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Archive for the ‘Chemical Biology and its relations to Metabolic Disease’ Category

The Evolution of Clinical Chemistry in the 20th Century

Curator: Larry H. Bernstein, MD, FCAP

Article ID #164: The Evolution of Clinical Chemistry in the 20th Century. Published on 12/13/2014

WordCloud Image Produced by Adam Tubman

This is a subchapter in the series on developments in diagnostics in the period from 1880 to 1980.

Otto Folin: America’s First Clinical Biochemist

(Extracted from Samuel Meites, AACC History Division; Apr 1996)

Forward by Wendell T. Caraway, PhD.

The first introduction to Folin comes with the Folin-Wu protein-free filktrate, a technique for removing proteins from whole blood or plasma that resulted in water-clear solutions suitable for the determination of glucose, creatinine, uric acid, non-protein nitrogen, and chloride. The major active ingredient used in the precipitation of protein was sodium tungstate prepared “according to Folin”.Folin-Wu sugar tubes were used for the determination of glucose. From these and subsequent encounters, we learned that Folin was a pioneer in methods for the chemical analysis of blood.  The determination of uric acid in serum was the Benedict method in which protein-free filtrate was mixed with solutions of sodium cyanide and arsenophosphotungstic acid and then heated in a water bath to develop a blue color.  A thorough review of the literature revealed that Folin and Denis had published, in 1912, a method for uric acid in which they used sodium carbonate, rather than sodium cyanide, which was modified and largely superceded the “cyanide”method.

Notes from the author.

Modern clinical chemistry began with the application of 20th century quantitative analysis and instrumentation to measure constituents of blood and urine, and relating the values obtained to human health and disease. In the United States, the first impetus propelling this new area of biochemistry was provided by the 1912 papers of Otto Folin.  The only precedent for these stimulating findings was his own earlier and certainly classic papers on the quantitative compositiuon of urine, the laws governing its composition, and studies on the catabolic end products of protein, which led to his ingenious concept of endogenous and exogenous metabolism.  He had already determined blood ammonia in 1902.  This work preceded the entry of Stanley Benedict and Donald Van Slyke into biochemistry.  Once all three of them were active contributors, the future of clinical biochemistry was ensured. Those who would consult the early volumes of the Journal of Biological Chemistry will discover the direction that the work of Otto Follin gave to biochemistry.  This modest, unobstrusive man of Harvard was a powerful stimulus and inspiration to others.

Quantitatively, in the years of his scientific productivity, 1897-1934, Otto Folin published 151 (+ 1) journal articles including a chapter in Aberhalden’s handbook and one in Hammarsten’s Festschrift, but excluding his doctoral dissertation, his published abstracts, and several articles in the proceedings of the Association of Life Insurance Directors of America. He also wrote one monograph on food preservatives and produced five editions of his laboratory manual. He published four articles while studying in Europe (1896-98), 28 while at the McLean Hospital (1900-7), and 119 at Harvard (1908-34). In his banner year of 1912 he published 20 papers. His peak period from 1912-15 included 15 papers, the monograph, and most of the work on the first edition of his laboratory manual.

The quality of Otto Folin’s life’s work relates to its impact on biochemistry, particularly clinical biochemistry.  Otto’s two brilliant collaborators, Willey Denis and Hsien Wu, must be acknowledged.  Without denis, Otto could not have achieved so rapidly the introduction and popularization of modern blood analysis in the U.S. It would be pointless to conjecture how far Otto would have progressed without this pair.

His work provided the basis of the modern approach to the quantitative analysis of blood and urine through improved methods that reduced the body fluid volume required for analysis. He also applied these methods to metabolic studies on tissues as well as body fluids. Because his interests lay in protein metabolism, his major contributions were directede toward measuring nitrogenous waste or end products.His most dramatic achievement was is illustrated by the study of blood nitrogen retention in nephritis and gout.

Folin introduced colorimetry, turbidimetry, and the use of color filters into quantitative clinical biochemistry. He initiated and applied ingeniously conceived reagents and chemical reactions that paved the way for a host of studies by his contemporaries. He introduced the use of phosphomolybdate for detecting phenolic compounds, and phosphomolybdate for uric acid.  These, in turn, led to the quantitation of epinephrine and tyrosin tryptophane, and cystine in protein. The molybdate suggested to Fiske and SubbaRow the determination of phosphate as phosphomolybdate, and the tungsten led to the use of tungstic acid as a protein precipitant.  Phosphomolybdate became the key reagent in thge blood sugar method.  Folin resurrected the abandoned Jaffe reaction and established creatine and creatinine analysis. He also laid the groundwork for the discovery of the discovery of creatine phosphate. Clinical chemistry owes to him the introductionb of Nessler’s reagent, permutit, Lloyd’s reagent, gum ghatti, and preservatives for standards, such as benzoic acid and formaldehyde. Among his distinguished graduate investigators were Bloor, Doisy, fiske, Shaffer, SubbaRow, Sumner and, Wu.

A Golden Age of Clinical Chemistry: 1948–1960

Louis Rosenfeld
Clinical Chemistry 2000; 46(10): 1705–1714

The 12 years from 1948 to 1960 were notable for introduction of the Vacutainer
tube, electrophoresis, radioimmunoassay, and the Auto-Analyzer. Also
appearing during this interval were new organizations, publications, programs,
and services that established a firm foundation for the professional status
of clinical chemists. It was a golden age.
Except for photoelectric colorimeters, the clinical chemistry laboratories
in 1948—and in many places even later—were not very different from
those of 1925. The basic technology and equipment were essentially
unchanged.There was lots of glassware of different kinds—pipettes,
burettes, wooden racks of test tubes, funnels, filter paper,
cylinders, flasks, and beakers—as well as visual colorimeters,
centrifuges, water baths, an exhaust hood for evaporating organic
solvents after extractions, a microscope for examining urine
sediments, a double-pan analytical beam balance for weighing
reagents and standard chemicals, and perhaps a pH meter. The
most complicated apparatus was the Van Slyke volumetric gas
device—manually operated. The emphasis was on classical chemical
and biological techniques that did not require instrumentation.
The unparalleled growth and wide-ranging research that began after
World War II and have continued into the new century, often aided by
government funding for biomedical research and development as civilian
health has become a major national goal, have impacted the operations
of the clinical chemistry laboratory. The years from 1948 to 1960 were
especially notable for the innovative technology that produced better
methods for the investigation of many diseases, in many cases
leading to better treatment.

AUTOMATION IN CLINICAL CHEMISTRY: CURRENT SUCCESSES AND TRENDS
FOR THE FUTURE
Pierangelo Bonini
Pure & Appl.Chem.,1982;.54, (11):, 2Ol7—2O3O,

the history of automation in clinical chemistry is the history of how and
when the techno logical progress in the field of analytical methodology
as well as in the field of instrumentation, has helped clinical chemists
to mechanize their procedures and to control them.

GENERAL STEPS OF A CLINICAL CHEMISTRY PROCEDURE –
1 – PRELIMINARY TREATMENT (DEPR0TEINIZATION)
2 – SAMPLE + REAGENT(S)
3 – INCUBATION
L – READING
5 – CALCULATION
Fig. 1 General steps of a clinical chemistry procedure
Especially in the classic clinical chemistry methods, a preliminary treatment
of the sample ( in most cases a deproteinization) was an essential step. This
was a major constraint on the first tentative steps in automation and we will
see how this problem was faced and which new problems arose from avoiding
deproteinization. Mixing samples and reagents is the next step; then there is
a more or less long incubation at different temperatures and finally reading,
which means detection of modifications of some physical property of the
mixture; in most cases the development of a colour can reveal the reaction
but, as well known, many other possibilities exist; finally the result is calculated.

Some 25 years ago, Skeggs (1) presented his paper on continuous flow
automation that was the basis of very successful instruments still used all over
the world. The continuous flow automation reactions take place in an hydraulic
route common to all samples.them after mechanization.

Standards and samples enter the analytical stream segmented by air bubbles
and, as they circulate, specific chemical reactions and physical manipulations
continuously take place in the stream. Finally, after the air bubbles are vented,
the colour intensity, proportional to the solute molecules, is monitored in a
detector flow cell.

It is evident that the most important aim of automation is to correctly process
as many samples in as short a time as possible. This result can be obtained
thanks to many technological advances either from analytical point of view or
from the instrument technology.

ANALYTICAL METHODOLOGY –
– VERY ACTIVE ENZYMATIC REAGENTS
–                          SHORTER REACTION TIME
– KINETIC AND FIXED TIME REACTIONS
–                        No NEED OF DEPROTEINIZATION
– SURFACTANTS
–                      AUTOMATIC SAtIPLE BLANK CALCULATION
– POLYCHROMATIC ANALYSIS

The introduction of very active enzymatic reagents for determination of
substrates resulted in shorter reaction times and possibly, in many cases,
of avoiding deproteinization.Reaction times are also reduced by using kinetic
and fixed time reactions instead of end points. In this case, the measurement
of sample blank does not need a separate tube with separate reaction
mixture. Deproteinization can be avoided also by using some surfac—
tants in the reagent mixture. An automatic calculation of sample blanks
is also possible by using polychromatic analysis. As we can see from this
figure, reduction of reaction times and elimination of tedious ope
rations like deproteinization, are the main results of this analytical progress.

Many relevant improvements in mechanics and optics over the last
twenty years and the tremendous advance in electronics have largely
contributed to the instrumental improvement of clinical chemistry automation.

A recent interesting innovation in the field of centrifugal analyzers consists
in the possibility of adding another reagent to an already mixed sample—
reagent solution. This innovation allows a preincubation to be made and
sample blanks to be read before adding the starter reagent.
The possibility to measure absorbances in cuvettes positioned longitudinally
to the light path, realized in a recent model of centrifugal analyzers, is claimed
to be advantageous to read absorbances in non homogeneous solutions, to
avoid any influence of reagent volume errors on the absorbance and to have
more suitable calculation factors. The interest of fluorimetric assays is
growing more and more, especially in connection with drugs immunofluorimetric
assays. This technology has been recently applied also to centrifugal analyzers
technology. A Xenon lamp generates a high energy light, reflected by a mirror
— holographic — grating operated by a stepping motor.
The selected wavelength of the exciting light passes through a split and
reaches the rotating cuvettes. Fluorescence is then filtered, read by
means of a photomultiplier and compared to the continuously monitored
fluorescence of an appropriate reference compound. In this way, eventual
instability due either to the electro—optical devices or to changes in
physicochemical properties of solution is corrected.

…more…

Dr. Yellapragada Subbarow – ATP – Energy for Life

One of the observations Dr SubbaRow made while testing the phosphorus method seemed to provide a clue to the mystery what happens to blood sugar when insulin is administered. Biochemists began investigating the problem when Frederick Banting showed that injections of insulin, the pancreatic hormone, keeps blood sugar under control and keeps diabetics alive.

SubbaRow worked for 18 months on the problem, often dieting and starving along with animals used in experiments. But the initial observations were finally shown to be neither significant nor unique and the project had to be scrapped in September 1926.

Out of the ashes of this project however arose another project that provided the key to the ancient mystery of muscular contraction. Living organisms resist degeneration and destruction with the help of muscles, and biochemists had long believed that a hypothetical inogen provided the energy required for the flexing of muscles at work.

Two researchers at Cambridge University in United Kingdom confirmed that lactic acid is formed when muscles contract and Otto Meyerhof of Germany showed that this lactic acid is a breakdown product of glycogen, the animal starch stored all over the body, particularly in liver, kidneys and muscles. When Professor Archibald Hill of the University College of London demonstrated that conversion of glycogen to lactic acid partly accounts for heat produced during muscle contraction everybody assumed that glycogen was the inogen. And, the 1922 Nobel Prize for medicine and physiology was divided between Hill and Meyerhof.

But how is glycogen converted to lactic acid? Embden, another German biochemist, advanced the hypothesis that blood sugar and phosphorus combine to form a hexose phosphoric ester which breaks down glycogen in the muscle to lactic acid.

In the midst of the insulin experiments, it occurred to Fiske and SubbaRow that Embden’s hypothesis would be supported if normal persons were found to have more hexose phosphate in their muscle and liver than diabetics. For diabetes is the failure of the body to use sugar. There would be little reaction between sugar and phosphorus in a diabetic body. If Embden was right, hexose (sugar) phosphate level in the muscle and liver of diabetic animals should rise when insulin is injected.

Fiske and SubbaRow rendered some animals diabetic by removing their pancreas in the spring of 1926, but they could not record any rise in the organic phosphorus content of muscles or livers after insulin was administered to the animals. Sugar phosphates were indeed produced in their animals but they were converted so quickly by enzymes to lactic acid that Fiske and SubbaRow could not detect them with methods then available. This was fortunate for science because, in their mistaken belief that Embden was wrong, they began that summer an extensive study of organic phosphorus compounds in the muscle “to repudiate Meyerhof completely”.

The departmental budget was so poor that SubbaRow often waited on the back streets of Harvard Medical School at night to capture cats he needed for the experiments. When he prepared the cat muscles for estimating their phosphorus content, SubbaRow found he could not get a constant reading in the colorimeter. The intensity of the blue colour went on rising for thirty minutes. Was there something in muscle which delayed the colour reaction? If yes, the time for full colour development should increase with the increase in the quantity of the sample. But the delay was not greater when the sample was 10 c.c. instead of 5 c.c. The only other possibility was that muscle had an organic compound which liberated phosphorus as the reaction in the colorimeter proceeded. This indeed was the case, it turned out. It took a whole year.

The mysterious colour delaying substance was a compound of phosphoric acid and creatine and was named Phosphocreatine. It accounted for two-thirds of the phosphorus in the resting muscle. When they put muscle to work by electric stimulation, the Phosphocreatine level fell and the inorganic phosphorus level rose correspondingly. It completely disappeared when they cut off the blood supply and drove the muscle to the point of “fatigue” by continued electric stimulation. And, presto! It reappeared when the fatigued muscle was allowed a period of rest.

Phosphocreatine created a stir among the scientists present when Fiske unveiled it before the American Society of Biological Chemists at Rochester in April 1927. The Journal of American Medical Association hailed the discovery in an editorial. The Rockefeller Foundation awarded a fellowship that helped SubbaRow to live comfortably for the first time since his arrival in the United States. All of Harvard Medical School was caught up with an enthusiasm that would be a life-time memory for con­temporary students. The students were in awe of the medium-sized, slightly stoop shouldered, “coloured” man regarded as one of the School’s top research workers.

SubbaRow’s carefully conducted series of experiments disproved Meyerhof’s assumptions about the glycogen-lactic acid cycle. His calculations fully accounted for the heat output during muscle contraction. Hill had not been able to fully account for this in terms of Meyerhof’s theory. Clearly the Nobel Committee was in haste in awarding the 1922 physiology prize, but the biochemistry orthodoxy led by Meyerhof and Hill themselves was not too eager to give up their belief in glycogen as the prime source of muscular energy.

Fiske and SubbaRow were fully upheld and the Meyerhof-Hill­ theory finally rejected in 1930 when a Danish physiologist showed that muscles can work to exhaustion without the aid of glycogen or the stimulation of lactic acid.

Fiske and SubbaRow had meanwhile followed a substance that was formed by the combination of phosphorus, liberated from Phosphocreatine, with an unidentified compound in muscle. SubbaRow isolated it and identified it as a chemical in which adenylic acid was linked to two extra molecules of phosphoric acid. By the time he completed the work to the satisfaction of Fiske, it was August 1929 when Harvard Medical School played host to the 13th International Physiological Congress.

ATP was presented to the gathered scientists before the Congress ended. To the dismay of Fiske and SubbaRow, a few days later arrived in Boston a German science journal, published 16 days before the Congress opened. It carried a letter from Karl Lohmann of Meyerhof’s laboratory, saying he had isolated from muscle a compound of adenylic acid linked to two molecules of phosphoric acid!

While Archibald Hill never adjusted himself to the idea that the basis of his Nobel Prize work had been demolished, Otto Meyerhof and his associates had seen the importance of Phosphocreatine discovery and plunged themselves into follow-up studies in competition with Fiske and SubbaRow. Two associates of Hill had in fact stumbled upon Phosphocreatine about the same time as Fiske and SubbaRow but their loyalty to Meyerhof-Hill theory acted as blinkers and their hasty and premature publications reveal their confusion about both the nature and significance of Phosphocreatine.

The discovery of ATP and its significance helped reveal the full story of muscular contraction: Glycogen arriving in muscle gets converted into lactic acid which is siphoned off to liver for re-synthesis of glycogen. This cycle yields three molecules of ATP and is important in delivering usable food energy to the muscle. Glycolysis or break up of glycogen is relatively slow in getting started and in any case muscle can retain ATP only in small quantities. In the interval between the begin­ning of muscle activity and the arrival of fresh ATP from glycolysis, ­Phosphocreatine maintains ATP supply by re-synthesizing it as fast as its energy terminals are used up by muscle for its activity.

Muscular contraction made possible by ATP helps us not only to move our limbs and lift weights but keeps us alive. The heart is after all a muscle pouch and millions of muscle cells embedded in the walls of arteries keep the life-sustaining blood pumped by the heart coursing through body organs. ATP even helps get new life started by powering the sperm’s motion toward the egg as well as the spectacular transformation of the fertilized egg in the womb.

Archibald Hill for long denied any role for ATP in muscle contraction, saying ATP has not been shown to break down in the intact muscle. This objection was also met in 1962 when University of Pennsylvania scientists showed that muscles can contract and relax normally even when glycogen and Phosphocreatine are kept under check with an inhibitor.

Michael Somogyi

Michael Somogyi was born in Reinsdorf, Austria-Hungary, in 1883. He received a degree in chemical engineering from the University of Budapest, and after spending some time there as a graduate assistant in biochemistry, he immigrated to the United States. From 1906 to 1908 he was an assistant in biochemistry at Cornell University.

Returning to his native land in 1908, he became head of the Municipal Laboratory in Budapest, and in 1914 he was granted his Ph.D. After World War I, the politically unstable situation in his homeland led him to return to the United States where he took a job as an instructor in biochemistry at Washington University in St. Louis, Missouri. While there he assisted Philip A. Shaffer and Edward Adelbert Doisy, Sr., a future Nobel Prize recipient, in developing a new method for the preparation of insulin in sufficiently large amounts and of sufficient purity to make it a viable treatment for diabetes. This early work with insulin helped foster Somogyi’s lifelong interest in the treatment and cure of diabetes. He was the first biochemist appointed to the staff of the newly opened Jewish Hospital, and he remained there as the director of their clinical laboratory until his retirement in 1957.

Arterial Blood Gases.  Van Slyke.

The test is used to determine the pH of the blood, the partial pressure of carbon dioxide and oxygen, and the bicarbonate level. Many blood gas analyzers will also report concentrations of lactate, hemoglobin, several electrolytes, oxyhemoglobin, carboxyhemoglobin and methemoglobin. ABG testing is mainly used in pulmonology and critical care medicine to determine gas exchange which reflect gas exchange across the alveolar-capillary membrane.

DONALD DEXTER VAN SLYKE died on May 4, 1971, after a long and productive career that spanned three generations of biochemists and physicians. He left behind not only a bibliography of 317 journal publications and 5 books, but also more than 100 persons who had worked with him and distinguished themselves in biochemistry and academic medicine. His doctoral thesis, with Gomberg at University of Michigan was published in the Journal of the American Chemical Society in 1907.  Van Slyke received an invitation from Dr. Simon Flexner, Director of the Rockefeller Institute, to come to New York for an interview. In 1911 he spent a year in Berlin with Emil Fischer, who was then the leading chemist of the scientific world. He was particularly impressed by Fischer’s performing all laboratory operations quantitatively —a procedure Van followed throughout his life. Prior to going to Berlin, he published the classic nitrous acid method for the quantitative determination of primary aliphatic amino groups, the first of the many gasometric procedures devised by Van Slyke, and made possible the determination of amino acids. It was the primary method used to study amino acid composition of proteins for years before chromatography. Thus, his first seven postdoctoral years were centered around the development of better methodology for protein composition and amino acid metabolism.

With his colleague G. M. Meyer, he first demonstrated that amino acids, liberated during digestion in the intestine, are absorbed into the bloodstream, that they are removed by the tissues, and that the liver alone possesses the ability to convert the amino acid nitrogen into urea.  From the study of the kinetics of urease action, Van Slyke and Cullen developed equations that depended upon two reactions: (1) the combination of enzyme and substrate in stoichiometric proportions and (2) the reaction of the combination into the end products. Published in 1914, this formulation, involving two velocity constants, was similar to that arrived at contemporaneously by Michaelis and Menten in Germany in 1913.

He transferred to the Rockefeller Institute’s Hospital in 2013, under Dr. Rufus Cole, where “Men who were studying disease clinically had the right to go as deeply into its fundamental nature as their training allowed, and in the Rockefeller Institute’s Hospital every man who was caring for patients should also be engaged in more fundamental study”.  The study of diabetes was already under way by Dr. F. M. Allen, but patients inevitably died of acidosis.  Van Slyke reasoned that if incomplete oxidation of fatty acids in the body led to the accumulation of acetoacetic and beta-hydroxybutyric acids in the blood, then a reaction would result between these acids and the bicarbonate ions that would lead to a lower than-normal bicarbonate concentration in blood plasma. The problem thus became one of devising an analytical method that would permit the quantitative determination of bicarbonate concentration in small amounts of blood plasma.  He ingeniously devised a volumetric glass apparatus that was easy to use and required less than ten minutes for the determination of the total carbon dioxide in one cubic centimeter of plasma.  It also was soon found to be an excellent apparatus by which to determine blood oxygen concentrations, thus leading to measurements of the percentage saturation of blood hemoglobin with oxygen. This found extensive application in the study of respiratory diseases, such as pneumonia and tuberculosis. It also led to the quantitative study of cyanosis and a monograph on the subject by C. Lundsgaard and Van Slyke.

In all, Van Slyke and his colleagues published twenty-one papers under the general title “Studies of Acidosis,” beginning in 1917 and ending in 1934. They included not only chemical manifestations of acidosis, but Van Slyke, in No. 17 of the series (1921), elaborated and expanded the subject to describe in chemical terms the normal and abnormal variations in the acid-base balance of the blood. This was a landmark in understanding acid-base balance pathology.  Within seven years after Van moved to the Hospital, he had published a total of fifty-three papers, thirty-three of them coauthored with clinical colleagues.

In 1920, Van Slyke and his colleagues undertook a comprehensive investigation of gas and electrolyte equilibria in blood. McLean and Henderson at Harvard had made preliminary studies of blood as a physico-chemical system, but realized that Van Slyke and his colleagues at the Rockefeller Hospital had superior techniques and the facilities necessary for such an undertaking. A collaboration thereupon began between the two laboratories, which resulted in rapid progress toward an exact physico-chemical description of the role of hemoglobin in the transport of oxygen and carbon dioxide, of the distribution of diffusible ions and water between erythrocytes and plasma, and of factors such as degree of oxygenation of hemoglobin and hydrogen ion concentration that modified these distributions. In this Van Slyke revised his volumetric gas analysis apparatus into a manometric method.  The manometric apparatus proved to give results that were from five to ten times more accurate.

A series of papers on the CO2 titration curves of oxy- and deoxyhemoglobin, of oxygenated and reduced whole blood, and of blood subjected to different degrees of oxygenation and on the distribution of diffusible ions in blood resulted.  These developed equations that predicted the change in distribution of water and diffusible ions between blood plasma and blood cells when there was a change in pH of the oxygenated blood. A significant contribution of Van Slyke and his colleagues was the application of the Gibbs-Donnan Law to the blood—regarded as a two-phase system, in which one phase (the erythrocytes) contained a high concentration of nondiffusible negative ions, i.e., those associated with hemoglobin, and cations, which were not freely exchaThe importance of Vanngeable between cells and plasma. By changing the pH through varying the CO2 tension, the concentration of negative hemoglobin charges changed in a predictable amount. This, in turn, changed the distribution of diffusible anions such as Cl” and HCO3″ in order to restore the Gibbs-Donnan equilibrium. Redistribution of water occurred to restore osmotic equilibrium. The experimental results confirmed the predictions of the equations.

As a spin-off from the physico-chemical study of the blood, Van undertook, in 1922, to put the concept of buffer value of weak electrolytes on a mathematically exact basis.

This proved to be useful in determining buffer values of mixed, polyvalent, and amphoteric electrolytes, and put the understanding of buffering on a quantitative basis. A monograph in Medicine entitled “Observation on the Courses of Different Types of Bright’s Disease, and on the Resultant Changes in Renal Anatomy,” was a landmark that related the changes occurring at different stages of renal deterioration to the quantitative changes taking place in kidney function. During this period, Van Slyke and R. M. Archibald identified glutamine as the source of urinary ammonia. During World War II, Van and his colleagues documented the effect of shock on renal function and, with R. A. Phillips, developed a simple method, based on specific gravity, suitable for use in the field.

Over 100 of Van’s 300 publications were devoted to methodology. The importance of Van Slyke’s contribution to clinical chemical methodology cannot be overestimated. These included the blood organic constituents (carbohydrates, fats, proteins, amino acids, urea, nonprotein nitrogen, and phospholipids) and the inorganic constituents (total cations, calcium, chlorides, phosphate, and the gases carbon dioxide, carbon monoxide, and nitrogen). It was said that a Van Slyke manometric apparatus was almost all the special equipment needed to perform most of the clinical chemical analyses customarily performed prior to the introduction of photocolorimeters and spectrophotometers for such determinations.

The progress made in the medical sciences in genetics, immunology, endocrinology, and antibiotics during the second half of the twentieth century obscures at times the progress that was made in basic and necessary biochemical knowledge during the first half. Methods capable of giving accurate quantitative chemical information on biological material had to be painstakingly devised; basic questions on chemical behavior and metabolism had to be answered; and, finally, those factors that adversely modified the normal chemical reactions in the body so that abnormal conditions arise that we characterize as disease states had to be identified.

Viewed in retrospect, he combined in one scientific lifetime (1) basic contributions to the chemistry of body constituents and their chemical behavior in the body, (2) a chemical understanding of physiological functions of certain organ systems (notably the respiratory and renal), and (3) how such information could be exploited in the understanding and treatment of disease. That outstanding additions to knowledge in all three categories were possible was in large measure due to his sound and broadly based chemical preparation, his ingenuity in devising means of accurate measurements of chemical constituents, and the opportunity given him at the Hospital of the Rockefeller Institute to study disease in company with physicians.

In addition, he found time to work collaboratively with Dr. John P. Peters of Yale on the classic, two-volume Quantitative Clinical Chemistry. In 1922, John P. Peters, who had just gone to Yale from Van Slyke’s laboratory as an Associate Professor of Medicine, was asked by a publisher to write a modest handbook for clinicians describing useful chemical methods and discussing their application to clinical problems. It was originally to be called “Quantitative Chemistry in Clinical Medicine.” He soon found that it was going to be a bigger job than he could handle alone and asked Van Slyke to join him in writing it. Van agreed, and the two men proceeded to draw up an outline and divide up the writing of the first drafts of the chapters between them. They also agreed to exchange each chapter until it met the satisfaction of both.At the time it was published in 1931, it contained practically all that could be stated with confidence about those aspects of disease that could be and had been studied by chemical means. It was widely accepted throughout the medical world as the “Bible” of quantitative clinical chemistry, and to this day some of the chapters have not become outdated.

Paul Flory

Paul J. Flory was born in Sterling, Illinois, in 1910. He attended Manchester College, an institution for which he retained an abiding affection. He did his graduate work at Ohio State University, earning his Ph.D. in 1934. He was awarded the Nobel Prize in Chemistry in 1974, largely for his work in the area of the physical chemistry of macromolecules.

Flory worked as a newly minted Ph.D. for the DuPont Company in the Central Research Department with Wallace H. Carothers. This early experience with practical research instilled in Flory a lifelong appreciation for the value of industrial application. His work with the Air Force Office of Strategic Research and his later support for the Industrial Affiliates program at Stanford University demonstrated his belief in the need for theory and practice to work hand-in-hand.

Following the death of Carothers in 1937, Flory joined the University of Cincinnati’s Basic Science Research Laboratory. After the war Flory taught at Cornell University from 1948 until 1957, when he became executive director of the Mellon Institute. In 1961 he joined the chemistry faculty at Stanford, where he would remain until his retirement.

Among the high points of Flory’s years at Stanford were his receipt of the National Medal of Science (1974), the Priestley Award (1974), the J. Willard Gibbs Medal (1973), the Peter Debye Award in Physical Chemistry (1969), and the Charles Goodyear Medal (1968). He also traveled extensively, including working tours to the U.S.S.R. and the People’s Republic of China.

Abraham Savitzky

Abraham Savitzky was born on May 29, 1919, in New York City. He received his bachelor’s degree from the New York State College for Teachers in 1941. After serving in the U.S. Air Force during World War II, he obtained a master’s degree in 1947 and a Ph.D. in 1949 in physical chemistry from Columbia University.

In 1950, after working at Columbia for a year, he began a long career with the Perkin-Elmer Corporation. Savitzky started with Perkin-Elmer as a staff scientist who was chiefly concerned with the design and development of infrared instruments. By 1956 he was named Perkin-Elmer’s new product coordinator for the Instrument Division, and as the years passed, he continued to gain more and more recognition for his work in the company. Most of his work with Perkin-Elmer focused on computer-aided analytical chemistry, data reduction, infrared spectroscopy, time-sharing systems, and computer plotting. He retired from Perkin-Elmer in 1985.

Abraham Savitzky holds seven U.S. patents pertaining to computerization and chemical apparatus. During his long career he presented numerous papers and wrote several manuscripts, including “Smoothing and Differentiation of Data by Simplified Least Squares Procedures.” This paper, which is the collaborative effort of Savitzky and Marcel J. E. Golay, was published in volume 36 of Analytical Chemistry, July 1964. It is one of the most famous, respected, and heavily cited articles in its field. In recognition of his many significant accomplishments in the field of analytical chemistry and computer science, Savitzky received the Society of Applied Spectroscopy Award in 1983 and the Williams-Wright Award from the Coblenz Society in 1986.

Samuel Natelson

Samuel Natelson attended City College of New York and received his B.S. in chemistry in 1928. As a graduate student, Natelson attended New York University, receiving a Sc.M. in 1930 and his Ph.D. in 1931. After receiving his Ph.D., he began his career teaching at Girls Commercial High School. While maintaining his teaching position, Natelson joined the Jewish Hospital of Brooklyn in 1933. Working as a clinical chemist for Jewish Hospital, Natelson first conceived of the idea of a society by and for clinical chemists. Natelson worked to organize the nine charter members of the American Association of Clinical Chemists, which formally began in 1948. A pioneer in the field of clinical chemistry, Samuel Natelson has become a role model for the clinical chemist. Natelson developed the usage of microtechniques in clinical chemistry. During this period, he served as a consultant to the National Aeronautics and Space Administration in the 1960s, helping analyze the effect of weightless atmospheres on astronauts’ blood. Natelson spent his later career as chair of the biochemistry department at Michael Reese Hospital and as a lecturer at the Illinois Institute of Technology.

Arnold Beckman

Arnold Orville Beckman (April 10, 1900 – May 18, 2004) was an American chemist, inventor, investor, and philanthropist. While a professor at Caltech, he founded Beckman Instruments based on his 1934 invention of the pH meter, a device for measuring acidity, later considered to have “revolutionized the study of chemistry and biology”.[1] He also developed the DU spectrophotometer, “probably the most important instrument ever developed towards the advancement of bioscience”.[2] Beckman funded the first transistor company, thus giving rise to Silicon Valley.[3]

He earned his bachelor’s degree in chemical engineering in 1922 and his master’s degree in physical chemistry in 1923. For his master’s degree he studied the thermodynamics of aqueous ammonia solutions, a subject introduced to him by T. A. White.. Beckman decided to go to Caltech for his doctorate. He stayed there for a year, before returning to New York to be near his fiancée, Mabel. He found a job with Western Electric’s engineering department, the precursor to the Bell Telephone Laboratories. Working with Walter A. Shewhart, Beckman developed quality control programs for the manufacture of vacuum tubes and learned about circuit design. It was here that Beckman discovered his interest in electronics.

In 1926 the couple moved back to California and Beckman resumed his studies at Caltech. He became interested in ultraviolet photolysis and worked with his doctoral advisor, Roscoe G. Dickinson, on an instrument to find the energy of ultraviolet light. It worked by shining the ultraviolet light onto a thermocouple, converting the incident heat into electricity, which drove a galvanometer. After receiving a Ph.D. in photochemistry in 1928 for this application of quantum theory to chemical reactions, Beckman was asked to stay on at Caltech as an instructor and then as a professor. Linus Pauling, another of Roscoe G. Dickinson’s graduate students, was also asked to stay on at Caltech.

During his time at Caltech, Beckman was active in teaching at both the introductory and advanced graduate levels. Beckman shared his expertise in glass-blowing by teaching classes in the machine shop. He also taught classes in the design and use of research instruments. Beckman dealt first-hand with the chemists’ need for good instrumentation as manager of the chemistry department’s instrument shop. Beckman’s interest in electronics made him very popular within the chemistry department at Caltech, as he was very skilled in building measuring instruments.

Over the time that he was at Caltech, the focus of the department increasingly moved towards pure science and away from chemical engineering and applied chemistry. Arthur Amos Noyes, head of the chemistry division, encouraged both Beckman and chemical engineer William Lacey to be in contact with real-world engineers and chemists, and Robert Andrews Millikan, Caltech’s president, referred technical questions to Beckman from government and businessess.

Sunkist Growers was having problems with its manufacturing process. Lemons that were not saleable as produce were made into pectin or citric acid, with sulfur dioxide used as a preservative. Sunkist needed to know the acidity of the product at any given time, Chemist Glen Joseph at Sunkist was attempting to measure the hydrogen-ion concentration in lemon juice electrochemically, but sulfur dioxide damaged hydrogen electrodes, and non-reactive glass electrodes produced weak signals and were fragile.

Joseph approached Beckman, who proposed that instead of trying to increase the sensitivity of his measurements, he amplify his results. Beckman, familiar with glassblowing, electricity, and chemistry, suggested a design for a vacuum-tube amplifier and ended up building a working apparatus for Joseph. The glass electrode used to measure pH was placed in a grid circuit in the vacuum tube, producing an amplified signal which could then be read by an electronic meter. The prototype was so useful that Joseph requested a second unit.

Beckman saw an opportunity, and rethinking the project, decided to create a complete chemical instrument which could be easily transported and used by nonspecialists. By October 1934, he had registered patent application U.S. Patent No. 2,058,761 for his “acidimeter”, later renamed the pH meter. Although it was priced expensively at $195, roughly the starting monthly wage for a chemistry professor at that time, it was significantly cheaper than the estimated cost of building a comparable instrument from individual components, about $500. The original pH meter weighed in at nearly 7 kg, but was a substantial improvement over a benchful of delicate equipment. The earliest meter had a design glitch, in that the pH readings changed with the depth of immersion of the electrodes, but Beckman fixed the problem by sealing the glass bulb of the electrode. The pH meter is an important device for measuring the pH of a solution, and by 11 May 1939, sales were successful enough that Beckman left Caltech to become the full-time president of National Technical Laboratories. By 1940, Beckman was able to take out a loan to build his own 12,000 square foot factory in South Pasadena.

In 1940, the equipment needed to analyze emission spectra in the visible spectrum could cost a laboratory as much as $3,000, a huge amount at that time. There was also growing interest in examining ultraviolet spectra beyond that range. In the same way that he had created a single easy-to-use instrument for measuring pH, Beckman made it a goal to create an easy-to-use instrument for spectrophotometry. Beckman’s research team, led by Howard Cary, developed several models.

The new spectrophotometers used a prism to spread light into its absorption spectra and a phototube to “read” the spectra and generate electrical signals, creating a standardized “fingerprint” for the material tested. With Beckman’s model D, later known as the DU spectrophotometer, National Technical Laboratories successfully created the first easy-to-use single instrument containing both the optical and electronic components needed for ultraviolet-absorption spectrophotometry. The user could insert a sample, dial up the desired frequency, and read the amount of absorption of that frequency from a simple meter. It produced accurate absorption spectra in both the ultraviolet and the visible regions of the spectrum with relative ease and repeatable accuracy. The National Bureau of Standards ran tests to certify that the DU’s results were accurate and repeatable and recommended its use.

Beckman’s DU spectrophotometer has been referred to as the “Model T” of scientific instruments: “This device forever simplified and streamlined chemical analysis, by allowing researchers to perform a 99.9% accurate biological assessment of a substance within minutes, as opposed to the weeks required previously for results of only 25% accuracy.” Nobel laureate Bruce Merrifield is quoted as calling the DU spectrophotometer “probably the most important instrument ever developed towards the advancement of bioscience.”

Development of the spectrophotometer also had direct relevance to the war effort. The role of vitamins in health was being studied, and scientists wanted to identify Vitamin A-rich foods to keep soldiers healthy. Previous methods involved feeding rats for several weeks, then performing a biopsy to estimate Vitamin A levels. The DU spectrophotometer yielded better results in a matter of minutes. The DU spectrophotometer was also an important tool for scientists studying and producing the new wonder drug penicillin. By the end of the war, American pharmaceutical companies were producing 650 billion units of penicillin each month. Much of the work done in this area during World War II was kept secret until after the war.

Beckman also developed the infrared spectrophotometer, first the the IR-1, then, in 1953, he redesigned the instrument. The result was the IR-4, which could be operated using either a single or double beam of infrared light. This allowed a user to take both the reference measurement and the sample measurement at the same time.

Beckman Coulter Inc., is an American company that makes biomedical laboratory instruments. Founded by Caltech professor Arnold O. Beckman in 1935 as National Technical Laboratories to commercialize a pH meter that he had invented, the company eventually grew to employ over 10,000 people, with $2.4 billion in annual sales by 2004. Its current headquarters are in Brea, California.

In the 1940s, Beckman changed the name to Arnold O. Beckman, Inc. to sell oxygen analyzers, the Helipot precision potentiometer, and spectrophotometers. In the 1950s, the company name changed to Beckman Instruments, Inc.

Beckman was contacted by Paul Rosenberg. Rosenberg worked at MIT’s Radiation Laboratory. The lab was part of a secret network of research institutions in both the United States and Britain that were working to develop radar, “radio detecting and ranging”. The project was interested in Beckman because of the high quality of the tuning knobs or “potentiometers” which were used on his pH meters. Beckman had trademarked the design of the pH meter knobs, under the name “helipot” for “helical potentiometer”. Rosenberg had found that the helipot was more precise, by a factor of ten, than other knobs. He redesigned the knob to have a continuous groove, in which the contact could not be jarred out of contact.

Beckman instruments were also used by the Manhattan Project to measure radiation in gas-filled, electrically charged ionization chambers in nuclear reactors.
The pH meter was adapted to do the job with a relatively minor adjustment – substituting an input-load resistor for the glass electrode. As a result, Beckman Instruments developed a new product, the micro-ammeter

After the war, Beckman developed oxygen analyzers that were used to monitor conditions in incubators for premature babies. Doctors at Johns Hopkins University used them to determine recommendations for healthy oxygen levels for incubators.

Beckman himself was approached by California governor Goodwin Knight to head a Special Committee on Air Pollution, to propose ways to combat smog. At the end of 1953, the committee made its findings public. The “Beckman Bible” advised key steps to be taken immediately:

In 1955, Beckman established the seminal Shockley Semiconductor Laboratory as a division of Beckman Instruments to begin commercializing the semiconductor transistor technology invented by Caltech alumnus William Shockley. The Shockley Laboratory was established in nearby Mountain View, California, and thus, “Silicon Valley” was born.

Beckman also saw that computers and automation offered a myriad of opportunities for integration into instruments, and the development of new instruments.

The Arnold and Mabel Beckman Foundation was incorporated in September 1977.  At the time of Beckman’s death, the Foundation had given more than 400 million dollars to a variety of charities and organizations. In 1990, it was considered one of the top ten foundations in California, based on annual gifts. Donations chiefly went to scientists and scientific causes as well as Beckman’s alma maters. He is quoted as saying, “I accumulated my wealth by selling instruments to scientists,… so I thought it would be appropriate to make contributions to science, and that’s been my number one guideline for charity.”

Wallace H. Coulter

Engineer, Inventor, Entrepreneur, Visionary

Wallace Henry Coulter was an engineer, inventor, entrepreneur and visionary. He was co-founder and Chairman of Coulter® Corporation, a worldwide medical diagnostics company headquartered in Miami, Florida. The two great passions of his life were applying engineering principles to scientific research, and embracing the diversity of world cultures. The first passion led him to invent the Coulter Principle™, the reference method for counting and sizing microscopic particles suspended in a fluid.

This invention served as the cornerstone for automating the labor intensive process of counting and testing blood. With his vision and tenacity, Wallace Coulter, was a founding father in the field of laboratory hematology, the science and study of blood. His global viewpoint and passion for world cultures inspired him to establish over twenty international subsidiaries. He recognized that it was imperative to employ locally based staff to service his customers before this became standard business strategy.

Wallace’s first attempts to patent his invention were turned away by more than one attorney who believed “you cannot patent a hole”. Persistent as always, Wallace finally applied for his first patent in 1949 and it was issued on October 20, 1953. That same year, two prototypes were sent to the National Institutes of Health for evaluation. Shortly after, the NIH published its findings in two key papers, citing improved accuracy and convenience of the Coulter method of counting blood cells. That same year, Wallace publicly disclosed his invention in his one and only technical paper at the National Electronics Conference, “High Speed Automatic Blood Cell Counter and Cell Size Analyzer”.

Leonard Skeggs was the inventor of the first continuous flow analyser way back in 1957. This groundbreaking event completely changed the way that chemistry was carried out. Many of the laborious tests that dominated lab work could be automated, increasing productivity and freeing personnel for other more challenging tasks

Continuous flow analysis and its offshoots and decedents are an integral part of modern chemistry. It might therefore be some conciliation to Leonard Skeggs to know that not only was he the beneficiary of an appellation with a long and fascinating history, he also created a revolution in wet chemistry that is still with us today.

Technicon

The AutoAnalyzer is an automated analyzer using a flow technique called continuous flow analysis (CFA), first made by the Technicon Corporation. The instrument was invented 1957 by Leonard Skeggs, PhD and commercialized by Jack Whitehead’s Technicon Corporation. The first applications were for clinical analysis, but methods for industrial analysis soon followed. The design is based on separating a continuously flowing stream with air bubbles.

In continuous flow analysis (CFA) a continuous stream of material is divided by air bubbles into discrete segments in which chemical reactions occur. The continuous stream of liquid samples and reagents are combined and transported in tubing and mixing coils. The tubing passes the samples from one apparatus to the other with each apparatus performing different functions, such as distillation, dialysis, extraction, ion exchange, heating, incubation, and subsequent recording of a signal. An essential principle of the system is the introduction of air bubbles. The air bubbles segment each sample into discrete packets and act as a barrier between packets to prevent cross contamination as they travel down the length of the tubing. The air bubbles also assist mixing by creating turbulent flow (bolus flow), and provide operators with a quick and easy check of the flow characteristics of the liquid. Samples and standards are treated in an exactly identical manner as they travel the length of the tubing, eliminating the necessity of a steady state signal, however, since the presence of bubbles create an almost square wave profile, bringing the system to steady state does not significantly decrease throughput ( third generation CFA analyzers average 90 or more samples per hour) and is desirable in that steady state signals (chemical equilibrium) are more accurate and reproducible.

A continuous flow analyzer (CFA) consists of different modules including a sampler, pump, mixing coils, optional sample treatments (dialysis, distillation, heating, etc.), a detector, and data generator. Most continuous flow analyzers depend on color reactions using a flow through photometer, however, also methods have been developed that use ISE, flame photometry, ICAP, fluorometry, and so forth.

Flow injection analysis (FIA), was introduced in 1975 by Ruzicka and Hansen.
Jaromir (Jarda) Ruzicka is a Professor  of Chemistry (Emeritus at the University of Washington and Affiliate at the University of Hawaii), and member of the Danish Academy of Technical Sciences. Born in Prague in 1934, he graduated from the Department of Analytical Chemistry, Facultyof Sciences, Charles University. In 1968, when Soviets occupied Czechoslovakia, he emigrated to Denmark. There, he joined The Technical University of Denmark, where, ten years  later, received a newly created Chair in Analytical Chemistry. When Jarda met Elo Hansen, they invented Flow Injection.

The first generation of FIA technology, termed flow injection (FI), was inspired by the AutoAnalyzer technique invented by Skeggs in early 1950s. While Skeggs’ AutoAnalyzer uses air segmentation to separate a flowing stream into numerous discrete segments to establish a long train of individual samples moving through a flow channel, FIA systems separate each sample from subsequent sample with a carrier reagent. While the AutoAnalyzer mixes sample homogeneously with reagents, in all FIA techniques sample and reagents are merged to form a concentration gradient that yields analysis results

Arthur Karmen.

Dr. Karmen was born in New York City in 1930. He graduated from the Bronx High School of Science in 1946 and earned an A.B. and M.D. in 1950 and 1954, respectively, from New York University. In 1952, while a medical student working on a summer project at Memorial-Sloan Kettering, he used paper chromatography of amino acids to demonstrate the presence of glutamic-oxaloacetic and glutaniic-pyruvic ransaminases (aspartate and alanine aminotransferases) in serum and blood. In 1954, he devised the spectrophotometric method for measuring aspartate aminotransferase in serum, which, with minor modifications, is still used for diagnostic testing today. When developing this assay, he studied the reaction of NADH with serum and demonstrated the presence of lactate and malate dehydrogenases, both of which were also later used in diagnosis. Using the spectrophotometric method, he found that aspartate aminotransferase increased in the period immediately after an acute myocardial infarction and did the pilot studies that showed its diagnostic utility in heart and liver diseases.  This became as important as the EKG. It was replaced in cardiology usage by the MB isoenzyme of creatine kinase, which was driven by Burton Sobel’s work on infarct size, and later by the troponins.

History of Laboratory Medicine at Yale University.

The roots of the Department of Laboratory Medicine at Yale can be traced back to John Peters, the head of what he called the “Chemical Division” of the Department of Internal Medicine, subsequently known as the Section of Metabolism, who co-authored with Donald Van Slyke the landmark 1931 textbook Quantitative Clinical Chemistry (2.3); and to Pauline Hald, research collaborator of Dr. Peters who subsequently served as Director of Clinical Chemistry at Yale-New Haven Hospital for many years. In 1947, Miss Hald reported the very first flame photometric measurements of sodium and potassium in serum (4). This study helped to lay the foundation for modern studies of metabolism and their application to clinical care.

The Laboratory Medicine program at Yale had its inception in 1958 as a section of Internal Medicine under the leadership of David Seligson. In 1965, Laboratory Medicine achieved autonomous section status and in 1971, became a full-fledged academic department. Dr. Seligson, who served as the first Chair, pioneered modern automation and computerized data processing in the clinical laboratory. In particular, he demonstrated the feasibility of discrete sample handling for automation that is now the basis of virtually all automated chemistry analyzers. In addition, Seligson and Zetner demonstrated the first clinical use of atomic absorption spectrophotometry. He was one of the founding members of the major Laboratory Medicine academic society, the Academy of Clinical Laboratory Physicians and Scientists.

Nathan Gochman.  Developer of Automated Chemistries.

Nathan Gochman, PhD, has over 40 years of experience in the clinical diagnostics industry. This includes academic teaching and research, and 30 years in the pharmaceutical and in vitro diagnostics industry. He has managed R & D, technical marketing and technical support departments. As a leader in the industry he was President of the American Association for Clinical Chemistry (AACC) and the National Committee for Clinical Laboratory Standards (NCCLS, now CLSI). He is currently a Consultant to investment firms and IVD companies.

William Sunderman

A doctor and scientist who lived a remarkable century and beyond — making medical advances, playing his Stradivarius violin at Carnegie Hall at 99 and being honored as the nation’s oldest worker at 100.

He developed a method for measuring glucose in the blood, the Sunderman Sugar Tube, and was one of the first doctors to use insulin to bring a patient out of a diabetic coma. He established quality-control techniques for medical laboratories that ended the wide variation in the results of laboratories doing the same tests.

He taught at several medical schools and founded and edited the journal Annals of Clinical and Laboratory Science. In World War II, he was a medical director for the Manhattan Project, which developed the atomic bomb.

Dr. Sunderman was president of the American Society of Clinical Pathologists and a founding governor of the College of American Pathologists. He also helped organize the Association of Clinical Scientists and was its first president.

Yale Department of Laboratory Medicine

The roots of the Department of Laboratory Medicine at Yale can be traced back to John Peters, the head of what he called the “Chemical Division” of the Department of Internal Medicine, subsequently known as the Section of Metabolism, who co-authored with Donald Van Slyke the landmark 1931 textbook Quantitative Clinical Chemistry; and to Pauline Hald, research collaborator of Dr. Peters who subsequently served as Director of Clinical Chemistry at Yale-New Haven Hospital for many years. In 1947, Miss Hald reported the very first flame photometric measurements of sodium and potassium in serum. This study helped to lay the foundation for modern studies of metabolism and their application to clinical care.

The Laboratory Medicine program at Yale had its inception in 1958 as a section of Internal Medicine under the leadership of David Seligson. In 1965, Laboratory Medicine achieved autonomous section status and in 1971, became a full-fledged academic department. Dr. Seligson, who served as the first Chair, pioneered modern automation and computerized data processing in the clinical laboratory. In particular, he demonstrated the feasibility of discrete sample handling for automation that is now the basis of virtually all automated chemistry analyzers. In addition, Seligson and Zetner demonstrated the first clinical use of atomic absorption spectrophotometry. He was one of the founding members of the major Laboratory Medicine academic society, the Academy of Clinical Laboratory Physicians and Scientists.

The discipline of clinical chemistry and the broader field of laboratory medicine, as they are practiced today, are attributed in no small part to Seligson’s vision and creativity.

Born in Philadelphia in 1916, Seligson graduated from University of Maryland and received a D.Sc. from Johns Hopkins University and an M.D. from the University of Utah. In 1953, he served as captain in the U.S. Army, chief of the Hepatic and Metabolic Disease Laboratory at Walter Reed Army Medical Center.

Recruited to Yale and Grace-New Haven Hospital in 1958 from the University of Pennsylvania as professor of internal medicine at the medical school and the first director of clinical laboratories at the hospital, Seligson subsequently established the infrastructure of the Department of Laboratory Medicine, creating divisions of clinical chemistry, microbiology, transfusion medicine (blood banking) and hematology – each with its own strong clinical, teaching and research programs.

Challenging the continuous flow approach, Seligson designed, built and validated “discrete sample handling” instruments wherein each sample was treated independently, which allowed better choice of methods and greater efficiency. Today continuous flow has essentially disappeared and virtually all modern automated clinical laboratory instruments are based upon discrete sample handling technology.

Seligson was one of the early visionaries who recognized the potential for computers in the clinical laboratory. One of the first applications of a digital computer in the clinical laboratory occurred in Seligson’s department at Yale, and shortly thereafter data were being transmitted directly from the laboratory computer to data stations on the patient wards. Now, such laboratory information systems represent the standard of care.

He was also among the first to highlight the clinical importance of test specificity and accuracy, as compared to simple reproducibility. One of his favorite slides was one that showed almost perfectly reproducible results for 10 successive measurements of blood sugar obtained with what was then the most widely used and popular analytical instrument. However, he would note, the answer was wrong; the assay was not accurate.

Seligson established one of the nation’s first residency programs focused on laboratory medicine or clinical pathology, and also developed a teaching curriculum in laboratory medicine for medical students. In so doing, he created a model for the modern practice of laboratory medicine in an academic environment, and his trainees spread throughout the country as leaders in the field.

Ernest Cotlove

Ernest Cotlove’s scientific and medical career started at NYU where, after finishing medicine in 1943, he pursued studies in renal physiology and chemistry. His outstanding ability to acquire knowledge and conduct innovative investigations earned him an invitation from James Shannon, then Director of the National Heart Institute at NIH. He continued studies of renal physiology and chemistry until 1953 when he became Head of Clinical Chemistry Laboratories in the new Department of Clinical Pathology being developed by George Z. Williams during the Clinical Center’s construction. Dr. Cotlove seized the opportunity to design and equip the most advanced and functional clinical chemistry facility in our country.

Dr. Cotlove’s career exemplified the progress seen in medical research and technology. He designed the electronic chloridometer that bears his name, in spite of published reports that such an approach was theoretically impossible. He used this innovative skill to develop new instruments and methods at the Clinical Center. Many recognized him as an expert in clinical chemistry, computer programming, systems design for laboratory operations, and automation of analytical instruments.

Effects of Automation on Laboratory Diagnosis

George Z. Williams

There are four primary effects of laboratory automation on the practice of medicine: The range of laboratory support is being greatly extended to both diagnosis and guidance of therapeutic management; the new feasibility of multiphasic periodic health evaluation promises effective health and manpower conservation in the future; and substantially lowered unit cost for laboratory analysis will permit more extensive use of comprehensive laboratory medicine in everyday practice. There is, however, a real and growing danger of naive acceptance of and overconfidence in the reliability and accuracy of automated analysis and computer processing without critical evaluation. Erroneous results can jeopardize the patient’s welfare. Every physician has the responsibility to obtain proof of accuracy and reliability from the laboratories which serve his patients.

. Mario Werner

Dr. Werner received his medical degree from the University of Zurich, Switzerland in 1956. After specializing in internal medicine at the University Clinic in Basel, he came to the United States–as a fellow of the Swiss Academy of Medical Sciences–to work at NIH and at the Rockefeller University. From 1964 to 1966, he served as chief of the Central Laboratory at the Klinikum Essen, Ruhr-University, Germany. In 1967, he returned to the US, joining the Division of Clinical Pathology and Laboratory Medicine at the University of California, San Francisco, as an assistant professor. Three years later, he became Associate Professor of Pathology and Laboratory Medicine at Washington University in St. Louis, where he was instrumental in establishing the training program in laboratory medicine. In 1972, he was appointed Professor of Pathology at The George Washington University in Washington, DC.

Norbert Tietz

Professor Norbert W. Tietz received the degree of Doctor of Natural Sciences from the Technical University Stuttgart, Germany, in 1950. In 1954 he immigrated to the United States where he subsequently held positions or appointments at several Chicago area institutions including the Mount Sinai Hospital Medical Center, Chicago Medical School/University of Health Sciences and Rush Medical College.

Professor Tietz is best known as the editor of the Fundamentals of Clinical Chemistry. This book, now in its sixth edition, remains a primary information source for both students and educators in laboratory medicine. It was the first modem textbook that integrated clinical chemistry with the basic sciences and pathophysiology.

Throughout his career, Dr. Tietz taught a range of students from the undergraduate through post-graduate level including (1) medical technology students, (2) medical students, (3) clinical chemistry graduate students, (4) pathology residents, and (5) practicing chemists. For example, in the late 1960’s he began the first master’s of science degree program in clinical chemistry in the United States at the Chicago Medical School. This program subsequently evolved into one of the first Ph.D. programs in clinical chemistry.

Automation and other recent developments in clinical chemistry.

Griffiths J.

http://www.ncbi.nlm.nih.gov/pubmed/1344702

The decade 1980 to 1990 was the most progressive period in the short, but
turbulent, history of clinical chemistry. New techniques and the instrumentation
needed to perform assays have opened a chemical Pandora’s box. Multichannel
analyzers, the base spectrophotometric key to automated laboratories, have
become almost perfect. The extended use of the antigen-monoclonal antibody
reaction with increasing sensitive labels has extended analyte detection
routinely into the picomole/liter range. Devices that aid the automation of
serum processing and distribution of specimens are emerging. Laboratory
computerization has significantly matured, permitting better integration of
laboratory instruments, improving communication between laboratory personnel
and the patient’s physician, and facilitating the use of expert systems and
robotics in the chemistry laboratory

Automation and Expert Systems in a Core Clinical Chemistry Laboratory
Streitberg, GT, et al.  JALA 2009;14:94–105

Clinical pathology or laboratory medicine has a great
influence on clinical decisions and 60e70% of the
most important decisions on admission, discharge,
and medication are based on laboratory results.1
As we learn more about clinical laboratory results
and incorporate them in outcome optimization
schemes, the laboratory will play a more pivotal role
in management of patients and the eventual outcomes.
2 It has been stated that the development of
information technology and automation in laboratory
medicine has allowed laboratory professionals
to keep in pace with the growth in workload.

Since the reasons to automate and the impact of automation have
similarities and these include reduction in errors, increase in productivity,
and improvement in safety. Advances in technology in clinical chemistry
that have included total laboratory automation call for changes in job
responsibilities to include skills in information technology, data management,
instrumentation, patient preparation for diagnostic analysis, interpretation
of pathology results, dissemination of knowledge and information to
patients and other health staff, as well as skills in research.

The clinical laboratory has become so productive, particularly in chemistry and immunology, and the labor, instrument and reagent costs are well determined, that today a physician’s medical decisions are 80% determined by the clinical laboratory.  Medical information systems have lagged far behind.  Why is that?  Because the decision for a MIS has historical been based on billing capture.  Moreover, the historical use of chemical profiles were quite good at validating healthy dtatus in an outpatient population, but the profiles became restricted under Diagnostic Related Groups.    Thus, it came to be that the diagnostics was considered a “commodity”.  In order to be competitive, a laboratory had to provide “high complexity” tests that were drawn in by a large volume of “moderate complexity” tests.

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Selected Contributions to Chemistry from 1880 to 1980

Curator: Larry H. Bernstein, MD, FCAP

 

FUNDAMENTALS OF CHEMISTRY – Vol. I  The Contribution of Nobel Laureates to Chemistry

– Ferruccio Trifiro

http://www.eolss.net/sample-chapters/c06/e6-11-01-04.pdf

This chapter deals with the contribution to the development of chemistry of all the Nobel Prize winners in chemistry up to the end of the twentieth century, together with some in physics and medicine or physiology that have had particular relevance for the advances achieved in chemistry. The contributions of the various Nobel laureates cited are briefly summarized. The Nobel laureates in physics dealt with in this chapter are those who made important contributions to ard the understanding of the properties of atoms, the development of theoretical tools to treat the chemical bond, or the development of new analytical instrumentation. The Nobel laureates in medicine or physiology cited here are those whose contributions have been in the area of using chemistry to understand natural processes, such as the physiological aspects of living organisms through electron and ion exchange processes, enzymatic catalysis, and DNA-based chemistry. Eight areas of thought or thematic areas were chosen into which the contributions of the Nobel laureates to chemistry can be subdivided.

  1. The Properties of Molecules

4.1. The Discovery of Coordination and Metallorganic Compounds

4.2. The Discovery of New Organic Molecules

4.3. The Emergence of Quantum Chemistry

  1. The Dynamics of Chemical Reactions

6.1. Kinetics of Heterogeneous and Homogeneous Processes

6.2. The Identification of the Activated State

  1. The Understanding of Natural Processes

8.1. From Ferments to Enzymes

8.2. Understanding the Mechanism of Action of Enzymes

8.3. Mechanisms of Important Natural Processes

8.4. Characterization of Biologically Important Molecules

  1. The Identification of Chemical Entities

9.1. Analytical Methods

9.2. New Separation Techniques

9.3. The Development of New Instrumentation for Structure Analysis

The Nobel Prize in Chemistry: The Development of Modern Chemistry

by Bo G. Malmström and Bertil Andersson*

http://www.nobelprize.org/nobel_prizes/themes/chemistry/malmstrom/

Introduction

1.1 Chemistry at the Borders to Physics and Biology

The turn of the century 1900 was also a turning point in the history of chemistry. A survey of the Nobel Prizes in Chemistry during this century provides a view toward important trends in the development of Chemistry at the center of the sciences, bordering onto physics, which provides its theoretical foundation, on one side, and onto biology on the other. The fact that chemistry flourished during the beginning of the 20th century is intimately connected with fundamental developments in physics.

In 1897 Sir Joseph John Thomson of Cambridge announced his discovery of the electron, for which he was awarded the Nobel Prize for Physics in 1906. It took a number of years before its relevance to chemistry was seen. In 1911 Ernest Rutherford, who had worked in Thomson’s laboratory in the 1890s, formulated an atomic model, which depicted a cloud of electrons circling around the nucleus. Rutherford had received the Nobel Prize for Chemistry in 1908 for his work on radioactivity.

In Rutherford’s atomic model the stability of atoms was at variance with the laws of classical physics. Niels Bohr from Copenhagen brought clarity to this dilemma in the distinct lines observed in the spectra of atoms, the regularities of which had been discovered in 1890 by the physics professor Johannes (Janne) Rydberg at Lund University. This was the basis for Bohr’s formulation (1913) of an alternative atomic model. Only certain circular orbits of the electrons are allowed. In this model light is emitted (or absorbed), when an electron makes a transition from one orbit to another. For this, Bohr received the Nobel Prize for Physics in 1922

Gilbert Newton Lewis next suggested in 1916 that strong (covalent) bonds between atoms involve a sharing of two electrons between these atoms (electron-pair bond). Lewis also contributed fundamental work in chemical thermodynamics, and his brilliant textbook, Thermodynamics (1923), written together with Merle Randall, is counted as one of the masterworks in the chemical literature. Lewis never received a Nobel Prize.

However, important work was published in the 1890s, considered by the first Nobel Committee for Chemistry (see Section 2). Three of the Laureates during the first decade, Jacobus Henricus van’t Hoff, Svante Arrhenius and Wilhelm Ostwald, are generally regarded as the founders of a new branch of chemistry, physical chemistry. Fundamental work was also recognized in organic chemistry and in the chemistry of natural products, which is clearly reflected in the early prizes. Further, the Nobel Committee, recognized the border towards biology in 1907, with the prize to Eduard Buchner “for his biochemical researches and his discovery of cell-free fermentation”.

  1. The First Decade of Nobel Prizes for Chemistry

So much fundamental work in chemistry had been carried out during the last two decades of the 19th century that a decision for the first several prizes was not easy.  In 1901 the Academy had to consider 20 nominations, but no less than 11 of these named van’t Hoff, who was selected. van’t Hoff had already established the four valences for the carbon atom in his PhD thesis in Utrecht in 1874, foundation work for  modern organic chemistry. But the Nobel Prize was awarded for his later work on chemical kinetics and equilibria and on the osmotic pressure in solution, published in 1884 and 1886.

In his 1886 work van’t Hoff showed that most dissolved chemical compounds give an osmotic pressure equal to the gas pressure they would have exerted in the absence of the solvent. An apparent exception was aqueous solutions of electrolytes (acids, bases and their salts), but in the following year Arrhenius showed that this anomaly could be explained, if it is assumed that electrolytes in water dissociate into ions. Arrhenius had already presented the rudiments of his dissociation theory in his doctoral thesis, which was defended in Uppsala in 1884 and was not entirely well received by the faculty. It was, however, strongly supported by Ostwald in Riga, who, in fact, travelled to Uppsala to initiate a collaboration with Arrhenius. In 1886-1990 Arrhenius did work with Ostwald, first in Riga and then in Leipzig, and also with van’t Hoff in Berlin. Arrhenius was awarded the Nobel Prize for Chemistry in 1903,  and he was also nominated for the Prize for Physics (see Section 1).

The award of the Nobel Prize for Chemistry in 1909 to Ostwald was chiefly in recognition of his work on catalysis and the rates of chemical reactions. Ostwald had in his investigations, following up observations in his thesis in 1878, shown that the rate of acid-catalyzed reactions is proportional to the square of the strength of the acid, as measured by titration with base. His work offered support not only to Arrhenius’ theory of dissociation but also to van’t Hoff’s theory for osmotic pressure. Ostwald was founder and editor of Zeitschrift für Physikalische Chemie, the publication of which is generally regarded as the birth of this new branch of chemistry.

Three of the Nobel Prizes for Chemistry during the first decade were awarded for pioneering work in organic chemistry. In 1902 Emil Fischer, then in Berlin, was given the prize for “his work on sugar and purine syntheses”. Fischer’s work is an example of the growing interest biologically important substances, and was a foundation for the development of biochemistry. Another major influence from organic chemistry was the development of chemical industry, and a chief contributor here was Fischer’s teacher, Adolf von Baeyer in Munich, who was awarded the prize in 1905 “in recognition of his services in the advancement of organic chemistry and the chemical industry, … ” His contributions include, in particular, structure determination of organic

Ernest Rutherford [Lord Rutherford since 1931], professor of physics in Manchester, was awarded the Nobel Prize for Chemistry in 1908. In his studies of uranium disintegration he found two types of radiation, named α- and β-rays, and by their deviation in electric and magnetic fields he could show that α-rays consist of positively charged particles. He had received many nominations for the Nobel Prize for Physics (see Section 1).

In 1897 Eduard Buchner, at the time professor in Tübingen, published results demonstrating that the fermentation of sugar to alcohol and carbon dioxide can take place in the absence of yeast cells. Louis Pasteur had earlier maintained that alcoholic fermentation can only occur in the presence of living yeast cells. Buchner’s experiments showed unequivocally that fermentation is a catalytic process caused by the action of enzymes, as had been suggested by Berzelius for all life processes. Because of Buchner’s experiment, 1897 is generally regarded as the birth date for biochemistry proper. Buchner was awarded the Nobel Prize for Chemistry in 1907, when he was professor at the agricultural college in Berlin. This confirmed the prediction of his former teacher, Adolf von Baeyer: “This will make him famous, in spite of the fact that he lacks talent as a chemist.”

  1. The Nobel Prizes for Chemistry 1911-2000

3.1 General and Physical Chemistry

The Nobel Prize for Chemistry in 1914 was awarded to Theodore William Richards of Harvard University for “his accurate determinations of the atomic weight of a large number of chemical elements”. In 1913 Richards had discovered that the atomic weight of natural lead and of that formed in radioactive decay of uranium minerals differ. This pointed to the existence of isotopes, i.e. atoms of the same element with different atomic weights, which was accurately demonstrated by Francis William Aston at Cambridge University, with the aid of an instrument developed by him, the mass spectrograph. For his achievements Aston received the Nobel Prize for Chemistry in 1922.

One branch of physical chemistry deals with chemical events at the interface of two phases, for example, solid and liquid, and phenomena at such interfaces have important applications all the way from technical to physiological processes. Detailed studies of adsorption on surfaces, were carried out by Irving Langmuir at the research laboratory of General Electric Company, who was awarded the Nobel Prize for Chemistry in 1932, the first industrial scientist to receive this distinction.

Two of the Prizes for Chemistry in more recent decades have been given for fundamental work in the application of spectroscopic methods (Prizes for Physics in 1952, 1955 and 1961) to chemical problems. Gerhard Herzberg, a physicist at the University of Saskatchewan, received the Nobel Prize for Chemistry in 1971 for his molecular spectroscopy studies “of the electronic structure and geometry of molecules, particularly free radicals”. The most used spectroscopic method in chemistry is undoubtedly NMR (nuclear magnetic resonance), and Richard R. Ernst at ETH in Zürich was given the Nobel Prize for Chemistry in 1991 for “the development of the methodology of high resolution nuclear magnetic resonance (NMR) spectroscopy”. Ernst’s methodology has now made it possible to determine the structure in solution (in contrast to crystals; cf. Section 3.5) of large molecules, such as proteins.

3.2 Chemical Thermodynamics

The Nobel Prize for Chemistry to van’t Hoff was in part for work in chemical thermodynamics, and many later contributions in this area have also been recognized with Nobel Prizes.  Walther Hermann Nernst of Berlin received this award in 1920 for work in thermochemistry, despite a 16-year opposition to this recognition from Arrhenius. Nernst had shown that it is possible to determine the equilibrium constant for a chemical reaction from thermal data, and in so doing he formulated what he himself called the third law of thermodynamics. This states that the entropy, a thermodynamic quantity, which is a measure of the disorder in the system, approaches zero as the temperature goes towards absolute zero. van’t Hoff had derived the mass action equation in 1886, with the aid of the second law which says, that the entropy increases in all spontaneous processes [this had already been done in 1876 by J. Willard Gibbs at Yale, who certainly had deserved a Nobel Prize].  Nernst showed in 1906 that it is possible with the aid of the third law, to derive the necessary parameters from the temperature dependence of thermochemical quantities. Nernst carried out thermo-chemical measurements at very low temperatures to prove his heat theorem. G.N. Lewis (see Section 1.1) in Berkeley extended these studies in the 1920s and his new formulation of the third law was confirmed by his student, William Francis Giauque, who extended the temperature range experimentally accessible by introducing the method of adiabatic demagnetization in 1933. He managed to reach temperatures a few thousandths of a degree above absolute zero and could thereby provide extremely accurate entropy estimates. He also showed that it is possible to determine entropies from spectroscopic data. Giauque was awarded the Nobel Prize for Chemistry in 1949 for his contributions to chemical thermodynamics.

The next Nobel Prize given for work in thermodynamics went to Lars Onsager of Yale University in 1968 for contributions to the thermodynamics of irreversible processes. Classical thermodynamics deals with systems at equilibrium, in which the chemical reactions are said to be reversible, but many chemical systems, for example, the most complex of all, living organisms, are far from equilibrium and their reactions are said to be irreversible. Onsager developed his so-called reciprocal relations in 1931, describing the flow of matter and energy in such systems, but the importance of his work was not recognized until the end of the 1940s. A further step forward in the development of non-equilibrium thermodynamics was taken by Ilya Prigogine in Bruxelles, whose theory of dissipative structures was awarded the Nobel Prize for Chemistry in 1977.

3.3 Chemical Change

The chief method to get information about the mechanism of chemical reactions is chemical kinetics, i.e. measurements of the rate of the reaction as a function of reactant concentrations as well as its dependence on temperature, pressure and reaction medium. Important work in this area had been done already in the 1880s by two of the early Laureates, van’t Hoff and Arrhenius, who showed that it is not enough for molecules to collide for a reaction to take place. Only molecules with sufficient kinetic energy in the collision do, in fact, react, and Arrhenius derived an equation in 1889 allowing the calculation of this activation energy from the temperature dependence of the reaction rate. With the advent of quantum mechanics in the 1920s (see Section 3.4), Eyring developed his transition-state theory in 1935 which showed that the activation entropy is also important. Strangely, Eyring never received a Nobel Prize (see Section 1.2).

In 1956 Sir Cyril Norman Hinshelwood of Oxford and Nikolay Nikolaevich Semenov from Moscow shared the Nobel Prize for Chemistry “for their researches into the mechanism of chemical reactions”.  A limit in investigating reaction rates is set by the speed with which the reaction can be initiated. If this is done by rapid mixing of the reactants, the time limit is about one thousandth of a second (millisecond). In the 1950s Manfred Eigen from Göttingen developed chemical relaxation methods that allow measurements in times as short as a thousandth or a millionth of a millisecond (microseconds or nanoseconds). The methods involve disturbing an equilibrium by rapid changes in temperature or pressure and then follow the passage to a new equilibrium. Another way to initiate some reactions rapidly is flash photolysis, i.e. by short light flashes, a method developed by Ronald G.W. Norrish at Cambridge and George Porter (Lord Porter since 1990) in London. Eigen received one-half and Norrish and Porter shared the other half of the Nobel Prize for Chemistry in 1967. The milli- to picosecond time scales gave important information on chemical reactions. However, it was not until it was possible to generate femtosecond laser pulses (10-15 s) that it became possible to reveal when chemical bonds are broken and formed. Ahmed Zewail (born 1946 in Egypt) at California Institute of Technology received the Nobel Prize for Chemistry in 1999 for his development of “femtochemistry” and in particular for being the first to experimentally demonstrate a transition state during a chemical reaction. His experiments relate back to 1889 when Arrhenius (Nobel Prize, 1903) made the important prediction that there must exist intermediates (transition states) in the transformation from reactants to products.

Henry Taube of Stanford University was awarded the Nobel Prize for Chemistry in 1983 “for his work on the mechanism of electron transfer reactions, especially in metal complexes”. Even if Taube’s work was on inorganic reactions, electron transfer is important in many catalytic processes used in industry and also in biological systems, for example, in respiration and photosynthesis.

3.4 Theoretical Chemistry and Chemical Bonding

Quantum mechanics, developed in the 1920s, offered a tool towards a more basic understanding of chemical bonds. In 1927 Walter Heitler and Fritz London showed that it is possible to solve exactly the relevant equations for the hydrogen molecule ion, i.e. two hydrogen nuclei sharing a single electron, and thereby calculate the attractive force between the nuclei. A pioneer in developing such methods was Linus Pauling at California Institute of Technology, who was awarded the Nobel Prize for Chemistry in 1954 “for his research into the nature of the chemical bond …” Pauling’s valence-bond (VB) method is rigorously described in his 1935 book Introduction to Quantum Mechanics (written together with E. Bright Wilson, Jr., at Harvard). A few years later (1939) he published an extensive non-mathematical treatment in The Nature of the Chemical Bond, a book which is one of the most read and influential in the entire history of chemistry. Pauling was not only a theoretician, but he also carried out extensive investigations of chemical structure by X-ray diffraction (see Section 3.5). On the basis of results with small peptides, which are building blocks of proteins, he suggested the α-helix as an important structural element. Pauling was awarded the Nobel Peace Prize for 1962, and he is the only person to date to have won two unshared Nobel Prizes.

α-helix   Pauling’s α-helix

α-carbon atoms are black, other carbon atoms grey, nitrogen atoms blue, oxygen atoms red and hydrogen atoms white; R designates amino-acid side chains. The dotted red lines are hydrogen bonds between amide and carbonyl groups in the peptide bonds.

Pauling’s VB method cannot give an adequate description of chemical bonding in many complicated molecules, and a more comprehensive treatment, the molecular-orbital (MO) method, was introduced already in 1927 by Robert S. Mulliken from Chicago and later developed further. MO theory considers, in quantum-mechanical terms, the interaction between all atomic nuclei and electrons in a molecule. Mulliken also showed that a combination of MO calculations with experimental (spectroscopic) results provides a powerful tool for describing bonding in large molecules. Mulliken received the Nobel Prize for Chemistry in 1966.

Theoretical chemistry has also contributed significantly to our understanding of chemical reaction mechanisms. In 1981 the Nobel Prize for Chemistry was shared between Kenichi Fukui in Kyoto and Roald Hoffmann of Cornell University “for their theories, developed independently, concerning the course of chemical reactions”. Fukui introduced in 1952 the frontier-orbital theory, according to which the occupied MO with the highest energy and the unoccupied one with the lowest energy have a dominant influence on the reactivity of a molecule. Hoffmann formulated in 1965, together with Robert B. Woodward (see Section 3.8), rules based on the conservation of orbital symmetry, for the reactivity and stereochemistry in chemical reactions.
3.5 Chemical Structure

The most commonly used method to determine the structure of molecules in three dimensions is X-ray crystallography. The diffraction of X-rays was discovered by Max von Laue in 1912, and this gave him the Nobel Prize for Physics in 1914. Its use for the determination of crystal structure was developed by Sir William Bragg and his son, Sir Lawrence Bragg, and they shared the Nobel Prize for Physics in 1915. The first Nobel Prize for Chemistry for the use of X-ray diffraction went to Petrus (Peter) Debye, then of Berlin, in 1936. Debye did not study crystals, however, but gases, which give less distinct diffraction patterns.

Many Nobel Prizes have been awarded for the determination of the structure of biological macromolecules (proteins and nucleic acids). Proteins are long chains of amino-acids, as shown by Emil Fischer (see Section 2), and the first step in the determination of their structure is to determine the order (sequence) of these building blocks. An ingenious method for this tedious task was developed by Frederick Sanger of Cambridge, and he reported the amino-acid sequence for a protein, insulin, in 1955. For this achievement he was awarded the Nobel Prize for Chemistry in 1958. Sanger later received part of a second Nobel Prize for Chemistry for a method to determine the nucleotide sequence in nucleic acids (see Section 3.12), and he is the only scientist so far who has won two Nobel Prizes for Chemistry.

The first protein crystal structures were reported by Max Perutz and Sir John Kendrew in 1960, and these two investigators shared the Nobel Prize for Chemistry in 1962. Perutz had started studying the oxygen-carrying blood pigment, hemoglobin, with Sir Lawrence Bragg in Cambridge already in 1937, and ten years later he was joined by Kendrew, who looked at crystals of the related muscle pigment, myoglobin. These proteins are both rich in Pauling’s α-helix (see Section 3.4), and this made it possible to discern the main features of the structures at the relatively low resolution first used. The same year that Perutz and Kendrew won their prize, the Nobel Prize for Physiology or Medicine went to Francis Crick, James Watson and Maurice Wilkins “for their discoveries concerning the molecular structure of nucleic acids … .” Two years later (1964) Dorothy Crowfoot Hodgkin received the Nobel Prize for Chemistry for determining the crystal structures of penicillin and vitamin B12.

Crystallographic electron microscopy was developed by Sir Aaron Klug in Cambridge, who was awarded the Nobel Prize for Chemistry in 1982. Attempts to prepare crystals of membrane proteins for structural studies were unsuccessful, but in 1982 Hartmut Michel managed to crystallize a photosynthetic reaction center after a painstaking series of experiments. He then proceeded to determine the three-dimensional structure of this protein complex in collaboration with Johann Deisenhofer and Robert Huber, and this was published in 1985. Deisenhofer, Huber and Michel shared the Nobel Prize for Chemistry in 1988. Michel has later also crystallized and determined the structure of the terminal enzyme in respiration, and his two structures have allowed detailed studies of electron transfer (cf. Sections 3.3 and 3.4) and its coupling to proton pumping, key features of the chemiosmotic mechanism for which Peter Mitchell had already received the Nobel Prize for Chemistry in 1978 (see Section 3.12). Functional and structural studies on the enzyme ATP synthase, connected to this proton pumping mechanism, was awarded one-half of the Nobel Prize for Chemistry in 1997, shared between Paul D. Boyer and John Walker (see Section 3.12).

3.6 Inorganic and Nuclear Chemistry

Much of the progress in inorganic chemistry during the 20th century has been associated with investigations of coordination compounds, i.e., a central metal ion surrounded by a number of coordinating groups, called ligands. In 1893 Alfred Werner in Zürich presented his coordination theory, and in 1905 he summarized his investigations in this new field in a book (Neuere Anschauungen auf dem Gebiete der anorganischen Chemie), which appeared in no less than five editions from 1905-1923. . Werner showed that a structure for compounds in which a metal ion binds several other molecules (ligands), all the ligand molecules are bound directly to the metal ion. Werner was awarded the Nobel Prize for Chemistry in 1913. Taube’s investigations of electron transfer, awarded in 1983 (see Section 3.3), were mainly carried out with coordination compounds, and vitamin B12 as well as the proteins hemoglobin and myoglobin, investigated by the Laureates Hodgkin, Perutz and Kendrew (see Section 3.5), also belong to this category.

Much inorganic chemistry in the early 1900s was a consequence of the discovery of radioactivity in 1896, for which Henri Becquerel from Paris was awarded the Nobel Prize for Physics in 1903, together with Pierre and Marie Curie. In 1911 Marie Curie received the Nobel Prize for Chemistry for her discovery of the elements radium and polonium and for the isolation of radium and studies of its compounds, and this made her the first investigator to be awarded two Nobel Prizes. The prize in 1921 went to Frederick Soddy of Oxford for his work on the chemistry of radioactive substances and on the origin of isotopes. In 1934 Frédéric Joliot and his wife Irène Joliot-Curie, the daughter of the Curies, discovered artificial radioactivity, i.e., new radioactive elements produced by the bombardment of non-radioactive elements with a-particles or neutrons. They were awarded the Nobel Prize for Chemistry in 1935 for “their synthesis of new radioactive elements”.

Many elements are mixtures of non-radioactive isotopes (see Section 3.1), and in 1934 Harold Urey of Columbia University had been given the Nobel Prize for Chemistry for his isolation of heavy hydrogen (deuterium). Urey had also separated uranium isotopes, and his work was an important basis for the investigations by Otto Hahn from Berlin. In attempts to make transuranium elements, i.e., elements with a higher atomic number than 92 (uranium), by radiating uranium atoms with neutrons, Hahn discovered that one of the products was barium, a lighter element. Lise Meitner, at the time a refugee from Nazism in Sweden, who had earlier worked with Hahn and taken the initiative for the uranium bombardment experiments, provided the explanation, namely, that the uranium atom was cleaved and that barium was one of the products. Hahn was awarded the Nobel Prize for Chemistry in 1944 “for his discovery of the fission of heavy nuclei”, and it can be wondered why Meitner was not included. Hahn’s original intention with his experiments was later achieved by Edwin M. McMillan and Glenn T. Seaborg of Berkeley, who were given the Nobel Prize for Chemistry in 1951 for “discoveries in the chemistry of transuranium elements”.

The use of stable as well as radioactive isotopes have important applications, not only in chemistry, but also in fields as far apart as biology, geology and archeology. In 1943 George de Hevesy from Stockholm received the Nobel Prize for Chemistry for his work on the use of isotopes as tracers, involving studies in inorganic chemistry and geochemistry as well as on the metabolism in living organisms. The prize in 1960 was given to Willard F. Libby of the University of California, Los Angeles (UCLA), for his method to determine the age of various objects (of geological or archeological origin) by measurements of the radioactive isotope carbon-14.

3.7 General Organic Chemistry

Contributions in organic chemistry have led to more Nobel Prizes for Chemistry than work in any other of the traditional branches of chemistry. Like the first prize in this area, that to Emil Fischer in 1902 (see Section 2), most of them have, however, been awarded for advances in the chemistry of natural products and will be treated separately (Section 3.9). Another large group, preparative organic chemistry, has also been given its own section (Section 3.8), and here only the prizes for more general contributions to organic chemistry will be discussed.

In 1969 the Nobel Prize for Chemistry went to Sir Derek H. R. Barton from London, and Odd Hassel from Oslo for developing the concept of conformation, i.e. the spatial arrangement of atoms in molecules, which differ only by the orientation of chemical groups by rotation around a single bond. This stereochemical concept rests on the original suggestion by van’t Hoff of the tetrahedral arrangement of the four valences of the carbon atom (see Section 2), and most organic molecules exist in two or more stable conformations.

The Nobel Prize for Chemistry in 1975 to Sir John Warcup Cornforth of the University of Sussex and Vladimir Prelog of ETH in Zürich was also based on research in stereochemistry. Not only can a compound have more than one geometric form, but chemical reactions can also have specificity in their stereochemistry, thereby forming a product with a particular three-dimensional arrangement of the atoms. This is especially true of reactions in living organisms, and Cornforth has mainly studied enzyme-catalyzed reactions, so his work borders onto biochemistry (Section 3.12). One of Prelog’s main contributions concerns chiral molecules, i.e. molecules that have two forms differing from one another as the right hand does from the left. Stereochemically specific reactions have great practical importance, as many drugs, for example, are active only in one particular geometric form.

Organometallic compounds constitute a group of organic molecules containing one or more carbon-metal bond, and they are thus the organic counterpart to Werner’s inorganic coordination. In 1952 Ernst Otto Fischer and Sir Geoffrey Wilkinson independently described a completely new group of organometallic molecules, called sandwich compounds in which compounds a metal ion is bound not to a single carbon atom but is “sandwiched” between two aromatic organic molecules. Fischer and Wilkinson shared the Nobel Prize for Chemistry in 1973.

3.8 Preparative Organic Chemistry

One of the chief goals of the organic chemist is to be able to synthesize increasingly complex compounds of carbon in combination with various other elements. The first Nobel Prize for Chemistry recognizing pioneering work in preparative organic chemistry was that to Victor Grignard from Nancy and Paul Sabatier from Toulouse in 1912. Grignard had discovered that organic halides can form compounds with magnesium. Sabatier was given the prize for developing a method to hydrogenate organic compounds in the presence of metallic catalysts. The prize in 1950 was presented to Otto Diels from Kiel and Kurt Alder from Cologne “for their discovery and development of the diene synthesis”, developed in 1928, by which organic compounds containing two double bonds (“dienes”) can effect the syntheses of many cyclic organic substances.

The German organic chemist Hans Fischer from Munich had already done significant work on the structure of hemin, the organic pigment in hemoglobin, when he synthesized it from simpler organic molecules in 1928. He also contributed much to the elucidation of the structure of chlorophyll, and for these important achievements he was awarded the Nobel Prize for Chemistry in 1930 (cf. Section 3.5). He finished his determination of the structure of chlorophyll in 1935, and by the time of his death he had almost completed its synthesis as well.

Robert Burns Woodward from Harvard is rightly considered the founder of the most advanced, modern art of organic synthesis. He designed methods for the total synthesis of a large number of complicated natural products, for example, cholesterol, chlorophyll and vitamin B12. He received the Nobel Prize for Chemistry in 1965, and he would probably have received a second chemistry prize in 1981 for his part in the formulation of the Woodward-Hoffmann rules (see Section 3.4), had it not been for his early death.

The Nobel Prize for Chemistry in 1984 was given to Robert Bruce Merrifield of Rockefeller University “for his development of methodology for chemical synthesis on a solid matrix”. Specifically, the synthesis of large peptides and small proteins.

3.9 Chemistry of Natural Product

The synthesis of complex organic molecules must be based on detailed knowledge of their structure. Early work on plant pigments was carried out by Richard Willstätter, a student of Adolf von Baeyer from Munich (see Section 2). Willstätter showed a structural relatedness between chlorophyll and hemin, and he demonstrated that chlorophyll contains magnesium as an integral component. He also carried out pioneering investigations on other plant pigments, such as the carotenoids, and he was awarded the Nobel Prize for Chemistry in 1915 for these achievements. Willstätter’s work laid the ground for the synthetic accomplishments of Hans Fischer (see Section 3.8). In addition, Willstätter contributed to the understanding of enzyme reactions.

The prizes for 1927 and 1928 were both presented to Heinrich Otto Wieland from Munich and Adolf Windaus from Göttingen, respectively, at the Nobel ceremony in 1928. These two chemists had done closely related work on the structure of steroids. The award to Wieland was primarily for his investigations of bile acids, whereas Windaus was recognized mainly for his work on cholesterol and his demonstration of the steroid nature of vitamin D. Wieland had already in 1912, before his prize-winning work, formulated a theory for biological oxidation, according to which removal of hydrogen (dehydrogenation) rather than reaction with oxygen is the dominating process.

Investigations on vitamins were recognized in 1937 and 1938 with the prizes to Sir Norman Haworth from Birmingham and Paul Karrer from Zürich and to Richard Kuhn from Heidelberg. Haworth did outstanding work in carbohydrate chemistry, establishing the ring structure of glucose. He was the first chemist to synthesize vitamin C, and this is the basis for the present large-scale production of this nutrient. Haworth shared the prize with Karrer, who determined the structure of carotene and of vitamin A. Kuhn also worked on carotenoids, and he published the structure of vitamin B2 at the same time as Karrer. He also isolated vitamin B6. In 1939 the Nobel Prize for Chemistry was shared between Adolf Butenandt from Berlin and Leopold Ruzicka (1887-1976) of ETH, Zurich. Butenandt was recognized “for his work on sex hormones”, having isolated estrone, progesterone and androsterone. Ruzicka synthesized androsterone and also testosterone.

The awards for outstanding work in natural-product chemistry continued after World War II. In 1947 Sir Robert Robinson from Oxford received the prize for his studies on plant substances, particularly alkaloids, such as morphine. Robinson also synthesized steroid hormones, and he elucidated the structure of penicillin. Many hormones are of a polypeptide nature, and in 1955 Vincent du Vigneaud of Cornell University was given the prize for his synthesis of two such hormones, vasopressin and oxytocin. Finally, in this area, Alexander R. Todd (Lord Todd since 1962) was recognized in 1957 “for his work on nucleotides and nucleotide co-enzymes”. Todd had synthesized ATP (adenosine triphosphate) and ADP (adenosine diphosphate), the main energy carriers in living cells, and he determined the structure of vitamin B12 (cf. Section 3.5) and of FAD (flavin-adenine dinucleotide).

3.10 Analytical Chemistry and Separation Science

A prize in analytical chemistry was given to Jaroslav Heyrovsky from Prague in 1959 for his development of polarographic methods of analysis. In these a dropping mercury electrode is employed to determine current-voltage curves for electrolytes. A given ion reacts at a specific voltage, and the current is a measure of the concentration of this ion.

The analysis of macromolecular constituents in living organisms requires specialized methods of separation. Ultracentrifugation wad developed by The Svedberg from Uppsala a few years before he was awarded the Nobel Prize for Chemistry in 1926 “for his work on disperse systems” (see Section 3.11). Svedberg’s student, Arne Tiselius, studied the migration of protein molecules in an electric field, and with this method, named electrophoresis, he demonstrated the complex nature of blood proteins. Tiselius also refined adsorption analysis, a method first used by the Russian botanist, Michail Tswett, for the separation of plant pigments and named chromatography by him. In 1948 Tiselius was given the prize for these achievements. A few years later (1952) Archer J.P. Martin from London and Richard L.M. Synge from Bucksburn (Scotland) shared the prize “for their invention of partition chromatography”, and this method was a major tool in many biochemical investigations later awarded with Nobel Prizes (see Section 3.12).

3.11 Polymers and Colloids

The Svedberg who received the Nobel Prize for Chemistry in 1926, also investigated gold sols. He used Zsigmond’s ultramicroscope to study the Brownian movement of colloidal particles, so named after the Scottish botanist Robert Brown, and confirmed a theory developed by Albert Einstein in 1905 and, independently, by M. Smoluchowski. His greatest achievement was, however, the construction of the ultracentrifuge, with which he studied not only the particle size distribution in gold sols but also determined the molecular weight of proteins, for example, hemoglobin. In the same year as Svedberg got the prize the Nobel Prize for Physics was awarded to Jean Baptiste Perrin of Sorbonne for developing equilibrium sedimentation in colloidal solutions, a method which Svedberg later perfected in his ultracentrifuge. Svedberg’s investigations with the ultracentrifuge and Tiselius’s electrophoresis studies (see Section 3.10) were instrumental in establishing that protein molecules have a unique size and structure, and this was a prerequisite for Sanger’s determination of their amino-acid sequence and the crystallographic work of Kendrew and Perutz (see Section 3.5).

3.12 Biochemistry

The second Nobel Prize for discoveries in biochemistry came in 1929, when Sir Arthur Harden from London and Hans von Euler-Chelpin from Stockholm shared the prize for investigations of sugar fermentation, which formed a direct continuation of Buchner’s work awarded in 1907. With his young co-worker, William John Young, Harden had shown in 1906 that fermentation requires a dialysable substance, called co-zymase, which is not destroyed by heat. Harden and Young also demonstrated that the process stops before all sugar (glucose) has been used up, but it starts again on addition of inorganic phosphate, and they suggested that hexose phosphates are formed in the early steps of fermentation. von Euler had done important work on the structure of co-zymase, shown to be nicotinamide adenine dinucleotide (NAD, earlier called DPN). As the number of Laureates can be three, it may seem appropriate for Young to have been included in the award, but Euler’s discovery was published together with Karl Myrbäck, and the number of Laureates is limited to three.

The next biochemical Nobel Prize was given in 1946 for work in the protein field. James B. Sumner of Cornell University received half the prize “for his discovery that enzymes can be crystallized” and John H. Northrop together with Wendell M. Stanley, both of the Rockefeller Institute, shared the other half “for their preparation of enzymes and virus proteins in a pure form”. Sumner had in 1926 crystalized an enzyme, urease, from jack beans and suggested that the crystals were the pure protein. His claim was, however, greeted with great scepticism, and the crystals were suggested to be inorganic salts with the enzyme adsorbed or occluded. Just a few years after Sumner’s discovery Northrop, however, managed to crystalize three digestive enzymes, pepsin, trypsin and chymotrypsin, and by painstaking experiments shown them to be pure proteins. Stanley started his attempt to purify virus proteins in the 1930s, but not until 1945 did he get virus crystals, and this then made it possible to show that viruses are complexes of protein and nucleic acid. The pioneering studies of these three investigators form the basis for the enormous number of new crystal structures of biological macromolecules, which have been published in the second half of the 20th century (cf. Section 3.5).

Several Nobel Prizes for Chemistry have been awarded for work in photosynthesis and respiration, the two main processes in the energy metabolism of living organisms (cf. Section 3.5). In 1961 Melvin Calvin of Berkeley received the prize for elucidating the carbon dioxide assimilation in plants. With the aid of carbon-14 (cf. Section 3.6) Calvin had shown that carbon dioxide is fixed in a cyclic process involving several enzymes. Peter Mitchell of the Glynn Research Laboratories in England was awarded in 1978 for his formulation of the chemiosmotic theory. According to this theory, electron transfer (cf. Sections 3.3 and 3.4) in the membrane-bound enzyme complexes in both respiration and photosynthesis, is coupled to proton translocation across the membranes, and the electrochemical gradient thus created is used to drive the synthesis of ATP (adenosine triphosphate), the energy storage molecule in all living cells. Paul D. Boyer of UCLA and John C. Walker of the MRC Laboratory in Cambridge shared one-half of the 1997 prize for their elucidation of the mechanism of ATP synthesis; the other half of the prize went to Jens C. Skou in Aarhus for the first discovery of an ion-transporting enzyme. Walker had determined the crystal structure of ATP synthase, and this structure confirmed a mechanism earlier proposed by Boyer, mainly on the basis of isotopic studies.

Luis F. Leloir from Buenos Aires was awarded in 1970 “for the discovery of sugar nucleotides and their role in the biosynthesis of carbohydrates”. In particular, Leloir had elucidated the biosynthesis of glycogen, the chief sugar reserve in animals and many microorganisms. Two years later the prize went with one half to Christian B. Anfinsen of NIH and the other half shared by Stanford Moore and William H. Stein, both from Rockefeller University, for fundamental work in protein chemistry. Anfinsen had shown, with the enzyme ribonuclease, that the information for a protein assuming a specific three-dimensional structure is inherent in its amino-acid sequence, and this discovery was the starting point for studies of the mechanism of protein folding, one of the major areas of present-day biochemical research. Moore and Stein had determined the amino-acid sequence of ribonuclease, but they received the prize for discovering anomalous properties of functional groups in the enzyme’s active site, which is a result of the protein fold.

Naturally a number of Nobel Prizes for Chemistry have been given for work in the nucleic acid field. In 1980 Paul Berg of Stanford received one half of the prize for studies of recombinant DNA, i.e. a molecule containing parts of DNA from different species, and the other half was shared by Walter Gilbert from Harvard and Frederick Sanger (see Section 3.5) for developing methods for the determination of the base sequences of nucleic acids. Berg’s work provides the basis of genetic engineering, which has led to the large biotechnology industry. Base sequence determinations are essential steps in recombinant-DNA technology, which is the rationale for Gilbert and Sanger sharing the prize with Berg.

Sidney Altman of Yale and Thomas R. Cech of the University of Colorado shared the prize in 1989 “for their discovery of the catalytic properties of RNA”. The central dogma of molecular biology is: DNA –> RNA –> enzyme. The discovery that not only enzymes but also RNA possesses catalytic properties have led to new ideas about the origin of life. The 1993 prize was shared by Kary B. Mullis from La Jolla and Michael Smith from Vancouver, who both have given important contributions to DNA technology. Mullis developed the PCR (“polymerase chain reaction”) technique, which makes it possible to replicate millions of times a specific DNA segment in a complicated genetic material. Smith’s work forms the basis for site-directed mutagenesis, a technique by which it is possible to change a specific amino-acid in a protein and thereby illuminate its functional role.

  1. Concluding Remarks

The first eighty years of Nobel Prizes for Chemistry outlines the development of modern chemistry. The prizes cover a broad spectrum of the basic chemical sciences, from theoretical chemistry to biochemistry, and also a number of contributions to applied chemistry. Organic chemistry dominates with no less than 25 awards. This is not surprising, since the special valence properties of carbon result in an almost infinite variation in the structure of organic compounds. Also, a large number of the prizes in organic chemistry were given for investigations of the chemistry of natural products of increasing complexity, and have lead to pharmaceutical development .

As many as 11 prizes have been awarded for biochemical discoveries. The first biochemical prize was already given in 1907 (Buchner), but only three awards in this area came in the first half of the century, illustrating the explosive growth of biochemistry in recent decades (8 prizes in 1970-1997). At the other end of the chemical spectrum, physical chemistry, including chemical thermodynamics and kinetics, dominates with 14 prizes, but there have also been 6 prizes in theoretical chemistry. Chemical structure is a large area with 8 prizes, including awards for methodological developments as well as for the determination of the structure of large biological molecules or molecular complexes. Industrial chemistry was first recognized in 1931 (Bergius, Bosch), but many more recent prizes for basic contributions lie close to industrial applications.

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Introduction to Impairments in Pathological States: Endocrine Disorders, Stress Hypermetabolism and Cancer

Author and Curator: Larry H. Bernstein, MD, FCAP 

 

This leads into a series of presentations and the metabolic imbalance central to findings of endocrine, metabolic, inflammatory, immune diseases and cancer.  All of this has been a result of discoveries based on the methods of study of genomiocs, proteomics, transcriptomics, and metabolomics that have preceded this.  In some cases there has been the use of knockout methods. The completion of the human genomic and other catalogues have been instrumental in the past few years.  In all cases there has been a thorough guidance by a biological concept of mechanism based on gene expression, metabolic disturbance, signaling pathways, and up- or down- regulation of metabolic circuits.  It is interesting to recall that a concept of metabolic circuits was not yet formulated at the time of the mid 20th century physiology, except perhaps with respect to the coagulation pathways, and to some extent, glycolysis, gluconeogenesis, the hexose monophosphate shunt, and mitochondrial respiration, which were linear strings of enzyme substrate reactions that intersected and that had flow restraints not then understood as to the complexity we now appreciate.  We did know the importance of cytochrome c, the adenine and pyridine nucleotides, and the energy balance.  Electron microscopy had opened the door to understanding the mechanism of contraction of skeletal muscle and myocardium, but it also opened the door to understanding kidney structure and function, explaining the “mesangium”.  The first cardiac maker was discovered by Arthur Karmen in the serum alanine and aspartate aminotransferases, with a consequent differentiation between hepatic and myocardial damage.  This was followed by lactic dehydrogenase and the H- and M-type isoenzymes in the 1960s, and in the next decade, by the MB-isoenzyme of creatine kinase.  Troponins T and then I would not be introduced until the mid 1980s, and they have become a gold standard for the diagnosis of myocardial infarction.

In the 1980s we also saw the development of antiplatelet therapy that rapidly advanced interventional cardiology.  But advances in surgical as well as medical intervention also proceeded as the understanding of the lipid metabolism was opened by the work of Brown and Goldstein, and UTSW Medical Campus, and major advances in treatment came at Baylor and UT Medical Center in Houston, and at the Cleveland Clinic.  The next important advance came with the discovery of nitric oxide synthase role in endothelium and oxidative stress.  The field of endocrinology saw advances as well for a solid period of 30 years in a comparable period for the adrenals, thyroid, and pituitary glands, and for the understanding of the male and female sex hormones, and discoveries in breast, ovarian, and prostate cancer.  There were cancer markers, such as, CA125 and CA15-3, and PSA.  This had more of an impact on timely surgical intervention, and if not that, post surgical followup.  Despite a long time into the war on cancer, introduced by President Lynden Johnson, the fundamental knowledge needed was not sufficient.  In the meantime, there were advances in the treatment of diabetes, with eventual introduction of the insulin pump for type I diabetes.  The problem of Type 2 DM increased in prevalence, reaching into the childhood age group, with ascendent obesity.  An epidemiological pattern of disease comorbidities was emergent.  Our population has aged out, and with it we are seeing an increase in dementias, especially Alzheimer’s disease.  But the knowledge of the brain has lagged far behind.

What follows is a series of chapters that address what has currently been advanced with repect to the alignment of our knowledge of the last decade and pharmacetical discovery.  Pharmaceuticals were suitable for bacterial infections until the 1990s, when we saw the rise of resistance to penicillins and Vancomycin, and we had issues with gram negative enterobacter, salmonella, and E. coli strains.  That has been and is a significant challenge.  The elucidation of the gut microbiome in recent years will help to relieve this problem.  The problem of the variety and different aggressive types of cancer has been another challenge.  The door has been opened to better diagnostic tools with respsct to imaging and targeted biomarkers for localization.  I am not dealing with imaging, which is not the subject here.

HLA targeting efficiency correlates with human T-cell response magnitude and with mortality from influenza A infection

From http://www.pnas.org –      Sep 3, 2013 4:24 PM

Experimental and computational evidence suggests that HLAs preferentially bind

  • conserved regions of viral proteins, a concept we term “targeting efficiency,” and
  • that this preference may provide improved clearance of infection in several viral systems.

To test this hypothesis, T-cell responses to A/H1N1 (2009)

  • were measured from peripheral blood mononuclear cells
  • obtained from a household cohort study performed during the 2009–2010 influenza season.

We found that HLA targeting efficiency scores

  • significantly correlated with IFN-γ
    enzyme-linked immunosorbent spot responses (P = 0.042, multiple regression).

A further population-based analysis found that

  • the carriage frequencies of the alleles with the lowest targeting efficiencies, A*24,
  • were associated with pH1N1 mortality (r = 0.37, P = 0.031) and
  • are common in certain indigenous populations in which
  • increased pH1N1 morbidity has been reported.

HLA efficiency scores and HLA use are associated with

  • CD8 T-cell magnitude in humans after influenza infection.

The computational tools used in this study may be useful predictors of

  • potential morbidity and identify immunologic differences of new variant influenza strains
  • more accurately than evolutionary sequence comparisons.

Population-based studies of the relative frequency of these alleles

  • in severe vs. mild influenza cases might advance clinical practices
  • for severe H1N1 infections among genetically susceptible populations.

A deeper look into cholesterol synthesis

By Swathi Parasuraman

The human body needs cholesterol to maintain membrane fluidity, and

  • it acts as a precursor molecule for several important biochemical pathways.

Its regulation requires strict control, as it can cause problems if it’s produced in excess. In 1964, Konrad Bloch received a Nobel Prize for his work elucidating the mechanisms of cholesterol synthesis. His work

  • eventually contributed to the discovery of statins, drugs used today to lower blood cholesterol levels.

The biosynthesis of cholesterol is a complex process with more than 20 steps. One of the first enzymes is

  • 3-hydroxy-3-methylglutaryl-CoA reductase, also known as HMGCR, the main target of statins.

As links between intermediates in cholesterol synthesis and various diseases are being discovered continually, more information about the regulatory role of the post-HMGCR pathway is needed.

In a recent minireview in The Journal of Biological Chemistry, Laura Sharpe and Andrew Brown of the University of New South Wales describe

  • multiple ways various enzymes other than HMGCR
  • are implicated in the modulation of cholesterol synthesis.

One such enzyme is squalene monooxygenase, which, like HMGCR, can be destroyed

  • by the proteasome when cholesterol levels are high.

The minireview also explains how pathway intermediates

  • can have functions distinct from those of cholesterol.

For example, intermediate 7-dehydrocholesterol usually is converted to cholesterol by the enzyme DHCR7

  • but is also a vitamin D precursor.

To synthesize the enzymes necessary to make cholesterol,

  • SREBPs, short for sterol regulatory element binding proteins, have special functions.

Along with transcriptional cofactors, they activate gene expression

  1. in response to low sterol levels and, conversely,
  2. are suppressed when there is enough cholesterol around.

Additionally, SREBPs control production of

  • nicotinamide adenine dinucleotide phosphate, or NADPH,
  • which is the reducing agent required to carry out the different steps in the pathway.

Lipid carrier proteins also can facilitate cholesterol synthesis. One example is SPF, or supernatant protein factor,

  1. which transfers substrate from an inactive to an active pool or
  2. from one enzyme site to another.

Furthermore, translocation of several cholesterogenic enzymes

  • from the endoplasmic reticulum to other cell compartments can occur under various conditions,
  • thereby regulating levels and sites of intracellular cholesterol accumulation.

Immunology in the gut mucosa:

20 Feb 2013 by Kausik Datta, posted in Immunology, Science (Nature)

The human gut can be the scene for devastating conditions such as inflammatory bowel disease,

  • which arises through an improperly controlled immune response.

The gut is often the body’s first point of contact with microbes; every mouthful of food is accompanied by a cargo of micro-organisms that go on to encounter the mucosa, the innermost layer of the gut. Most microbes are destroyed by the harsh acidic environment in the stomach, but a hardy few make it through to the intestines.

The intestinal surface is covered with finger-like protrusions called villi,

whose primary function is the absorption of nutrients.

These structures and the underlying tissues

  • host the body’s largest population of immune cells.

Scattered along the intestinal mucosa are

  • dome-like structures called Peyer’s Patches.

These are enriched in lymphoid tissue, making them key sites for

  • coordinating immune responses to pathogens,
  • whilst promoting tolerance to harmless microbes and food.

The villi contain a network of blood vessels to transport nutrients from food to the rest of the body. Lymphatics

  • from both the Peyer’s Patches and the villi
  • drain into the mesenteric lymph nodes.

Within the villi is a network of loose connective tissue called the lamina propria, and

  • at the base of the villi are the crypts which host the stem cells that replenish the epithelium.

The epithelium together with its overlying mucus forms

  • a barrier against microbial invasion.

A mix of immune cells including T- and B-lymphocytes, macrophages, and dendritic cells are

  • embedded within the matrix of the Peyer’s Patches, .

A key function of the Peyer’s Patch is the sampling of antigens present in the gut. The Peyer’s Patch has a thin mucous layer and specialized phagocytic cells, called M-cells, which

  • transport material across the epithelial barrier via a process called transcytosis.

Dendritic cells extend dendrites between epithelial cells to sample antigens that are then

  • broken down and used for presenting to lymphocytes.

Sampling antigens in this way typically results in so-called tolerogenic activation, where

  • the immune system initiates an anti-inflammatory response.

With their cargo of antigens, these Dendritic Cells then

  • traffic to the T-cell zones of the Peyer’s Patch.

Upon encounter with specific T-cells, the Dendritic Cells

  • convert them into an immunomodulatory cell called regulatory T-cell or T-reg.

Defects in the function of these cells are associated with

  • inflammatory bowel disease in both animals and humans.

These T-regs migrate to lamina propria of the villi via the lymphatics. Here, the T-regs

  • secrete a molecule called Interleukin (IL)-10,
  • which exerts a suppressive action on immune cells within the lamina propria
  • and upon the epithelial layer itself.

IL10 is, therefore, critical in maintaining immune quiescence

  • and preventing unnecessary inflammation.

However, a breakdown in this process of immune homeostasis results in gut pathology and

  • when this occurs over a prolonged period and in an uncontrolled manner,
  • it can lead to inflammatory bowel disease.

Chemical, mechanical or pathogen-triggered barrier disruption

  • coupled with particular genetic susceptibilities may all combine to set off inflammation.

Epithelium coming into contact with bacteria

  • is activated, leading to bacterial influx.

Alarm molecules released by the epithelium

  • activates immune cells, and T-regs in the vicinity
  • scale down their IL10 secretion to enable an immune response to proceed.

Dendritic cells are also activated by this environment, and

  • start to release key inflammatory molecules,
  • such as IL6, IL12, and IL23.

Effector T-cells also appear on the scene and

  • these coordinate an escalation of the immune response
  • by secreting their own inflammatory molecules,
  • Tumor Necrosis Factor (TNF)-α, Interferon (IFN)-γ and IL17.

Soon after the effector T-cells are arrived, a voracious phagocyte called a neutrophil is recruited. Neutrophils are critical for the clearance of the bacteria. One weapon in the neutrophil armory is

  • the ability to undergo self-destruction.

This leaves behind a jumble of DNA saturated with enzymes, called the Neutrophil Extracellular Trap.

Although this can effectively destroy the bacterial invaders

  • and plug any breaches in the epithelial wall,
  • it also causes collateral damage to tissues.

Slowly the tide begins to turn and the bacterial invasion is repulsed. Any remaining neutrophils die off,

  • and are cleared by macrophages.

Epithelial integrity is restored by replacement of damaged cells with new ones from the intestinal crypts. Finally T-regs are recruited once again to calm the immune response.

Targeting the molecules involved in gut pathology is leading to

  • effective therapies for inflammatory bowel disease.

Notes:

T- and B-lymphocytes, Macrophages, and Dendritic Cells: These are all important immune effector cells. Macrophages and Dendritic cells are primary defence cells that can eat up (‘phagocytosis’) microbes and destroy them; they also can present parts of these microbes to lymphocytes. T-lymphocytes or T-cells help B-lymphocytes or B-cells recognize the antigen and form antibodies against it. Other types of T-cells can themselves kill microbes. All these cells also secrete various chemical substances, called cytokines and chemokines, which act as molecular messengers in recruiting various immune cells, coordinating and fine-tuning the immune response. Some of these cytokines are called Interleukins, shortened to IL.

Anti-inflammatory response: A type of immune response in which molecular messengers are used to scale down heavy-handed immune cell activity and switch off processes that recruit immune cells. This helps the body recognize and selectively tolerate beneficial substances such as commensalic microbes that live in the gut.

Neutrophils: These are highly versatile immune effector cells. Usually, they are one of the first cells recruited to the site of infection or tissue damage via message spread by molecular messengers. Neutrophils can themselves elaborate cytokines and chemokines, and have the ability to directly kill microbes.

Oxazoloisoindolinones with in vitro antitumor activity selectively activate a p53-pathway through potential inhibition of the p53-MDM2 interaction.

J Soares, et al. Eur J Pharm Sci 10/2014; http://dx.doi.org:/10.1016/j.ejps.2014.10.006

An appealing target for anticancer treatment is

  • the p53 tumor suppressor protein.

This protein is inactivated in half of human tumors

  • due to endogenous negative regulators such as MDM2.

Therefore, restoring the p53 activity through

  • the inhibition of its interaction with MDM2
  • is considered a valuable therapeutic strategy
  • against cancers with a wild-type p53 status.

We report the synthesis of nine enantiopure phenylalaninol-derived oxazolopyrrolidone lactams

  • and the evaluation of their biological effects as p53-MDM2 interaction inhibitors.

Using a yeast-based screening assay, two oxazoloisoindolinones,

  • were identified as potential p53-MDM2 inhibitors.

The molecular mechanism of oxazoloisoindolinone 3a validated

  • in human colon adenocarcinoma HCT116 cells with wild-type p53 (HCT116 p53(+/+)) and
  • in its isogenic derivative without p53 (HCT116 p53(-/-)).

we demonstrated that oxazoloisoindolinone 3a exhibited

  • a p53-dependent in vitro antitumor activity through
  • induction of G0/G1-phase cell cycle arrest and apoptosis.

The selective activation of a p53-apoptotic pathway by oxazoloisoindolinone 3a was further supported

  • by the occurrence of PARP cleavage only in p53-expressing HCT116 cells.

Oxazoloisoindolinone 3a led

  • to p53 protein stabilization
  • to the up-regulation of p53 transcriptional activity &
  • increased expression levels of several p53 target genes,
  • as p21, MDM2, BAX and PUMA,
  • in p53(+/+) but not in p53(-/-) HCT116 cells.

the ability of oxazoloisoindolinone 3a to block the p53-MDM2 interaction in HCT116 p53(+/+) cells was confirmed by co-immunoprecipitation.

molecular docking analysis of the interactions

  • between the compounds and MDM2 revealed that
  • oxazoloisoindolinone 3a binds to MDM2.

this work adds the oxazoloisoindolinone scaffold to the activators of a wild-type p53-pathway with promising antitumor activity.

it may open the way to the development of

  • a new class of p53-MDM2 interaction inhibitors.

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei.

Sanu Shameer, et al. Nucleic Acids Research10/2014;
http://dx.doi.org/10.1093/nar/gku944

The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells under particular conditions and as technologies advance to allow detailed measurements of the cellular metabolome.

Metabolic network databases are important in allowing us to

  • contextualise data sets emerging from transcriptomic, proteomic and metabolomic experiments.

Here we present a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describes

  • the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan
  • responsible for human and animal African trypanosomiasis.

In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have implemented a network

  • representation of the information through MetExplore,

yielding a novel environment in which to visualise the metabolism of this important parasite.

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Summary to Metabolomics

Summary to Metabolomics

Author and Curator: Larry H. Bernstein, MD, FCAP 

This concludes a long step-by-step journey into rediscovering biological processes from the genome as a framework to the remodeled and reconstituted cell through a number of posttranscription and posttranslation processes that modify the proteome and determine the metabolome.  The remodeling process continues over a lifetime. The process requires a balance between nutrient intake, energy utilization for work in the lean body mass, energy reserves, endocrine, paracrine and autocrine mechanisms, and autophagy.  It is true when we look at this in its full scope – What a creature is man?

http://masspec.scripps.edu/metabo_science/recommended_readings.php
 Recommended Readings and Historical Perspectives

Metabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the “systematic study of the unique chemical fingerprints that specific cellular processes leave behind”, the study of their small-molecule metabolite profiles.[1] The metabolome represents the collection of all metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes.[2] mRNA gene expression data and proteomic analyses reveal the set of gene products being produced in the cell, data that represents one aspect of cellular function. Conversely, metabolic profiling can give an instantaneous snapshot of the physiology of that cell. One of the challenges of systems biology and functional genomics is to integrate proteomic, transcriptomic, and metabolomic information to provide a better understanding of cellular biology.

The term “metabolic profile” was introduced by Horning, et al. in 1971 after they demonstrated that gas chromatography-mass spectrometry (GC-MS) could be used to measure compounds present in human urine and tissue extracts. The Horning group, along with that of Linus Pauling and Arthur B. Robinson led the development of GC-MS methods to monitor the metabolites present in urine through the 1970s.

Concurrently, NMR spectroscopy, which was discovered in the 1940s, was also undergoing rapid advances. In 1974, Seeley et al. demonstrated the utility of using NMR to detect metabolites in unmodified biological samples.This first study on muscle highlighted the value of NMR in that it was determined that 90% of cellular ATP is complexed with magnesium. As sensitivity has improved with the evolution of higher magnetic field strengths and magic angle spinning, NMR continues to be a leading analytical tool to investigate metabolism. Efforts to utilize NMR for metabolomics have been influenced by the laboratory of Dr. Jeremy Nicholson at Birkbeck College, University of London and later at Imperial College London. In 1984, Nicholson showed 1H NMR spectroscopy could potentially be used to diagnose diabetes mellitus, and later pioneered the application of pattern recognition methods to NMR spectroscopic data.

In 2005, the first metabolomics web database, METLIN, for characterizing human metabolites was developed in the Siuzdak laboratory at The Scripps Research Institute and contained over 10,000 metabolites and tandem mass spectral data. As of September 2012, METLIN contains over 60,000 metabolites as well as the largest repository of tandem mass spectrometry data in metabolomics.

On 23 January 2007, the Human Metabolome Project, led by Dr. David Wishart of the University of Alberta, Canada, completed the first draft of the human metabolome, consisting of a database of approximately 2500 metabolites, 1200 drugs and 3500 food components. Similar projects have been underway in several plant species, most notably Medicago truncatula and Arabidopsis thaliana for several years.

As late as mid-2010, metabolomics was still considered an “emerging field”. Further, it was noted that further progress in the field depended in large part, through addressing otherwise “irresolvable technical challenges”, by technical evolution of mass spectrometry instrumentation.

Metabolome refers to the complete set of small-molecule metabolites (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites) to be found within a biological sample, such as a single organism. The word was coined in analogy with transcriptomics and proteomics; like the transcriptome and the proteome, the metabolome is dynamic, changing from second to second. Although the metabolome can be defined readily enough, it is not currently possible to analyse the entire range of metabolites by a single analytical method. The first metabolite database(called METLIN) for searching m/z values from mass spectrometry data was developed by scientists at The Scripps Research Institute in 2005. In January 2007, scientists at the University of Alberta and the University of Calgary completed the first draft of the human metabolome. They catalogued approximately 2500 metabolites, 1200 drugs and 3500 food components that can be found in the human body, as reported in the literature. This information, available at the Human Metabolome Database (www.hmdb.ca) and based on analysis of information available in the current scientific literature, is far from complete.

Each type of cell and tissue has a unique metabolic ‘fingerprint’ that can elucidate organ or tissue-specific information, while the study of biofluids can give more generalized though less specialized information. Commonly used biofluids are urine and plasma, as they can be obtained non-invasively or relatively non-invasively, respectively. The ease of collection facilitates high temporal resolution, and because they are always at dynamic equilibrium with the body, they can describe the host as a whole.

Metabolites are the intermediates and products of metabolism. Within the context of metabolomics, a metabolite is usually defined as any molecule less than 1 kDa in size.
A primary metabolite is directly involved in the normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes.  By contrast, in human-based metabolomics, it is more common to describe metabolites as being either endogenous (produced by the host organism) or exogenous. Metabolites of foreign substances such as drugs are termed xenometabolites. The metabolome forms a large network of metabolic reactions, where outputs from one enzymatic chemical reaction are inputs to other chemical reactions.

Metabonomics is defined as “the quantitative measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification”. The word origin is from the Greek μεταβολή meaning change and nomos meaning a rule set or set of laws. This approach was pioneered by Jeremy Nicholson at Imperial College London and has been used in toxicology, disease diagnosis and a number of other fields. Historically, the metabonomics approach was one of the first methods to apply the scope of systems biology to studies of metabolism.

There is a growing consensus that ‘metabolomics’ places a greater emphasis on metabolic profiling at a cellular or organ level and is primarily concerned with normal endogenous metabolism. ‘Metabonomics’ extends metabolic profiling to include information about perturbations of metabolism caused by environmental factors (including diet and toxins), disease processes, and the involvement of extragenomic influences, such as gut microflora. This is not a trivial difference; metabolomic studies should, by definition, exclude metabolic contributions from extragenomic sources, because these are external to the system being studied.

Toxicity assessment/toxicology. Metabolic profiling (especially of urine or blood plasma samples) detects the physiological changes caused by toxic insult of a chemical (or mixture of chemicals).

Functional genomics. Metabolomics can be an excellent tool for determining the phenotype caused by a genetic manipulation, such as gene deletion or insertion. Sometimes this can be a sufficient goal in itself—for instance, to detect any phenotypic changes in a genetically-modified plant intended for human or animal consumption. More exciting is the prospect of predicting the function of unknown genes by comparison with the metabolic perturbations caused by deletion/insertion of known genes.

Nutrigenomics is a generalised term which links genomics, transcriptomics, proteomics and metabolomics to human nutrition. In general a metabolome in a given body fluid is influenced by endogenous factors such as age, sex, body composition and genetics as well as underlying pathologies. The large bowel microflora are also a very significant potential confounder of metabolic profiles and could be classified as either an endogenous or exogenous factor. The main exogenous factors are diet and drugs. Diet can then be broken down to nutrients and non- nutrients.

http://en.wikipedia.org/wiki/Metabolomics

Jose Eduardo des Salles Roselino

The problem with genomics was it was set as explanation for everything. In fact, when something is genetic in nature the genomic reasoning works fine. However, this means whenever an inborn error is found and only in this case the genomic knowledge afterwards may indicate what is wrong and not the completely way to put biology upside down by reading everything in the DNA genetic as well as non-genetic problems.

Coordination of the transcriptome and metabolome by the circadian clock PNAS 2012

Coordination of the transcriptome and metabolome by the circadian clock PNAS 2012

analysis of metabolomic data and differential metabolic regulation for fetal lungs, and maternal blood plasma

conformational changes leading to substrate efflux.img

conformational changes leading to substrate efflux.img

The cellular response is defined by a network of chemogenomic response signatures.

The cellular response is defined by a network of chemogenomic response signatures.

Dynamic Construct of the –Omics

Dynamic Construct of the –Omics

 genome cartoon

genome cartoon

central dogma phenotype

central dogma phenotype

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Summary of Cell Structure, Anatomic Correlates of Metabolic Function

Author and Curator: Larry H. Bernstein, MD, FCAP  

 

This chapter has been concerned with the subcellular ultrastructure of organelles, and importantly, their function.  There is no waste in the cell structure. The nucleus has the instructions necessary to carry out the cell’s functions.  In the Eukaryotic cell there is significant differentiation so that the cells are regulated for the needs that they uniquely carry out.  When there is disregulation, it leads to remodeling or to cell death.

Here I shall note some highlights of this chapter.

  1. In every aspect of cell function, proteins are involved embedded in the structure, for most efficient functioning.
  2. Metabolic regulation is dependent on pathways that are also linkages of proteins.
  3. Energy utilization is dependent on enzymatic reactions, often involving essential metal ions of high valence numbers, which facilitates covalent and anion binding, and has an essential role in allostericity.

Mitochondria

Mitochondria,_mammalian_lung

Mitochondria,_mammalian_lung

http://en.wikipedia.org/wiki/File:Mitochondria,_mammalian_lung_-_TEM.jpg

Mitochondria range from 0.5 to 1.0 micrometer (μm) in diameter. These structures are sometimes described as “cellular power plants” because they generate most of the cell’s supply of adenosine triphosphate (ATP), used as a source of chemical energy. In addition to supplying cellular energy, mitochondria are involved in other tasks such as signaling, cellular differentiation, cell death, as well as the control of the cell cycle and cell growth. Mitochondria have been implicated in several human diseases, including mitochondrial disorders and cardiac dysfunction.

The number of mitochondria in a cell can vary widely by organism, tissue, and cell type. For instance, red blood cells have no mitochondria, whereas liver cells can have more than 2000. The organelle is composed of compartments that carry out specialized functions. These compartments or regions include the outer membrane, the intermembrane space, the inner membrane, and the cristae and matrix. Mitochondrial proteins vary depending on the tissue and the species. The mitochondrial proteome is thought to be dynamically regulated. Although most of a cell’s DNA is contained in the cell nucleus, the mitochondrion has its own independent genome. Further, its DNA shows substantial similarity to bacterial genomes.

In 1913 particles from extracts of guinea-pig liver were linked to respiration by Otto Heinrich Warburg, which he called “grana”. Warburg and Heinrich Otto Wieland, who had also postulated a similar particle mechanism, disagreed on the chemical nature of the respiration. It was not until 1925 when David Keilin discovered cytochromes that the respiratory chain was described.  In 1939, experiments using minced muscle cells demonstrated that one oxygen atom can form two adenosine triphosphate molecules, and, in 1941, the concept of phosphate bonds being a form of energy in cellular metabolism was developed by Fritz Albert Lipmann. In the following years, the mechanism behind cellular respiration was further elaborated, although its link to the mitochondria was not known. The introduction of tissue fractionation by Albert Claude allowed mitochondria to be isolated from other cell fractions and biochemical analysis to be conducted on them alone. In 1946, he concluded that cytochrome oxidase and other enzymes responsible for the respiratory chain were isolated to the mitchondria.

The first high-resolution micrographs appeared in 1952, replacing the Janus Green stains as the preferred way of visualising the mitochondria. This led to a more detailed analysis of the structure of the mitochondria, including confirmation that they were surrounded by a membrane. It also showed a second membrane inside the mitochondria that folded up in ridges dividing up the inner chamber and that the size and shape of the mitochondria varied from cell to cell.  In 1967, it was discovered that mitochondria contained ribosomes. In 1968, methods were developed for mapping the mitochondrial genes, with the genetic and physical map of yeast mitochondria being completed in 1976.

A mitochondrion contains outer and inner membranes composed of phospholipid bilayers and proteins. The two membranes have different properties. Because of this double-membraned organization, there are five distinct parts to a mitochondrion. They are:

  1. the outer mitochondrial membrane,
  2. the intermembrane space (the space between the outer and inner membranes),
  3. the inner mitochondrial membrane,
  4. the cristae space (formed by infoldings of the inner membrane), and
  5. the matrix (space within the inner membrane).

Mitochondria stripped of their outer membrane are called mitoplasts.

Mitochondrion_structure_drawing

Mitochondrion_structure_drawing

http://upload.wikimedia.org/wikipedia/commons/thumb/9/9e/Mitochondrion_structure_drawing.svg/500px-Mitochondrion_structure_drawing.svg.png

Mitochondrion ultrastructure (interactive diagram) A mitochondrion has a double membrane; the inner one contains its chemiosmotic apparatus and has deep grooves which increase its surface area. While commonly depicted as an “orange sausage with a blob inside of it” (like it is here), mitochondria can take many shapes and their intermembrane space is quite thin.

The intermembrane space is the space between the outer membrane and the inner membrane. It is also known as perimitochondrial space. Because the outer membrane is freely permeable to small molecules, the concentrations of small molecules such as ions and sugars in the intermembrane space is the same as the cytosol. However, large proteins must have a specific signaling sequence to be transported across the outer membrane, so the protein composition of this space is different from the protein composition of the cytosol. One protein that is localized to the intermembrane space in this way is cytochrome c.

The inner mitochondrial membrane contains proteins with five types of functions:

  1. Those that perform the redox reactions of oxidative phosphorylation
  2. ATP synthase, which generates ATP in the matrix
  3. Specific transport proteins that regulate metabolite passage into and out of the matrix
  4. Protein import machinery.
  5. Mitochondria fusion and fission protein.

It contains more than 151 different polypeptides, and has a very high protein-to-phospholipid ratio (more than 3:1 by weight, which is about 1 protein for 15 phospholipids). The inner membrane is home to around 1/5 of the total protein in a mitochondrion. In addition, the inner membrane is rich in an unusual phospholipid, cardiolipin. This phospholipid was originally discovered in cow hearts in 1942, and is usually characteristic of mitochondrial and bacterial plasma membranes. Cardiolipin contains four fatty acids rather than two, and may help to make the inner membrane impermeable. Unlike the outer membrane, the inner membrane doesn’t contain porins, and is highly impermeable to all molecules. Almost all ions and molecules require special membrane transporters to enter or exit the matrix. Proteins are ferried into the matrix via the translocase of the inner membrane (TIM) complex or via Oxa1. In addition, there is a membrane potential across the inner membrane, formed by the action of the enzymes of the electron transport chain.

The inner mitochondrial membrane is compartmentalized into numerous cristae, which expand the surface area of the inner mitochondrial membrane, enhancing its ability to produce ATP. For typical liver mitochondria, the area of the inner membrane is about five times as large as the outer membrane. This ratio is variable and mitochondria from cells that have a greater demand for ATP, such as muscle cells, contain even more cristae. These folds are studded with small round bodies known as F1 particles or oxysomes. These are not simple random folds but rather invaginations of the inner membrane, which can affect overall chemiosmotic function. One recent mathematical modeling study has suggested that the optical properties of the cristae in filamentous mitochondria may affect the generation and propagation of light within the tissue.

Mitochondrion

Mitochondrion

http://upload.wikimedia.org/wikipedia/commons/thumb/d/d8/MitochondrionCAM.jpg/250px-MitochondrionCAM.jpg

The matrix is the space enclosed by the inner membrane. It contains about 2/3 of the total protein in a mitochondrion. The matrix is important in thThe MAM is enriched in enzymes involved in lipid biosynthesis, such as phosphatidylserine synthase on the ER face and phosphatidylserine decarboxylase on the mitochondrial face.[28][29] Because mitochondria are dynamic organelles constantly undergoing fission and fusion events, they require a constant and well-regulated supply of phospholipids for membrane integrity.[30][31] But mitochondria are not only a destination for the phospholipids they finish synthesis of; rather, this organelle also plays a role in inter-organelle trafficking of the intermediates and products of phospholipid biosynthetic pathways, ceramide and cholesterol metabolism, and glycosphingolipid anabolisme production of ATP with the aid of the ATP synthase contained in the inner membrane. The matrix contains a highly concentrated mixture of hundreds of enzymes, special mitochondrial ribosomes, tRNA, and several copies of the mitochondrial DNA genome. Of the enzymes, the major functions include oxidation of pyruvate and fatty acids, and the citric acid cycle.

Purified MAM from subcellular fractionation has shown to be enriched in enzymes involved in phospholipid exchange, in addition to channels associated with Ca2+ signaling. The mitochondria-associated ER membrane (MAM) is another structural element that is increasingly recognized for its critical role in cellular physiology and homeostasis. Once considered a technical snag in cell fractionation techniques, the alleged ER vesicle contaminants that invariably appeared in the mitochondrial fraction have been re-identified as membranous structures derived from the MAM—the interface between mitochondria and the ER. Physical coupling between these two organelles had previously been observed in electron micrographs and has more recently been probed with fluorescence microscopy. Such studies estimate that at the MAM, which may comprise up to 20% of the mitochondrial outer membrane, the ER and mitochondria are separated by a mere 10–25 nm and held together by protein tethering complexes.

Such trafficking capacity depends on the MAM, which has been shown to facilitate transfer of lipid intermediates between organelles. In contrast to the standard vesicular mechanism of lipid transfer, evidence indicates that the physical proximity of the ER and mitochondrial membranes at the MAM allows for lipid flipping between opposed bilayers. Despite this unusual and seemingly energetically unfavorable mechanism, such transport does not require ATP. Instead, in yeast, it has been shown to be dependent on a multiprotein tethering structure termed the ER-mitochondria encounter structure, or ERMES, although it remains unclear whether this structure directly mediates lipid transfer or is required to keep the membranes in sufficiently close proximity to lower the energy barrier for lipid flipping.

A critical role for the ER in calcium signaling was acknowledged before such a role for the mitochondria was widely accepted, in part because the low affinity of Ca2+ channels localized to the outer mitochondrial membrane seemed to fly in the face of this organelle’s purported responsiveness to changes in intracellular Ca2+ flux. But the presence of the MAM resolves this apparent contradiction: the close physical association between the two organelles results in Ca2+ microdomains at contact points that facilitate efficient Ca2+ transmission from the ER to the mitochondria. Transmission occurs in response to so-called “Ca2+ puffs” generated by spontaneous clustering and activation of IP3R, a canonical ER membrane Ca2+ channel.

The properties of the Ca2+ pump SERCA and the channel IP3R present on the ER membrane facilitate feedback regulation coordinated by MAM function. In particular, clearance of Ca2+ by the MAM allows for spatio-temporal patterning of Ca2+ signaling because Ca2+ alters IP3R activity in a biphasic manner. SERCA is likewise affected by mitochondrial feedback: uptake of Ca2+ by the MAM stimulates ATP production, thus providing energy that enables SERCA to reload the ER with Ca2+ for continued Ca2+ efflux at the MAM. Thus, the MAM is not a passive buffer for Ca2+ puffs; rather it helps modulate further Ca2+ signaling through feedback loops that affect ER dynamics.

Regulating ER release of Ca2+ at the MAM is especially critical because only a certain window of Ca2+ uptake sustains the mitochondria, and consequently the cell, at homeostasis. Sufficient intraorganelle Ca2+ signaling is required to stimulate metabolism by activating dehydrogenase enzymes critical to flux through the citric acid cycle. However, once Ca2+ signaling in the mitochondria passes a certain threshold, it stimulates the intrinsic pathway of apoptosis in part by collapsing the mitochondrial membrane potential required for metabolism.  Studies examining the role of pro- and anti-apoptotic factors support this model; for example, the anti-apoptotic factor Bcl-2 has been shown to interact with IP3Rs to reduce Ca2+ filling of the ER, leading to reduced efflux at the MAM and preventing collapse of the mitochondrial membrane potential post-apoptotic stimuli. Given the need for such fine regulation of Ca2+ signaling, it is perhaps unsurprising that dysregulated mitochondrial Ca2+ has been implicated in several neurodegenerative diseases, while the catalogue of tumor suppressors includes a few that are enriched at the MAM.

…more

http://en.wikipedia.org/wiki/Mitochondrion

Lysosome and Apoptosis

Role of autophagy in cancer

R Mathew, V Karantza-Wadsworth & E White

Nature Reviews Cancer 7, 961-967 (Dec 2007) |  http://dx.doi.org:/10.1038/nrc2254

Autophagy is a cellular degradation pathway for the clearance of damaged or superfluous proteins and organelles. The recycling of these intracellular constituents also serves as an alternative energy source during periods of metabolic stress to maintain homeostasis and viability. In tumour cells with defects in apoptosis, autophagy allows prolonged survival. Paradoxically, autophagy defects are associated with increased tumorigenesis, but the mechanism behind this has not been determined. Recent evidence suggests that autophagy provides a protective function to limit tumour necrosis and inflammation, and to mitigate genome damage in tumour cells in response to metabolic stress.

Sustained Activation of mTORC1 in Skeletal Muscle Inhibits Constitutive and Starvation-Induced Autophagy and Causes a Severe, Late-Onset Myopathy

P Castets, S Lin, N Rion, S Di Fulvio, et al.
cell-metabolism 7 May, 2013; 17(5): p731–744   http://dx.doi.org/10.1016/j.cmet.2013.03.015

  • mTORC1 inhibition is required for constitutive and starvation-induced autophagy
  • Sustained activation of mTORC1 causes a severe myopathy due to autophagy impairment
  • TSC1 depletion is sufficient to activate mTORC1 irrespective of other stimuli
  • mTORC1 inactivation is sufficient to trigger LC3 lipidation

Autophagy is a catabolic process that ensures homeostatic cell clearance and is deregulated in a growing number of myopathological conditions. Although FoxO3 was shown to promote the expression of autophagy-related genes in skeletal muscle, the mechanisms triggering autophagy are unclear. We show that TSC1-deficient mice (TSCmKO), characterized by sustained activation of mTORC1, develop a late-onset myopathy related to impaired autophagy. In young TSCmKO mice,

  • constitutive and starvation-induced autophagy is blocked at the induction steps via
  • mTORC1-mediated inhibition of Ulk1, despite FoxO3 activation.

Rapamycin is sufficient to restore autophagy in TSCmKO mice and

  • improves the muscle phenotype of old mutant mice.

Inversely, abrogation of mTORC1 signaling by

  • depletion of raptor induces autophagy regardless of FoxO inhibition.

Thus, mTORC1 is the dominant regulator of autophagy induction in skeletal muscle and

  • ensures a tight coordination of metabolic pathways.

These findings may open interesting avenues for therapeutic strategies directed toward autophagy-related muscle diseases.

Histone deacetylases 1 and 2 regulate autophagy flux and skeletal muscle homeostasis in mice

Viviana Moresi, et al.   PNAS Jan 31, 2012; 109(5): 1649-1654
http://dx.doi.org:/10.1073/pnas.1121159109
http://www.pnas.org/content/109/5/1649/F6.medium.gif

HDAC1 activates FoxO and is both sufficient and required for skeletal muscle atrophy

Beharry, PB. Sandesara, BM. Roberts, et al.
J. Cell Sci. Apr 2014 127 (7) 1441-1453   http://dx.doi.org:/10.1242/​jcs.136390

The Forkhead box O (FoxO) transcription factors are activated, and necessary for the muscle atrophy, in several pathophysiological conditions, including muscle disuse and cancer cachexia. However, the mechanisms that lead to FoxO activation are not well defined. Recent data from our laboratory and others indicate that

  • the activity of FoxO is repressed under basal conditions via reversible lysine acetylation,
  • which becomes compromised during catabolic conditions.

Therefore, we aimed to determine how histone deacetylase (HDAC) proteins contribute to

  • activation of FoxO and induction of the muscle atrophy program.

Through the use of various pharmacological inhibitors to block HDAC activity, we demonstrate that

  • class I HDACs are key regulators of FoxO and the muscle-atrophy program
  • during both nutrient deprivation and skeletal muscle disuse.

Furthermore, we demonstrate, through the use of wild-type and dominant-negative HDAC1 expression plasmids,

  • that HDAC1 is sufficient to activate FoxO and induce muscle fiber atrophy in vivo and
  • is necessary for the atrophy of muscle fibers that is associated with muscle disuse.

The ability of HDAC1 to cause muscle atrophy required its deacetylase activity and

  • was linked to the induction of several atrophy genes by HDAC1,
  • including atrogin-1, which required deacetylation of FoxO3a.

Moreover, pharmacological inhibition of class I HDACs during muscle disuse, using MS-275,

  • significantly attenuated both disuse muscle fiber atrophy and contractile dysfunction.

Together, these data solidify the importance of class I HDACs in the muscle atrophy program and

  • indicate that class I HDAC inhibitors are feasible countermeasures to impede muscle atrophy and weakness.

Autophagy and thyroid carcinogenesis: genetic and epigenetic links
F Morani, R Titone, L Pagano, et al.  Endocr Relat Cancer Feb 1, 2014 21 R13-R29
http://dx.doi.org:/10.1530/ERC-13-0271

Autophagy is a vesicular process for the lysosomal degradation of protein aggregates and

  • of damaged or redundant organelles.

Autophagy plays an important role in cell homeostasis, and there is evidence that

  • this process is dysregulated in cancer cells.

Recent in vitro preclinical studies have indicated that autophagy is

  • involved in the cytotoxic response to chemotherapeutics in thyroid cancer cells.

Indeed, several oncogenes and oncosuppressor genes implicated in thyroid carcinogenesis

  • also play a role in the regulation of autophagy.

In addition, some epigenetic modulators involved in thyroid carcinogenesis also influence autophagy. In this review, we highlight the genetic and epigenetic factors that

  • mechanistically link thyroid carcinogenesis and autophagy, thus substantiating the rationale for
  • an autophagy-targeted therapy of aggressive and radio-chemo-resistant thyroid cancers.

Read Full Post »

Transcription Modulation

Author and Curator: Larry H. Bernstein, MD, FCAP 

 

This portion of the transcription series deals with transcription factors and the effects of their binding on metabolism. This also has implications for pharmaceutical target identification.

The Functional Consequences of Variation in Transcription Factor Binding
DA. Cusanovich, B Pavlovic, JK. Pritchard*, Y Gilad*
1 Department of Human Genetics, 2 Howard Hughes Medical Institute, University of Chicago, Chicago, IL 3 Departments of Genetics and Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA.
PLoS Genet 2014;10(3):e1004226.  http://dx.doi.org:/10.1371/journal.pgen.1004226

One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly

  • play an important role in determining gene expression outputs, yet
  • the regulatory logic underlying functional transcription factor binding is poorly understood.

An important question in genomics is to understand how a class of proteins called ‘‘transcription factors’’ controls the expression level of other genes in the genome in a cell type-specific manner – a process that is essential to human development. One major approach to this problem is to study where these transcription factors bind in the genome, but this does not tell us about the effect of that binding on gene expression levels and

  • it is generally accepted that much of the binding does not strongly influence gene expression.

To address this issue, we artificially reduced the concentration of 59 different transcription factors in the cell and then

  • examined which genes were impacted by the reduced transcription factor level.

Our results implicate some attributes

  • that might influence what binding is functional, but they also suggest that
  • a simple model of functional vs. non-functional binding may not suffice.

Many studies have focused on characterizing the genomic locations of TF binding, but

  • it is unclear whether TF binding at any specific locus has
  • functional consequences with respect to gene expression output.

We knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line

  • to evaluate the context of functional TF binding.

We then identified genes whose expression was affected by the knockdowns

  • by intersecting the gene expression data with transcription factor binding data
    (based on ChIP-seq and DNase-seq)
  • within 10 kb of the transcription start sites of expressed genes.

This combination of data allowed us to infer functional TF binding.
Only a small subset of genes bound by a factor were

  • differentially expressed following the knockdown of that factor,
  • suggesting that most interactions between TF and chromatin
  • do not result in measurable changes in gene expression levels
  • of putative target genes.

We found that functional TF binding is enriched

  • in regulatory elements that harbor a large number of TF binding sites,
  • at sites with predicted higher binding affinity, and
  • at sites that are enriched in genomic regions annotated as ‘‘active enhancers.’’

We aim to be able to predict the expression pattern of a gene based on its regulatory
sequence alone. However, the regulatory code of the human genome is much more complicated than

  • the triplet code of protein coding sequences, and is highly context-specific,
  • depending on cell-type and other factors.

Moreover, regulatory regions are not necessarily organized into

  • discrete, easily identifiable regions of the genome and
  • may exert their influence on genes over large genomic distances

Genomic studies addressing questions of the regulatory logic of the human genome have largely taken one of two approaches.

  1. collecting transcription factor binding maps using techniques such as ChIPseq
    and DNase-seq
  2. mapping various quantitative trait loci (QTL), such as gene expression levels
    (eQTLs) [7], DNA methylation (meQTLs) [8] and chromatin accessibility (dsQTLs)

Cumulatively, binding map studies and QTL map studies have

  • led to many insights into the principles and mechanisms of gene regulation.

However, there are questions that neither mapping approach on its own is well equipped to address. One outstanding issue is

  • the fraction of factor binding in the genome that is ‘‘functional’’,
    which we define here to mean that
  • disturbing the protein-DNA interaction leads to a measurable
  • downstream effect on gene regulation.

Transcription factor knockdown could be used to address this problem, whereby

  • the RNA interference pathway is employed to greatly reduce
  • the expression level of a specific target gene by using small interfering RNAs (siRNAs).

The response to the knockdown can then be measured by collecting RNA after the knockdown and

  • measuring global changes in gene expression patterns
  • after specifically attenuating the expression level of a given factor.

Combining a TF knockdown approach with TF binding data can help us to

  • distinguish functional binding from non-functional binding

This approach has previously been applied to the study of human TFs, although for the most part studies have only focused on

  • the regulatory relationship of a single factor with its downstream targets.

The FANTOM consortium knocked down 52 different transcription factors in

  • the THP-1 cell line, an acute monocytic leukemia-derived cell line, and
  • used a subset of these to validate certain regulatory predictions based on binding motif enrichments.

We and others previously studied the regulatory architecture of gene expression in

  • the model system of HapMap lymphoblastoid cell lines (LCLs) using both
  • binding map strategies and QTL mapping strategies.

We now sought to use knockdown experiments targeting transcription factors in a HapMap LCL

  • to refine our understanding of the gene regulatory circuitry of the human genome.

Therefore, We integrated the results of the knockdown experiments with previous data on TF binding to

  • better characterize the regulatory targets of 59 different factors and
  • to learn when a disruption in transcription factor binding
  • is most likely to be associated with variation in the expression level of a nearby gene.

Gene expression levels following the knockdown were compared to

  • expression data collected from six samples that were transfected with negative control siRNA.

The expression data from all samples were normalized together using

  • quantile  normalization followed by batch correction using the RUV-2 method.

We then performed several quality control analyses to confirm

  1. that the quality of the data was high,
  2. that there were no outlier samples, and
  3. that the normalization methods reduced the influence of confounders

In order to identify genes that were expressed at a significantly different level

  • in the knockdown samples compared to the negative controls,
  • we used likelihood-ratio tests within the framework of a fixed effect linear model.

Following normalization and quality control of the arrays,

  • we identified genes that were differentially expressed between
  • the three knockdown replicates of each factor and the six controls.

Depending on the factor targeted, the knockdowns resulted in

  • between 39 and 3,892 differentially expressed genes at an FDR of 5%
    (Figure 1B; see Table S3 for a summary of the results).

The knockdown efficiency for the 59 factors ranged

  • from 50% to 90% (based on qPCR; Table S1).

The qPCR measurements of the knockdown level were significantly

  • correlated with estimates of the TF expression levels
  • based on the microarray data (P =0.001; Figure 1C).

Reassuringly, we did not observe a significant correlation between

  • the knockdown efficiency of a given factor and
  • the number of genes classified as differentially expressed foci.

Because we knocked down 59 different factors in this experiment

  • we were able to assess general patterns associated with the perturbation of transcription factors
  • beyond merely the number of affected target genes.

Globally, despite the range in the number of genes we identified as

  • differentially expressed in each knockdown,
  • the effect sizes of the differences in expression were relatively modest and
  • consistent in magnitude across all knockdowns.

The median effect size following the knockdown experiment for genes classified as

  • differentially expressed at an FDR of 5% in any knockdown was
  • a 9.2% difference in expression level between the controls and the knockdown (Figure 2),
  • while the median effect size for any individual knockdown experiment ranged between 8.1% and 11.0%.
    (this was true whether we estimated the knockdown effect based on qPCR (P = 0.10; Figure 1D) or microarray (P = 0.99; not shown) data.

Nor did we observe a correlation between

  • variance in qPCR-estimated knockdown efficiency (between replicates) and
  • the number of genes differentially expressed (P = 0.94; Figure 1E).

We noticed that the large variation in the number of differentially expressed genes

  • extended even to knockdowns of factors from the same gene family.

Figure 1. Differential expression analysis.
(a) Examples of differential expression analysis results for the genes HCST and IRF4. The top two panels are ‘MA plots’ of the mean Log2(expression level) between the knockdown arrays and the controls for each gene (x-axis) to the Log2(Fold-Change) between the knockdowns and controls (y-axis). Differentially expressed genes at an FDR of 5% are plotted in yellow (points 50% larger). The gene targeted by the siRNA is highlighted in red. The bottom two panels are ‘volcano plots’ of the Log2(Fold-Change) between the knockdowns and controls (x-axis) to the P-value for differential expression (y-axis). The dashed line marks the 5% FDR threshold. Differentially expressed genes at an FDR of 5% are plotted in yellow (points 50% larger). The red dot marks the gene targeted by the siRNA.
(b) Barplot of number of differentially expressed genes in each knockdown experiment.
(c) Comparison of the knockdown level measured by qPCR (RNA sample collected 48 hours posttransfection) and the knockdown level measured by microarray.
(d) Comparison of the level of knockdown of the transcription factor at 48 hrs (evaluated by qPCR; x-axis) and the number of genes differentially expressed in the knockdown experiment (y-axis).
(e) Comparison of the variance in knockdown efficiency between replicates for each transcription factor (evaluated by qPCR; x-axis) and the number of differentially expressed genes in the knockdown experiment (y-axis).

Differential expression analysis

Differential expression analysis

http://dx.doi.org:/10.1371/journal.pgen.1004226.g001

Figure 2. Effect sizes for differentially expressed genes.
Boxplots of absolute Log2(fold-change) between knockdown arrays and control arrays for all genes identified as differentially expressed in each experiment. Outliers are not plotted. The gray bar indicates the interquartile range across all genes differentially expressed in all knockdowns. Boxplots are ordered by the number of genes differentially expressed in each experiment. Outliers were not plotted.

Effect sizes for differentially expressed genes

Effect sizes for differentially expressed genes

http://dx.doi.org:/10.1371/journal.pgen.1004226.g002

Knocking down SREBF2 (1,286 genes differentially expressed), a key regulator of cholesterol homeostasis,

  • results in changes in the expression of genes that are
  • significantly enriched for cholesterol and sterol biosynthesis annotations.

While not all factors exhibited striking enrichments for relevant functional categories and pathways,

  • the overall picture is that perturbations of many of the factors
  • primarily affected pathways consistent with their known biology.

In order to assess functional TF binding, we next incorporated

  • binding maps together with the knockdown expression data.

We combined binding data based on DNase-seq footprints in 70 HapMap LCLs, reported by Degner et al. (Table S5)

  • and from ChIP-seq experiments in LCL GM12878, published by ENCODE.

We were thus able to obtain genome wide binding maps for a total of 131 factors that were either

  • directly targeted by an siRNA in our experiment (29 factors) or were
  • differentially expressed in one of the knockdown experiments.

We classified a gene as a bound target of a particular factor when

  • binding of that factor was inferred within 10kb of the transcription start site (TSS) of the target gene.

Using this approach, we found that the 131 TFs were bound

  • in proximity to a median of 1,922 genes per factor (range 11 to 7,053 target genes).

We considered binding of a factor to be functional if the target gene

  • was differentially expressed after perturbing the expression level the bound transcription factor.

We then asked about the concordance between

  • the transcription factor binding data and the knockdown expression data.
  •  the extent to which differences in gene expression levels following the knockdowns
  • might be predicted by binding of the transcription factors
  • within the putative regulatory regions of the responsive genes. and also
  • what proportion of putative target (bound) genes of a given TF were
  • differentially expressed following the knockdown of the factor.

Focusing only on the binding sites classified using the DNase-seq data
(which were assigned to a specific instance of the binding motif, unlike the ChIP data),

  • we examined sequence features that might distinguish functional binding.

In particular, whether binding at conserved sites was more likely to be functional  and

  • whether binding sites that better matched the known PWM for the factor were more likely to be functional.

We did not observe a significant shift in the conservation of functional binding sites (Wilcoxon rank sum P = 0.34),

  • but we did observe that binding around differentially expressed genes occurred at sites
  • that were significantly better matches to the canonical binding motif.

Figure 3. Intersecting binding data and expression data for each knockdown.
(a) Example Venn diagrams showing the overlap of binding and differential expression for the knockdowns of HCST and IRF4 (the same genes as in Figure 1).
(b) Boxplot summarizing the distribution of the fraction of all expressed genes that are bound by the targeted gene or downstream factors.
(c) Boxplot summarizing the distribution of the fraction of bound genes that are classified as differentially expressed, using an FDR of either 5% or 20%.

Intersecting binding data and expression data for each knockdown

Intersecting binding data and expression data for each knockdown

http://dx.doi.org:/10.1371/journal.pgen.1004226.g003

Considering bound targets determined from either the ChIP-seq or DNase-seq data, we observed that

  • differentially expressed genes were associated with both
  • a higher number of binding events for the relevant factors within 10 kb of the TSS (P,10216; Figure 4A)
  • as well as with a larger number of different binding factors
    (considering the siRNA-targeted factor and any TFs that were DE in the knockdown; P,10216; Figure 4B).

Figure 4. Degree of binding correlated with function. Boxplots comparing
(a) the number of sites bound, and
(b) the number of differentially expressed transcription factors binding events near functionally or non-functionally bound genes. We considered binding for siRNA-targeted factor and any factor differentially expressed in the knockdown.
(c) Focusing only on genes differentially expressed in common between each pairwise set of knockdowns we tested for enrichments of functional binding (y-axis). Pairwise comparisons between knockdown experiments were binned by the fraction of differentially expressed transcription factors in common between the two experiments. For these boxplots, outliers were not plotted.

Degree of binding correlated with function

Degree of binding correlated with function

http://dx.doi.org:/10.1371/journal.pgen.1004226.g004

We examined the distribution of binding about the TSS. Most factor binding was concentrated

  • near the TSS whether or not the genes were classified as differentially expressed (Figure 5A).
  • the distance from the TSS to the binding sites was significantly longer for differentially expressed genes (P,10216; Fig. 5B).

Figure 5. Distribution of functional binding about the TSS.
(a) A density plot of the distribution of bound sites within 10 kb of the TSS for both functional and non-functional genes. Inset is a zoom-in of the region +/21 kb from the TSS (b) Boxplots comparing the distances from the TSS to the binding sites for functionally bound genes and non-functionally bound genes. For the boxplots, 0.001 was added before log10 transforming the distances and outliers were not plotted.

Distribution of functional binding about the TSS

Distribution of functional binding about the TSS

http://dx.doi.doi:/10.1371/journal.pgen.1004226.g005

We investigated the distribution of factor binding across various chromatin states, as defined by Ernst et al. This dataset lists

  • regions of the genome that have been assigned to different activity states
  • based on ChIP-seq data for various histone modifications and CTCF binding.

For each knockdown, we separated binding events

  • by the genomic state in which they occurred and then
  • tested whether binding in that state was enriched around differentially expressed genes.

After correcting for multiple testing of genes that were differentially expressed.

  • 19 knockdowns showed significant enrichment for binding in ‘‘strong enhancers’’
  • four knockdowns had significant enrichments for ‘‘weak enhancers’’,
  • eight knockdowns showed significant depletion of binding in ‘‘active promoters’’ ,
  • six knockdowns had significant depletions for ‘‘transcription elongation’’,

Did the factors tended to have a consistent effect (either up- or down-regulation)

  • on the expression levels of genes they purportedly regulated?

All factors we tested are associated with both up- and down-regulation of downstream targets (Figure 6).

A slight majority of downstream target genes were expressed at higher levels

  • following the knockdown for 15 of the 29 factors for which we had binding information (Figure 6B).

The factor that is associated with the largest fraction (68.8%) of up-regulated target genes following the knockdown is EZH2,

  • the enzymatic component of the Polycomb group complex.

On the other end of the spectrum was JUND, a member of the AP-1 complex, for which

  • 66.7% of differentially expressed targets were down-regulated following the knockdown.

Figure 6. Magnitude and direction of differential expression after knockdown.
(a) Density plot of all Log2(fold-changes) between the knockdown arrays and controls for genes that are differentially expressed at 5% FDR in one of the knockdown experiments as well as bound by the targeted transcription factor.
(b) Plot of the fraction of differentially expressed putative direct targets that were up-regulated in each of the knockdown experiments.

Magnitude and direction of differential expression after knockdown

Magnitude and direction of differential expression after knockdown

http://dx.doi.org:/10.1371/journal.pgen.1004226.g006

We found no correlation between the number of paralogs and the fraction of bound targets that were differentially expressed. We also did not observe a significant correlation when we considered whether

  • the percent identity of the closest paralog might be predicative of
  • the fraction of bound genes that were differentially expressed following the knockdown (Figure S8).

While there is compelling evidence for our inferences, the current chromatin functional annotations

  • do not fully explain the regulatory effects of the knockdown experiments.

For example, the enrichments for binding in ‘‘strong enhancer’’ regions of the genome range from 7.2% to 50.1% (median = 19.2%),

  • much beyond what is expected by chance alone, but far from accounting for all functional binding.

In addition to considering

  • the distinguishing characteristics of functional binding, we also examined
  • the direction of effect that perturbing a transcription factor had on the expression level of its direct targets.

We specifically addressed whether

  • knocking down a particular factor tended to drive expression of its putatively direct (namely, bound) targets up or down,
  • which can be used to infer that the factor represses or activates the target, respectively.

Transcription factors have traditionally been thought of primarily as activators, and previous work from our group is consistent with that notion. Surprisingly, the most straightforward inference from the present study is that

  • many of the factors function as repressors at least as often as they function as activators.
  1. EZH2 had a negative regulatory relationship with the largest fraction of direct targets (68.8%),
    consistent with – the known role of EZH2 as the active member of the Polycomb group complex PC2
  2. while JUND seemed to have a positive regulatory relationship with the largest fraction of direct targets (66.7%),
    and with – the biochemical characterization of the AP-1 complex (of which JUND is a component) as a transactivator.

More generally, however, our results, combined with the previous work from our group and others make for a complicated view

  • of the role of transcription factors in gene regulation as
  • it seems difficult to reconcile the inference from previous work that
  • many transcription factors should primarily act as activators with the results presented here.

One somewhat complicated hypothesis, which nevertheless can resolve the apparent discrepancy, is that

  • the ‘‘repressive’’ effects we observe for known activators may be
  • at sites in which the activator is acting as a weak enhancer of transcription and
  • that reducing the cellular concentration of the factor
  • releases the regulatory region to binding by an alternative, stronger activator.

To more explicitly address the effect that our proximity-based definition of target genes might have on our analyses, we reanalyzed

  • the overlap between factor binding and differential expression following the knockdowns
  • using an independent, empirically determined set of target genes.

Thurman et al. used correlations in DNase hypersensitivity between

  • intergenic hypersensitive sites and promoter hypersensitive sites across diverse tissues
  • to assign intergenic regulatory regions to specific genes,
  • independently of proximity to a particular promoter.

We performed this alternative analysis in which we

  • assigned binding events to genes based on the classification of Thurman et al.

We then considered the overlap between binding and differential expression in this new data set. The results were largely

  • consistent with our proximity-based observations.

A median of 9.5% of genes that were bound by a factor were

  • also differentially expressed following the knockdown of that factor
    (compared to 11.1% when the assignment of binding sites to genes is based on proximity).

From the opposite perspective, a median of 28.0% of differentially expressed genes were bound by that factor
(compared to 32.3% for the proximity based definition). The results of this analysis are summarized in Table S7.

Our results should not be considered a comprehensive census of regulatory events in the human genome. Instead, we adopted a gene-centric approach,

  • focusing only on binding events near the genes for which we could measure expression
  • to learn some of the principles of functional transcription factor binding.

In light of our observations a reassessment of our estimates of binding may be warranted. In particular, because functional binding is skewed away from promoters (our system is apparently not well-suited to observe functional promoter binding, perhaps because of protection by large protein complexes),

  • a more conservative estimate of the fraction of binding that is indeed functional would not consider data within the promoter.

Importantly, excluding the putative promoter region from our analysis (i.e. only considering a window .1 kb from the TSS and ,10 kb from the TSS)

  • does not change our conclusions.

Considering this smaller window,

  • a median of 67.0% of expressed genes are still classified as bound by
  1. either the knocked down transcription factor or
  2. a downstream factors that is differentially expressed in each experiment,

yet a median of only 8.1% of the bound genes are

  • also differentially expressed after the knockdowns.

Much of what distinguishes functional binding (as we define it) has yet to be explained. We are unable to explain much of the differential expression observed in our experiments by the presence of least one relevant binding event. This may not be altogether surprising, as

  • we are only considering binding in a limited window around the transcription start site.

To address these issues, more factors should be perturbed to further evaluate the robustness of our results and to add insight. Together, such studies will help us develop a more sophisticated understanding of functional transcription factor binding in particular, the gene regulatory logic more generally.

Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale

E Shmelkov, Z Tang, I Aifantis, A Statnikov*
Biology Direct 2011; 6(15).  http://www.biology-direct.com/content/6/1/15

Recently the biological pathways have become a common and probably the most popular form of representing biochemical information for hypothesis generation and validation. These maps store wide knowledge of complex molecular interactions and regulations occurring in the living organism in a simple and obvious way, often using intuitive graphical notation. Two major types of biological pathways could be distinguished.

  1. Metabolic pathways incorporate complex networks of protein-based interactions and modifications, while
  2. signal transduction and transcriptional regulatory pathways are usually considered to provide information on mechanisms of transcription

While there are a lot of data collected on human metabolic processes,

  • the content of signal transduction and transcriptional regulatory pathways varies greatly in quality and completeness.

An indicative comparison of MYC transcriptional targets reported in ten different pathway databases reveals that these databases differ greatly from each other (Figure 1). Given that MYC is involved

  • in the transcriptional regulation of approximately 15% of all genes,

one cannot argue that the majority of pathway databases that contain

  • less than thirty putative transcriptional targets of MYC are even close to complete.

More importantly, to date there have been no prior genome-wide evaluation studies (that are based on genome-wide binding and gene expression assays) assessing pathway databases

Background: While pathway databases are becoming increasingly important in most types of biological and translational research, little is known about the quality and completeness of pathways stored in these databases. The present study conducts a comprehensive assessment of transcriptional regulatory pathways in humans for seven well-studied transcription factors:

  1. MYC,
  2. NOTCH1,
  3. BCL6,
  4. TP53,
  5. AR,
  6. STAT1,
  7. RELA.

The employed benchmarking methodology first involves integrating

  • genome-wide binding with functional gene expression data
  • to derive direct targets of transcription factors.

Then the lists of experimentally obtained direct targets

  • are compared with relevant lists of transcriptional targets from 10 commonly used pathway databases.

Results: The results of this study show that for the majority of pathway databases,

  • the overlap between experimentally obtained target genes and
  • targets reported in transcriptional regulatory pathway databases is
  • surprisingly small and often is not statistically significant.

The only exception is MetaCore pathway database which

  • yields statistically significant intersection with experimental results in 84% cases.

The lists of experimentally derived direct targets obtained in this study can be used

  • to reveal new biological insight in transcriptional regulation,  and we
  • suggest novel putative therapeutic targets in cancer.

Conclusions: Our study opens a debate on validity of using many popular pathway databases to obtain transcriptional regulatory targets. We conclude that the choice of pathway databases should be informed by

  • solid scientific evidence and rigorous empirical evaluation.

In the current study we perform

(1) an evaluation of ten commonly used pathway databases,

  • assessing the transcriptional regulatory pathways, considered in the current study as
  • the interactions of the type ‘transcription factor-transcriptional targets’.

This involves integration of human genome wide functional microarray or RNA-seq gene expression data with

  • protein-DNA binding data from ChIP-chip, ChIP-seq, or ChIP-PET platforms
  • to find direct transcriptional targets of the seven well known transcription factors:
  • MYC, NOTCH1, BCL6, TP53, AR, STAT1, and RELA.

The choice of transcription factors is based on their important role in oncogenesis and availability of binding and expression data in the public domain.

(2) the lists of experimentally derived direct targets are used to assess the quality and completeness of 84 transcriptional regulatory pathways from four publicly available (BioCarta, KEGG, WikiPathways and Cell Signaling Technology) and six commercial (MetaCore, Ingenuity Pathway Analysis, BKL TRANSPATH, BKL TRANSFAC, Pathway Studio and GeneSpring Pathways) pathway databases.

(3) We measure the overlap between pathways and experimentally obtained target genes and assess statistical significance of this overlap, and we demonstrate that experimentally derived lists of direct transcriptional targets

  • can be used to reveal new biological insight on transcriptional regulation.

We show this by analyzing common direct transcriptional targets of

  • MYC, NOTCH1 and RELA
  • that act in interconnected molecular pathways.

Detection of such genes is important as it could reveal novel targets of cancer therapy.

Figure 1 Number of genes in common between MYC transcriptional targets derived from ten different pathway databases. Cells are colored according to their values from white (low values) to red (high values). (not shown)

statistical methodology for comparison

statistical methodology for comparison

Figure 2 Illustration of statistical methodology for comparison between a gold-standard and a pathway database

Since we are seeking to compare gene sets from different studies/databases, it is essential to transform genes to standard identifiers. That is why we transformed all
gene sets to the HUGO Gene Nomenclature Committee approved gene symbols and names. In order to assess statistical significance of the overlap between the resulting gene sets, we used the hypergeometric test at 5% a-level with false discovery rate correction for multiple comparisons by the method of Benjamini and Yekutieli. The alternative hypothesis of this test is that two sets of genes (set A from pathway
database and set B from experiments) have greater number of genes in common than two randomly selected gene sets with the same number of genes as in sets A and B. For example, consider that for some transcription factor there are 300 direct targets in the pathway database #1 and 700 in the experimentally derived list (gold-standard), and their intersection is 16 genes (Figure 2a). If we select on random from a total of
20,000 genes two sets with 300 and 700 genes each, their overlap would be greater or equal to 16 genes in 6.34% times. Thus, this overlap will not be statistically significant at 5% a-level (p = 0.0634). On the other hand, consider that for the pathway database #2, there are 30 direct targets of that transcription factor, and their intersection with the 700-gene gold-standard is only 6 genes. Even though the size of this intersection is rather small, it is unlikely to randomly select 30 genes (out of 20,000) with an overlap greater or equal to 6 genes with a 700-gene gold-standard (p = 0.0005, see Figure 2a). This overlap is statistically significant at 5% a-level.

We also calculate an enrichment fold change ratio (EFC) for every intersection between a gold-standard and a pathway database. For a given pair of a gold-standard and a pathway database, EFC is equal to the observed number of genes in their intersection, divided by the expected size of intersection under the null hypothesis (plus machine epsilon, to avoid division by zero). Notice however that larger values of EFC may correspond to databases that are highly incomplete and contain only a few relations. For example, consider that for some transcription factor there are 300 direct targets in the pathway database #1 and 50 in the experimentally derived list (gold-standard), and their intersection is 30 genes (Figure 2b). If we select on random from a total of 20,000 genes two sets with 300 and 50 genes each, their expected overlap under the null hypothesis will be equal to 0.75. Thus, the EFC ratio will be equal to 40 (= 30/0.75). On the other hand, consider that for the pathway database #2, there are 2 direct
targets of that transcription factor, and their intersection with the 50-gene gold-standard is only 1 gene. Even though the expected overlap under the null hypothesis will be equal to 0.005 and EFC equal to 200 (5 times bigger than for the database #1), the size of this intersection with the gold-standard is 30 times less than for database #1 (Figure 2b).

Figure 3 Comparison between different pathway databases and experimentally derived gold-standards for all considered transcription factors. Value in a given cell is a number of overlapping genes between a gold-standard and a pathway-derived gene set. Cells
are colored according to their values from white (low values) to red (high values). Underlined values in red represent statistically significant intersections. (not shown)

Figure 4 Summary of the pathway databases assessment. Green cells represent statistically significant intersections between experimentally derived gold-standards and transcriptional regulatory pathways. White cells denote results that are not statistically significant. Numbers are the enrichment fold change ratios (EFC) calculated for each intersection. (not shown)

At the core of this study was creation of gold-standards of transcriptional regulation in humans that can be compared with target genes reported in transcriptional regulatory pathways. We focused on seven well known transcription factors and obtained gold-standards

  • by integrating genome-wide transcription factor-DNA binding data (from ChIP-chip, ChIP-seq, or ChIP-PET platforms)
  • with functional gene expression microarray and RNA-seq data.

The latter data allows to survey changes in the transcriptomes on a genome-wide scale

  • after the inhibition or over-expression of the transcription factor in question.

However, change in the expression of a particular gene could be caused either by the direct effect of the removal or introduction of a given transcription factor, as well as by an indirect effect, through the change in expression level of some other gene(s). It is essential

  • to integrate data from these two sources to
  • obtain an accurate list of gene targets that are directly regulated by a transcription factor.

It is worth noting that tested pathway databases typically do not give distinction between cell-lines, experimental conditions, and other details relevant to experimental systems in which data were obtained. These databases in a sense propose a ‘universal’ list of transcriptional targets. However, it is known that

  • transcriptional regulation in a cell is dynamic and works differently for different systems and stimuli.

This accentuates the major limitation of pathway databases and emphasizes

  • importance of deriving a specific list of transcriptional targets for the current experimental system.

In this study we followed the latter approach by developing gold-standards for specific cell characterized biological systems and experimental conditions.

The approach used here  for building gold-standards of direct mechanistic knowledge has several limitations. (see article).  Nevertheless, our results suggest that multiple transcription factors can co-operate and control both physiological differentiation and malignant transformation, as demonstrated utilizing combinatorial gene-profiling for

  • NOTCH1, MYC and RELA targets.

These studies might lead us to multi-pathway gene expression “signatures”

  • essential for the prediction of genes that could be targeted in cancer treatments.

In agreement with this hypothesis, several of the genes identified in our analysis have been suggested to be putative therapeutic targets in leukemia, with either preclinical or clinical trials underway (CDK4, CDK6, GSK3b, MYC, LCK, NFkB2, BCL2L1, NOTCH1).

Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus

I Izeddin†, V Récamier†‡, L Bosanac, II Cissé, L Boudarene, et al.
1Functional Imaging of Transcription, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Inserm, and CNRS UMR; 2Laboratoire Kastler Brossel, CNRS UMR, Departement de Physique et Institut de Biologie
de l’Ecole Normale Supérieure (IBENS), Paris, Fr; 3Transcription Imaging Consortium, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, US; + more.
Biophysics and structural biology | Cell biology eLife 2014;3:e02230. http://dx.doi.org:/10.7554/eLife.02230

Transcription factors are

  • proteins that control the expression of genes in the nucleus, and
  • they do this by binding to other proteins or DNA.

First, however, these regulatory proteins need to overcome the challenge of

  • finding their targets in the nucleus, which is crowded with other proteins and DNA.

Much research to date has focused on measuring how fast proteins can diffuse and spread out throughout the nucleus. However these measurements only make sense if these proteins have access to the same space within the nucleus.

Now, Izeddin, Récamier et al. have developed a new technique to track

  • single protein molecules in the nucleus of mammalian cells.

A transcription factor called c-Myc and another protein called P-TEFb

  • were tracked and while they diffused at similar rates,
  • they ‘explored’ the space inside the nucleus in very different ways.

Izeddin, Récamier et al. found that c-Myc explores the nucleus in a so-called ‘non-compact’ manner: this means that it

  • can move almost everywhere inside the nucleus, and has an equal chance
  • of reaching any target regardless of its position in this space.

P-TEFb, on the other hand, searches

  • the nucleus in a ‘compact’ way.

This means that it is constrained to follow a specific path

  • through the nucleus and is therefore guided to its potential targets.

Izeddin, Récamier et al. explain that

  • the different ‘search strategies’ used by these two proteins
  • influence how long it takes them to find their targets and
  • how far they can travel in a given time.

These findings, together with information about

  • where and when different proteins interact in the nucleus,

will be essential to understand how the organization of the genome within the nucleus

  • can control the expression of genes.

The next challenge will now be to

  • uncover what determines a
  • protein’s search strategy in the nucleus, as well as
  • the potential ways that this strategy might be regulated.

Mueller et al., 2010; Normanno et al., 2012). These transient interactions are essential to ensure a fine regulation of binding site occupancy—by competition or by altering the TF concentration—but must also be persistent enough to enable the assembly of multicomponent complexes (Dundr, 2002; Darzacq and Singer, 2008; Gorski et al., 2008; Cisse et al., 2013).
In parallel to the experimental evidence of the fast diffusive motion of nuclear factors, our understanding of the intranuclear space has evolved from a homogeneous environment to an organelle where spatial arrangement among genes and regulatory sequences play an important role in transcriptional control (Heard and Bickmore, 2007). The nucleus of eukaryotes displays a hierarchy of organized structures (Gibcus and Dekker, 2013) and is often referred to as a
crowded environment.
How crowding influences transport properties of macromolecules and organelles in the cell is a fundamental question in quantitative molecular biology. While a restriction of the available space for diffusion can slow down transport processes, it can also channel molecules towards their targets increasing their chance to meet interacting partners. A widespread observation in quantitative cell biology is that the diffusion of molecules is anomalous, often attributed to crowding in the nucleoplasm, cytoplasm, or in the membranes of the cell (Höfling and Franosch, 2013). An open debate remains on how to determine whether diffusion is anomalous or normal (Malchus and Weiss, 2009; Saxton, 2012), and the mechanisms behind anomalous diffusion (Saxton, 2007). The answer to these questions bears important consequences for the understanding of the biochemical reactions of the cell.
The problem of diffusing molecules in non-homogenous media has been investigated in different fields. Following the seminal work of de Gennes (1982a), (1982b) in polymer physics, the study of diffusivity of particles and their reactivity has been generalized to random or disordered media (Kopelman, 1986; Lindenberg et al., 1991). These works have set a framework to interpret the mobility of macromolecular complexes in the cell, and recently in terms of kinetics of biochemical reactions (Condamin et al., 2007). Experimental evidence has also been found, showing the influence
of the glass-like properties of the bacterial cytoplasm in the molecular dynamics of intracellular processes (Parry et al., 2014). These studies demonstrate that the geometry of the medium in which diffusion takes place has important repercussions for the search kinetics of molecules. The notion of compact and non-compact exploration was introduced by de Gennes (1982a) in the context of dense polymers and describes two fundamental types of diffusive behavior. While a non-compact explorer leaves a significant number of available sites unvisited, a compact explorer performs a redundant
exploration of the space. In chemistry, the influence of compactness is well established to describe dimensional effects on reaction rates (Kopelman, 1986).
In this study, we aim to elucidate the existence of different types of mobility of TFs in the eukaryotic nucleus, as well as the principles governing nuclear exploration of factors relevant to transcriptional control. To this end, we used single-molecule (SM) imaging to address the relationship between the nuclear geometry and the search dynamics of two nuclear factors having distinct functional roles: the proto-oncogene c-Myc and the positive transcription elongation factor (P-TEFb). c-Myc is a basic helix-loop-helix DNA-binding transcription factor that binds to E-Boxes; 18,000 E-boxes are found in the genome, and c-Myc affects the transcription of numerous genes (Gallant and Steiger, 2009).
Recently, c-Myc has been demonstrated to be a general transcriptional activator upregulating transcription of nearly all genes (Lin et al., 2012; Nie et al., 2012). P-TEFb is an essential actor in the transcription regulation driven by RNA Polymerase II. P-TEFb is a cyclin-dependent kinase, comprising a CDK9 and a Cyclin T subunit. It phosphorylates the elongation control factors SPT5 and NELF to allow productive elongation of class II gene transcription (Wada et al., 1998). The carboxy-terminal domain (CTD) of the catalytic subunit RPB1 of polymerase II is also a major target of P-TEFb (Zhou et al., 2012). c-Myc and P-TEFb are therefore two good examples of transcriptional regulators binding to numerous sites in the nucleus; the latter binds to the transcription machinery itself and the former directly to DNA.

Single particle tracking (SPT) constitutes a powerful method to probe the mobility of molecules in living cells (Lord et al., 2010). In the nucleus, SPT has been first employed to investigate the dynamics of mRNAs (Fusco et al., 2003; Shav-Tal et al., 2004) or for rheological measurements of the nucleoplasm using inert probes (Bancaud et al., 2009). Recently, the tracking of single nuclear factors has been facilitated by the advent of efficient in situ tagging methods such as Halo
tags (Mazza et al., 2012). An alternative approach takes advantage of photoconvertible tags (Lippincott-Schwartz and Patterson, 2009) and photoactivated localization microscopy (PALM) (Betzig et al., 2006; Hess et al., 2006). Single particle tracking PALM (sptPALM) was first used to achieve high-density diffusion maps of membrane proteins (Manley et al., 2008). However, spt-PALM experiments have typically been limited to proteins with slow mobility (Manley et al., 2008) or those that undergo restricted motions (Frost et al., 2010; English et al., 2011).

Recently, by inclusion of light-sheet illumination, it has been used to determine the binding characteristics of TFs to DNA (Gebhardt et al., 2013). In this study, we developed a new sptPALM procedure adapted for the recording of individual proteins rapidly diffusing in the nucleus of mammalian cells. We used the photoconvertible fluorophore Dendra2 (Gurskaya et al., 2006) and took advantage of tilted illumination (Tokunaga et al., 2008). A careful control of the photoconversion rate minimized the background signal due to out-of-focus activated molecules, and we could thus follow the motion of individual proteins freely diffusing within the nuclear volume. With this sptPALM technique, we recorded large data sets (on the order of 104 single translocations in a single imaging session), which were essential for a proper statistical analysis of the search dynamics.
We applied our technique to several nuclear proteins and found that diffusing factors do not sense a unique nucleoplasmic architecture: c-Myc and P-TEFb adopt different nuclear space-exploration strategies, which drastically change the way they reach their specific targets. The differences observed between the two factors were not due to their diffusive kinetic parameters but to the geometry of their exploration path. c-Myc and our control protein, ‘free’ Dendra2, showed free diffusion in a three-dimensional nuclear space. In contrast, P-TEFb explored the nuclear volume by sampling a space of reduced dimensionality, displaying characteristics of exploration constrained in fractal structures.
The role of the space-sampling mode in the search strategy has long been discussed from a theoretical point of view (de Gennes, 1982a; Kopelman, 1986; Lindenberg et al., 1991). Our experimental results support the notion that it could indeed be a key parameter for diffusion-limited chemical reactions in the closed environment of the nucleus (Bénichou et al., 2010). We discuss the implications of our observations in terms of gene expression control, and its relation to the spatial organization of genes within the nucleus.

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Functional Correlates of Signaling Pathways

Author and Curator: Larry H. Bernstein, MD, FCAP

 

We here move on to a number of specific, key published work on signaling, and look at the possible therapeutic applications to disease states.

Scripps Research Professor Wolfram Ruf and colleagues have identified a key connection between

  • the signaling pathways and the immune system spiraling out of control involving
  • the coagulation system and vascular endothelium that,
  • if disrupted may be a target for sepsis. (Science Daily, Feb 29, 2008).

It may be caused by a bacterial infection that enters the bloodstream, but

  • we now recognize the same cascade not triggered by bacterial invasion.

The acute respiratory distress syndrome (ARDS) has been defined as

  • a severe form of acute lung injury featuring
  • pulmonary inflammation and increased capillary leak.

ARDS is associated with a high mortality rate and accounts for 100,000 deaths annually in the United States. ARDS may arise in a number of clinical situations, especially in patients with sepsis. A well-described pathophysiological model of ARDS is one form of

  • the acute lung inflammation mediated by
  1. neutrophils,
  2. cytokines, and
  3. oxidant stress.

Neutrophils are major effect cells at the frontier of

  • innate immune responses, and they play
  • a critical role in host defense against invading microorganisms.

The tissue injury appears to be related to

  • proteases and toxic reactive oxygen radicals
  • released from activated neutrophils.

In addition, neutrophils can produce cytokines and chemokines that

enhance the acute inflammatory response.

Neutrophil accumulation in the lung plays a pivotal role in the pathogenesis of acute lung injury during sepsis. Directed movement of neutrophils is

  • mediated by a group of chemoattractants,
  • especially CXC chemokines.

Local lung production of CXC chemokines is intensified during experimental sepsis induced by cecal ligation and puncture (CLP).

Sepsis, Multi-organ Dysfunction Syndrome, and Septic Shock: A Conundrum of Signaling Pathways Cascading Out of Control

http://pharmaceuticalintelligence.com/2012/10/13/sepsis-multi-organ-dysfunction-syndrome-and-septic-shock-a-conundrum-of-signaling-pathways-cascading-out-of-control/

Integrins and extracellular matrix in mechanotransduction

ligand binding of integrins

ligand binding of integrins

Integrins are a family of cell surface receptors which

mediate cell–matrix and cell–cell adhesions.

Among other functions they provide an important

mechanical link between the cells external and intracellular environments while

the adhesions that they form also have critical roles in cellular signal-transduction.

Cell–matrix contacts occur at zones in the cell surface where

adhesion receptors cluster and when activated

the receptors bind to ligands in the extracellular matrix.

The extracellular matrix surrounds the cells of tissues and forms the

structural support of tissue which is particularly important in connective tissues.

Cells attach to the extracellular matrix through

specific cell-surface receptors and molecules

including integrins and transmembrane proteoglycans.

The integrin family of αβ heterodimeric receptors act as

cell adhesion molecules

connecting the ECM to the actin cytoskeleton.

The actin cytoskeleton is involved in the regulation of

1.cell motility,

2.cell polarity,

3.cell growth, and

4.cell survival.

The combination of αβ subunits determines

binding specificity and

signaling properties.

Both α and β integrin subunits contain two separate tails, which

penetrate the plasma membrane and possess small cytoplasmic domains which facilitate

the signaling functions of the receptor.

There is some evidence that the β subunit is the principal site for

binding of cytoskeletal and signaling molecules,

whereas the α subunit has a regulatory role. The integrin tails

link the ECM to the actin cytoskeleton within the cell and with cytoplasmic proteins,

such as talin, tensin, and filamin. The extracellular domains of integrin receptors bind the ECM ligands.

binding of integrins depends on ECM divalent cations ch19

binding of integrins depends on ECM divalent cations ch19

integrin coupled to F-actin via linker

integrin coupled to F-actin via linker

http://www.nature.com/nrm/journal/vaop/ncurrent/images/nrm3896-f4.jpg

Schematic of the ‘focal adhesion clutch’ on stiff (a) versus soft (b) extracellular matrix (ECM). In all cases, integrins are coupled to F-actin via linker proteins (for example, talin and vinculin). The linker proteins move backwards (as indicated by the small arrows) as F-actin also moves backwards, under pushing forces from actin polymerization and/or pulling forces from myosin II activity. This mechanism transfers force from actin to integrins, which pull on the ECM. A stiff ECM (a) resists this force so that the bound integrins remain immobile. A compliant matrix (b) deforms under this force (as indicated by the compressed ECM labelled as deformed matrix) so that the bound integrins can also move backwards. Their movement reduces the net loading rate on all the force-bearing elements, which results in altered cellular responses

The ECM is a complex mixture of matrix molecules, including –

  • glycoproteins, collagens, laminins, glycosaminoglycans, proteoglycans,
  • and nonmatrix proteins, – including growth factors

The integrin receptor formed from the binding of α and β subunits is

  • shaped like a globular head supported by two rod-like legs (Figure 1).

Most of the contact between the two subunits occurs in the head region, with

  • the intracellular tails of the subunits forming the legs of the receptor.

Integrin recognition of ligands is not constitutive but

  • is regulated by alteration of integrin affinity for ligand binding.

For integrin binding to ligands to occur

  • the integrin must be primed and activated, both of which involve
  • conformational changes to the receptor.

Linking integrin conformation to function

Figure  Integrin binding to extracellular matrix (ECM). Conformational changes to integrin structure and clustering of subunits which allow enhanced function of the receptor.

Integrins work alongside other proteins such as

cadherins,

immunoglobulin superfamily

cell adhesion molecules,

selectins, and

syndecans

to mediate

cell–cell and

cell–matrix interactions and communication.

Activation of adhesion receptors triggers the formation of matrix contacts in which

bound matrix components,

adhesion receptors,

and associated intracellular cytoskeletal and signaling molecules

form large functional, localized multiprotein complexes.

Cell–matrix contacts are important in a variety of different cell and

tissue properties including

1.embryonic development,

2.inflammatory responses,

3.wound healing,

4.and adult tissue homeostasis.

Integrin extracellular binding activity is regulated from inside the cell and binding to the ECM induces signals that are transmitted into the cell. This bidirectional signaling requires

dynamic,

spatially, and

temporally regulated formation and

disassembly of multiprotein complexes that

form around the short cytoplasmic tails of integrins.

Ligand binding to integrin family members leads to clustering of integrin molecules in the plasma membrane and recruitment of actin filaments and intracellular signaling molecules to the cytoplasmic domain of the integrins. This forms focal adhesion complexes which are able to maintain

not only adhesion to the ECM

but are involved in complex signaling pathways

which include establishing

1.cell polarity,

2.directed cell migration, and

3.maintaining cell growth and survival.

Initial activation through integrin adhesion to matrix recruits up to around 50 diverse signaling molecules

to assemble the focal adhesion complex

which is capable of responding to environmental stimuli efficiently.

Mapping of the integrin

adhesome binding and signaling interactions

a network of 156 components linked together which can be modified by 690 interactions.

Genetic programming occurs with the binding of integrins to the ECM

Signal transduction pathway activation arising from integrin-ECM binding results in

  • changes in gene expression of cells and
  • leads to alterations in cell and tissue function.

Various different effects can arise depending on the

1.cell type,

2.matrix composition, and

3.integrins activated

It has been suggested that integrin-type I collagen interaction is necessary for

  • the phosphorylation and activation of osteoblast-specific transcription factors
  • present in committed osteoprogenitor cells.

During mechanical loading/stimulation of chondrocytes there is an

  1. influx of ions across the cell membrane resulting from
  2. activation of mechanosensitive ion channels
  3. which can be inhibited by subunit-specific anti-integrin blocking antibodies or RGD peptides.

Using these strategies it was identified that

  • α5β1 integrin is a major mechanoreceptor in articular chondrocyte
  • responses to mechanical loading/stimulation.

Osteoarthritic chondrocytes show a depolarization response to 0.33 Hz stimulation

  • in contrast to the hyperpolarization response of normal chondrocytes.

The mechanotransduction pathway in chondrocytes derived from normal and osteoarthritic cartilage

  • both involve recognition of the mechanical stimulus
  • by integrin receptors resulting in
  • the activation of integrin signaling pathways
  • leading to the generation of a cytokine loop.

Normal and osteoarthritic chondrocytes show differences

  • at multiple stages of the mechanotransduction cascade.
Signaling pathways activated in chondrocytes

Signaling pathways activated in chondrocytes

http://dx.doi.org/10.1016/j.matbio.2014.08.007

Chondrocyte integrins are important mediators of cell–matrix interactions in cartilage

  • by regulating the response of the cells to signals from the ECM that
  1. control cell proliferation,
  2. survival,
  3. differentiation,
  4. matrix remodeling.

Integrins participate in development and maintenance of the tissue but also

  • in pathological processes related to matrix destruction, where
  • they likely play a role in the progression of OA.

Cellular adaptation to mechanical stress: role of integrins, Rho, cytoskeletal tension and mechanosensitive ion channels

Cells exhibited four types of mechanical responses:

(1) an immediate viscoelastic response;

(2) early adaptive behavior characterized by pulse-to-pulse attenuation in response to oscillatory forces;

(3) later adaptive cell stiffening with sustained (>15 second) static stresses; and

(4) a large-scale repositioning response with prolonged (>1 minute) stress.

Importantly, these adaptation responses differed biochemically.

The immediate and early responses were affected by

chemically dissipating cytoskeletal prestress (isometric tension), whereas

the later adaptive response was not.

The repositioning response was prevented by

inhibiting tension through interference with Rho signaling,

similar to the case of the immediate and early responses, but it was also prevented by

blocking mechanosensitive ion channels or

by inhibiting Src tyrosine kinases.

All adaptive responses were suppressed by cooling cells to 4°C to slow biochemical remodeling. Thus, cells use multiple mechanisms to sense and respond to static and dynamic changes in the level of mechanical stress applied to integrins.

Microtubule-Stimulated ADP Release, ATP Binding, and Force Generation In Transport Kinesins

All three classes of molecular motor proteins are now known to be

  • large protein families with diverse cellular functions.

Both the kinesin family and the myosin family have been defined and their proteins grouped into subfamilies. Finally, the elusive cytoplasmic version of dynein was identified and a multigene family of flagellar and cytoplasmic dyneins defined. Members of a given motor protein family share

  • significant homology in their motor domains with the defining member,
  • kinesin, dynein or myosin; but they also contain
  • unique protein domains that are specialized for interaction with different cargoes.

This large number of motor proteins may reflect

  • the number of cellular functions that require force generation or movement,
  • ranging from mitosis to morphogenesis to transport of vesicles.

Kinesins are a large family of microtubule (MT)-based motors that play important roles in many cellular activities including

mitosis,

motility, and

intracellular transport

Their involvement in a range of pathological processes

  • also highlights their significance as therapeutic targets and
  • the importance of understanding the molecular basis of their function

They are defined by their motor domains that contain both

  • the microtubule (MT) and
  • ATP binding sites.

Three ATP binding motifs—

  1. the P-loop,
  2. switch I,
  3. switch II–

are highly conserved among

  1. kinesins,
  2. myosin motors, and
  • small GTPases.

They share a conserved mode of MT binding such that

  • MT binding,
  • ATP binding, and
  • hydrolysis

are functionally coupled for efficient MT-based work.

The interior of a cell is a hive of activity, filled with

  • proteins and other items moving from one location to another.

A network of filaments called microtubules forms tracks

  • along which so-called motor proteins carry these items.

Kinesins are one group of motor proteins, and a typical kinesin protein has

  • one end (called the ‘motor domain’) that can attach itself to the microtubules.

The other end links to the cargo being carried, and a ‘neck’ connects the two. When two of these proteins work together,

  • flexible regions of the neck allow the two motor domains to move past one another,
  • which enable the kinesin to essentially walk along a microtubule in a stepwise manner.

Although the two kinesins have been thought to move along the microtubule tracks in different ways, Atherton et al. find that the core mechanism used by their motor domains is the same.

When a motor domain binds to the microtubule, its shape changes,

  • first stimulating release of the breakdown products of ATP from the previous cycle.

This release makes room for a new ATP molecule to bind. The structural changes caused by ATP binding

  • produce larger changes in the flexible neck region that
  • enable individual motor domains within a kinesin pair to
  • co-ordinate their movement and move in a consistent direction.

The major and largely invariant point of contact between kinesin motor domains and the MT is helix-α4,

  • which lies at the tubulin intradimer interface.

The conformational changes in functionally important regions of each motor domain are described,

  • starting with the nucleotide-binding site,
  • from which all other conformational changes emanate.

The nucleotide-binding site (Figure 2) has three major elements:

(1) the P-loop (brown) is visible in all our reconstructions;

(2) loop9 (yellow, contains switch I) undergoes major conformational changes through the ATPase cycle; and

(3) loop11 (red, contains switch II) that connects strand-β7 to helix-α4, the conformation and flexibility of which is

  • determined by MT binding and motor nucleotide state.

Movement and extension of helix-α6 controls neck linker docking

the N-terminus of helix-α6 is closely associated with elements of the nucleotide binding site suggesting that

  • its conformation alters in response to different nucleotide states.

Further,

  • because the orientation of helix-α6 with respect to helix-α4 controls neck linker docking and
  • because helix-α4 is held against the MT during the ATPase cycle,
    • conformational changes in helix-α6 control movement of the neck linker.

Mechanical amplification and force generation involves conformational changes across the motor domain

A key conformational change in the motor domain following Mg-ATP binding is

  • peeling of the central β-sheet from the C-terminus of helix-α4 increasing their separation;
  • this is required to accommodate rotation of helix-α6 and consequent neck linker docking

ATP binding draws loop11 and loop9 closer together; causing

(1) tilting of most of the motor domain not contacting the MT towards the nucleotide-binding site,

(2) rotation, translation, and extension of helix-α6 which we propose contributes to force generation, and

(3) allows neck linker docking and biases movement of the 2nd head towards the MT plus end.

In both motors, microtubule binding promotes

ordered conformations of conserved loops that

stimulate ADP release,

enhance microtubule affinity and

prime the catalytic site for ATP binding.

ATP binding causes only small shifts of these nucleotide-coordinating loops but induces

large conformational changes elsewhere that

allow force generation and

neck linker docking towards the microtubule plus end.

The study presents evidence provide evidence for a conserved ATP-driven

mechanism for kinesins and

reveals the critical mechanistic contribution of the microtubule interface.

Phosphorylation at endothelial cell–cell junctions: Implications for VE-cadherin function

This review summarizes the role of VE-cadherin phosphorylation in the regulation of endothelial cell–cell junctions and highlights how this affects vascular permeability and leukocyte extravasation.

The vascular endothelium is the inner lining of blood vessels and

forms a physical barrier between the vessel lumen and surrounding tissue;

controlling the extravasation of fluids,

plasma proteins and leukocytes.

Changes in the permeability of the endothelium are tightly regulated. Under basal physiological conditions, there is a continuous transfer of substances across the capillary beds. In addition the endothelium can mediate inducible,

transient hyperpermeability

in response to stimulation with inflammatory mediators,

which takes place primarily in post-capillary venules

However, when severe, inflammation may result in dysfunction of the endothelial barrier

  • in various parts of the vascular tree, including large veins, arterioles and capillaries.

Dysregulated permeability is observed in various pathological conditions, such as

  • tumor-induced angiogenesis,
  • cerebrovascular accident and
  • atherosclerosis.

Two fundamentally different pathways regulate endothelial permeability,

  1. the transcellular and
  2. paracellular pathways.

Solutes and cells can pass through the body of endothelial cells via the transcellular pathway, which includes

  • vesicular transport systems,
  • fenestrae, and
  • biochemical transporters.

The paracellular route is controlled by

  • the coordinated opening and closing of endothelial junctions and
  • thereby regulates traffic across the intercellular spaces between endothelial cells.

Endothelial cells are connected by

tight, gap and

adherens junctions,

of which the latter, and particularly the adherens junction component,

vascular endothelial (VE)-cadherin,

are of central importance for the initiation and stabilization of cell–cell contacts.

Although multiple adhesion molecules are localized at endothelial junctions,

  • blocking the adhesive function of VE-cadherin using antibodies
  • is sufficient to disrupt endothelial junctions and
  • to increase endothelial monolayer permeability both in vitro and in vivo.

Like other cadherins, VE-cadherin mediates adhesion via

  • homophilic, calcium-dependent interactions.

This cell–cell adhesion

is strengthened by binding of cytoplasmic proteins, the catenins,

to the C-terminus of VE-cadherin.

VE-cadherin can directly bind

  • β-catenin and plakoglobin, which
  • both associate with the actin binding protein α-catenin.

Initially, α-catenin was thought to directly anchor cadherins to the actin cytoskeleton, but recently it became clear that

  • α-catenin cannot bind to both β-catenin and actin simultaneously.

Numerous lines of evidence indicate that p120-catenin

  • promotes VE-cadherin surface expression and stability at the plasma membrane.

Different models are proposed that describe how

  • p120-catenin regulates cadherin membrane dynamics, including the hypothesis
  • that p120-catenin functions as a ‘cap’ that prevents the interaction of VE-cadherin
  • with the endocytic membrane trafficking machinery.

In addition, p120-catenin might regulate VE-cadherin internalization

  • through interactions with small GTPases.

Cytoplasmic p120-catenin, which is not bound to VE-cadherin, has been shown to

decrease RhoA activity,

elevate active Rac1 and Cdc42, and thereby is thought

to regulate actin cytoskeleton organization and membrane trafficking.

The intact cadherin-catenin complex is required for proper functioning of the adherens junction.

Several mechanisms may be involved in the

  • regulation of the organization and function of the cadherin–catenin complex, including
  1. endocytosis of the complex,
  2. VE-cadherin cleavage and
  3. actin cytoskeleton reorganization.

The remainder of this review primarily focuses on the

role of tyrosine phosphorylation in the control of VE-cadherin-mediated cell–cell adhesion.

Regulation of the adhesive function of VE-cadherin by tyrosine phosphorylation

It is a widely accepted concept that tyrosine phosphorylation of

  • components of the VE–cadherin-catenin complex
  • Correlates with the weakening of cell–cell adhesion.

A general idea has emerged that

tyrosine phosphorylation of the VE-cadherin complex

leads to the uncoupling of VE-cadherin from the actin cytoskeleton

through dissociation of catenins from the cadherin.

However, tyrosine phosphorylation of VE-cadherin

  • is required for efficient transmigration of leukocytes.

This suggests that VE-cadherin-mediated cell–cell contacts

1.are not just pushed open by the migrating leukocytes, but play

2.a more active role in the transmigration process.

A schematic overview of leukocyte adhesion-induced signals leading to VE-cadherin phosphorylation

Regulation of the integrity of endothelial cell–cell contacts by phosphorylation of VE-cadherin.

Regulation of the integrity of endothelial cell–cell contacts by phosphorylation of VE-cadherin

Regulation of the integrity of endothelial cell–cell contacts by phosphorylation of VE-cadherin

N-glycosylation status of E-cadherin controls cytoskeletal dynamics through the organization of distinct β-catenin- and γ-catenin-containing AJs

N-glycosylation of E-cadherin has been shown to inhibit cell–cell adhesion.

Specifically, our recent studies have provided evidence that

  • the reduction of E-cadherin N-glycosylation
  • promoted the recruitment of stabilizing components,
  • vinculin and serine/ threonine protein phosphatase 2A (PP2A), to adherens junctions (AJs)
  • and enhanced the association of AJs with the actin cytoskeleton.

Here, we examined the details of how

N-glycosylation of E-cadherin affected the molecular organization of AJs and their cytoskeletal interactions.

Using the hypoglycosylated E-cadherin variant, V13, we show that

V13/β-catenin complexes preferentially interacted with PP2A and with the microtubule motor protein dynein.

This correlated with dephosphorylation of the microtubule-associated protein tau, suggesting that

increased association of PP2A with V13-containing AJs promoted their tethering to microtubules.

These studies provide the first mechanistic insights into how N-glycosylation of E-cadherin drives changes in AJ composition through

  • the assembly of distinct β-catenin- and γ-catenin-containing scaffolds that impact the interaction with different cytoskeletal components

Cytoskeletal Basis of Ion Channel Function in Cardiac Muscle

MacKinnon. Fig 1  Ion channels exhibit three basic properties

MacKinnon. Fig 1 Ion channels exhibit three basic properties

In order to contract and accommodate the repetitive morphological changes induced by the cardiac cycle, cardiomyocytes

depend on their highly evolved and specialized cytoskeletal apparatus.

Defects in components of the cytoskeleton, in the long term,

affect the ability of the cell to compensate at both functional and structural levels.

In addition to the structural remodeling,

the myocardium becomes increasingly susceptible to altered electrical activity leading to arrhythmogenesis.

The development of arrhythmias secondary to structural remodeling defects has been noted, although the detailed molecular mechanisms are still elusive.

subjects with severe left ventricular chamber dilation such as in DCM can have left bundle branch block (LBBB), while right bundle branch block (RBBB) is more characteristic of right ventricular failure.  LBBB and RBBB have both been repeatedly associated with AV block in heart failure.

The impact of volume overload on structural and electro-cardiographic alterations has been noted in cardiomyopathy patients treated with left ventricular assist device (LVAD) therapy, which puts the heart at mechanical rest.

In LVAD-treated subjects,

QRS- and both QT- and QTc duration decreased,

suggesting that QRS- and QT-duration are significantly influenced by mechanical load and

that the shortening of the action potential duration contributes to the improved contractile performance after LVAD support.

An early postoperative period study after cardiac unloading therapy in 17 HF patients showed that in the first two weeks after LVAD implantation,

HF was associated with a relatively high incidence of ventricular arrhythmias associated with QTc interval prolongation.

In addition, a recent retrospective study of 100 adult patients with advanced HF, treated with an axial-flow HeartMate LVAD suggested that

  • the rate of new-onset monomorphic ventricular tachycardia (MVT) was increased in LVAD treated patients compared to patients given only medical treatment,

The myocardium is exposed to severe and continuous biomechanical stress during each contraction-relaxation cycle. When fiber tension remains uncompensated or simply unbalanced,

it may represent a trigger for arrhythmogenesis caused by cytoskeletal stretching,

which ultimately leads to altered ion channel localization, and subsequent action potential and conduction alterations.

Cytoskeletal proteins not only provide the backbone of the cellular structure, but they also

maintain the shape and flexibility of the different sub-cellular compartments, including the

1.plasma membrane,

2.the double lipid layer, which defines the boundaries of the cell and where

ion channels are mainly localized.

The interaction between the sarcomere, which is the basic for the passive force during diastole and for the restoring force during systole.

Sarcomeric Proteins and Ion Channels

besides fiber stretch associated with mechanical and hemodynamic impairment, cytoskeletal alterations due to primary genetic defects or indirectly to alterations in response to cellular injury can potentially

1.affect ion channel anchoring, and trafficking, as well as

2.functional regulation by second messenger pathways,

3.causing an imbalance in cardiac ionic homeostasis that will trigger arrhythmogenesis.

Intense investigation of

the sarcomeric actin network,

the Z-line structure, and

chaperone molecules docking in the plasma membrane,

has shed new light on the molecular basis of

  • cytoskeletal interactions in regulating ion channels

Actin disruption using cytochalasin D, an agent that interferes with actin polymerization, increased Na+ channel activity in 90% of excised patches tested within 2 min, which indicated that

the integrity of the filamentous actin (F-actin) network was essential for the maintenance of normal Na+ channel function

These data were the first to support a role for the cytoskeleton in cardiac arrhythmias.

Molecular interactions between the cytoskeleton and ion channels

The figure illustrates the interactions between the ion channels on the sarcolemma, and the sarcomere in cardiac myocytes. Note that the Z-line is connected to the cardiac T-tubules. The diagram illustrates the complex protein-protein interactions that occur between structural components of the cytoskeleton and ion channels. The cytoskeleton is involved in regulating the metabolism of ion channels, modifying their expression, localization, and electrical properties.

sarcomere structure

sarcomere structure

It is important to be aware of the enormous variety of clinical presentations that derive from distinct variants in the same pool of genetic factors. Knowledge of these variants could facilitate tailoring the therapy of choice for each patient. In particular,

the recent findings of structural and functional links between

the cytoskeleton and ion channels

could expand the therapeutic interventions in

arrhythmia management in structurally abnormal myocardium, where aberrant binding

between cytoskeletal proteins can directly or indirectly alter ion channel function.

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Summary of Signaling and Signaling Pathways

Summary of Signaling and Signaling Pathways

Author and Curator: Larry H Bernstein, MD, FCAP

In the imtroduction to this series of discussions I pointed out JEDS Rosalino’s observation about the construction of a complex molecule of acetyl coenzyme A, and the amount of genetic coding that had to go into it.  Furthermore, he observes –  Millions of years later, or as soon as, the information of interaction leading to activity and regulation could be found in RNA, proteins like reverse transcriptase move this information to a more stable form (DNA). In this way it is easier to understand the use of CoA to make two carbon molecules more reactive.

acetylCoA

acetylCoA

In the tutorial that follows we find support for the view that mechanisms and examples from the current literature, which give insight into the developments in cell metabolism, are achieving a separation from inconsistent views introduced by the classical model of molecular biology and genomics, toward a more functional cellular dynamics that is not dependent on the classic view.  The classical view fits a rigid framework that is to genomics and metabolomics as Mendelian genetics if to multidimentional, multifactorial genetics.  The inherent difficulty lies in two places:

  1. Interactions between differently weighted determinants
  2. A large part of the genome is concerned with regulatory function, not expression of the code

The goal of the tutorial was to achieve an understanding of how cell signaling occurs in a cell.  Completion of the tutorial would provide

  1. a basic understanding signal transduction and
  2. the role of phosphorylation in signal transduction.
Regulation of the integrity of endothelial cell–cell contacts by phosphorylation of VE-cadherin

Regulation of the integrity of endothelial cell–cell contacts by phosphorylation of VE-cadherin

In addition – detailed knowledge of –

  1. the role of Tyrosine kinases and
  2. G protein-coupled receptors in cell signaling.
serine

serine

threonine

threonine

protein kinase

protein kinase

We are constantly receiving and interpreting signals from our environment, which can come

  • in the form of light, heat, odors, touch or sound.

The cells of our bodies are also

  • constantly receiving signals from other cells.

These signals are important to

  • keep cells alive and functioning as well as
  • to stimulate important events such as
  • cell division and differentiation.

Signals are most often chemicals that can be found

  • in the extracellular fluid around cells.

These chemicals can come

  • from distant locations in the body (endocrine signaling by hormones), from
  • nearby cells (paracrine signaling) or can even
  • be secreted by the same cell (autocrine signaling).

Notch-mediated juxtacrine signal between adjacent cells. 220px-Notchccr

Signaling molecules may trigger any number of cellular responses, including

  • changing the metabolism of the cell receiving the signal or
  • result in a change in gene expression (transcription) within the nucleus of the cell or both.
controlling the output of ribosomes.

controlling the output of ribosomes.

To which I would now add..

  • result in either an inhibitory or a stimulatory effect

The three stages of cell signaling are:

Cell signaling can be divided into 3 stages:

Reception: A cell detects a signaling molecule from the outside of the cell.

Transduction: When the signaling molecule binds the receptor it changes the receptor protein in some way. This change initiates the process of transduction. Signal transduction is usually a pathway of several steps. Each relay molecule in the signal transduction pathway changes the next molecule in the pathway.

Response: Finally, the signal triggers a specific cellular response.

signal transduction

signal transduction

http://www.hartnell.edu/tutorials/biology/images/signaltransduction_simple.jpg

The initiation is depicted as follows:

Signal Transduction – ligand binds to surface receptor

Membrane receptors function by binding the signal molecule (ligand) and causing the production of a second signal (also known as a second messenger) that then causes a cellular response. These types of receptors transmit information from the extracellular environment to the inside of the cell.

  • by changing shape or
  • by joining with another protein
  • once a specific ligand binds to it.

Examples of membrane receptors include

  • G Protein-Coupled Receptors and
Understanding these receptors and identifying their ligands and the resulting signal transduction pathways represent a major conceptual advance.

Understanding these receptors and identifying their ligands and the resulting signal transduction pathways represent a major conceptual advance.

  • Receptor Tyrosine Kinases.
intracellular signaling

intracellular signaling

http://www.hartnell.edu/tutorials/biology/images/membrane_receptor_tk.jpg

Intracellular receptors are found inside the cell, either in the cytopolasm or in the nucleus of the target cell (the cell receiving the signal).

Note that though change in gene expression is stated, the change in gene expression does not here imply a change in the genetic information – such as – mutation.  That does not have to be the case in the normal homeostatic case.

This point is the differentiating case between what JEDS Roselino has referred as

  1. a fast, adaptive reaction, that is the feature of protein molecules, and distinguishes this interaction from
  2. a one-to-one transcription of the genetic code.

The rate of transcription can be controlled, or it can be blocked.  This is in large part in response to the metabolites in the immediate interstitium.

This might only be

  • a change in the rate of a transcription or a suppression of expression through RNA.
  • Or through a conformational change in an enzyme
 Swinging domains in HECT E3 enzymes

Swinging domains in HECT E3 enzymes

Since signaling systems need to be

  • responsive to small concentrations of chemical signals and act quickly,
  • cells often use a multi-step pathway that transmits the signal quickly,
  • while amplifying the signal to numerous molecules at each step.

Signal transduction pathways are shown (simplified):

Signal Transduction

Signal Transduction

Signal transduction occurs when an

  1. extracellular signaling molecule activates a specific receptor located on the cell surface or inside the cell.
  2. In turn, this receptor triggers a biochemical chain of events inside the cell, creating a response.
  3. Depending on the cell, the response alters the cell’s metabolism, shape, gene expression, or ability to divide.
  4. The signal can be amplified at any step. Thus, one signaling molecule can cause many responses.

In 1970, Martin Rodbell examined the effects of glucagon on a rat’s liver cell membrane receptor. He noted that guanosine triphosphate disassociated glucagon from this receptor and stimulated the G-protein, which strongly influenced the cell’s metabolism. Thus, he deduced that the G-protein is a transducer that accepts glucagon molecules and affects the cell. For this, he shared the 1994 Nobel Prize in Physiology or Medicine with Alfred G. Gilman.

Guanosine monophosphate structure

Guanosine monophosphate structure

In 2007, a total of 48,377 scientific papers—including 11,211 e-review papers—were published on the subject. The term first appeared in a paper’s title in 1979. Widespread use of the term has been traced to a 1980 review article by Rodbell: Research papers focusing on signal transduction first appeared in large numbers in the late 1980s and early 1990s.

Signal transduction involves the binding of extracellular signaling molecules and ligands to cell-surface receptors that trigger events inside the cell. The combination of messenger with receptor causes a change in the conformation of the receptor, known as receptor activation.

This activation is always the initial step (the cause) leading to the cell’s ultimate responses (effect) to the messenger. Despite the myriad of these ultimate responses, they are all directly due to changes in particular cell proteins. Intracellular signaling cascades can be started through cell-substratum interactions; examples are the integrin that binds ligands in the extracellular matrix and steroids.

Integrin

Integrin

Most steroid hormones have receptors within the cytoplasm and act by stimulating the binding of their receptors to the promoter region of steroid-responsive genes.

steroid hormone receptor

steroid hormone receptor

Various environmental stimuli exist that initiate signal transmission processes in multicellular organisms; examples include photons hitting cells in the retina of the eye, and odorants binding to odorant receptors in the nasal epithelium. Certain microbial molecules, such as viral nucleotides and protein antigens, can elicit an immune system response against invading pathogens mediated by signal transduction processes. This may occur independent of signal transduction stimulation by other molecules, as is the case for the toll-like receptor. It may occur with help from stimulatory molecules located at the cell surface of other cells, as with T-cell receptor signaling. Receptors can be roughly divided into two major classes: intracellular receptors and extracellular receptors.

Signal transduction cascades amplify the signal output

Signal transduction cascades amplify the signal output

Signal transduction cascades amplify the signal output

G protein-coupled receptors (GPCRs) are a family of integral transmembrane proteins that possess seven transmembrane domains and are linked to a heterotrimeric G protein. Many receptors are in this family, including adrenergic receptors and chemokine receptors.

Arrestin binding to active GPCR kinase (GRK)-phosphorylated GPCRs blocks G protein coupling

signal transduction pathways

signal transduction pathways

Arrestin binding to active GPCR kinase (GRK)-phosphorylated GPCRs blocks G protein coupling

Arrestin binding to active GPCR kinase (GRK)-phosphorylated GPCRs blocks G protein coupling

Signal transduction by a GPCR begins with an inactive G protein coupled to the receptor; it exists as a heterotrimer consisting of Gα, Gβ, and Gγ. Once the GPCR recognizes a ligand, the conformation of the receptor changes to activate the G protein, causing Gα to bind a molecule of GTP and dissociate from the other two G-protein subunits.

The dissociation exposes sites on the subunits that can interact with other molecules. The activated G protein subunits detach from the receptor and initiate signaling from many downstream effector proteins such as phospholipases and ion channels, the latter permitting the release of second messenger molecules.

Receptor tyrosine kinases (RTKs) are transmembrane proteins with an intracellular kinase domain and an extracellular domain that binds ligands; examples include growth factor receptors such as the insulin receptor.

 insulin receptor and and insulin receptor signaling pathway (IRS)

insulin receptor and and insulin receptor signaling pathway (IRS)

To perform signal transduction, RTKs need to form dimers in the plasma membrane; the dimer is stabilized by ligands binding to the receptor.

RTKs

RTKs

The interaction between the cytoplasmic domains stimulates the autophosphorylation of tyrosines within the domains of the RTKs, causing conformational changes.

Allosteric_Regulation.svg

Subsequent to this, the receptors’ kinase domains are activated, initiating phosphorylation signaling cascades of downstream cytoplasmic molecules that facilitate various cellular processes such as cell differentiation and metabolism.

Signal-Transduction-Pathway

Signal-Transduction-Pathway

As is the case with GPCRs, proteins that bind GTP play a major role in signal transduction from the activated RTK into the cell. In this case, the G proteins are

  • members of the Ras, Rho, and Raf families, referred to collectively as small G proteins.

They act as molecular switches usually

  • tethered to membranes by isoprenyl groups linked to their carboxyl ends.

Upon activation, they assign proteins to specific membrane subdomains where they participate in signaling. Activated RTKs in turn activate

  • small G proteins that activate guanine nucleotide exchange factors such as SOS1.

Once activated, these exchange factors can activate more small G proteins, thus

  • amplifying the receptor’s initial signal.

The mutation of certain RTK genes, as with that of GPCRs, can result in the expression of receptors that exist in a constitutively activate state; such mutated genes may act as oncogenes.

Integrin

 

Integrin

Integrin

Integrin-mediated signal transduction

An overview of integrin-mediated signal transduction, adapted from Hehlgens et al. (2007).

Integrins are produced by a wide variety of cells; they play a role in

  • cell attachment to other cells and the extracellular matrix and
  • in the transduction of signals from extracellular matrix components such as fibronectin and collagen.

Ligand binding to the extracellular domain of integrins

  • changes the protein’s conformation,
  • clustering it at the cell membrane to
  • initiate signal transduction.

Integrins lack kinase activity; hence, integrin-mediated signal transduction is achieved through a variety of intracellular protein kinases and adaptor molecules, the main coordinator being integrin-linked kinase.

As shown in the picture, cooperative integrin-RTK signaling determines the

  1. timing of cellular survival,
  2. apoptosis,
  3. proliferation, and
  4. differentiation.
integrin-mediated signal transduction

integrin-mediated signal transduction

Integrin signaling

Integrin signaling

ion channel

A ligand-gated ion channel, upon binding with a ligand, changes conformation

  • to open a channel in the cell membrane
  • through which ions relaying signals can pass.

An example of this mechanism is found in the receiving cell of a neural synapse. The influx of ions that occurs in response to the opening of these channels

  1. induces action potentials, such as those that travel along nerves,
  2. by depolarizing the membrane of post-synaptic cells,
  3. resulting in the opening of voltage-gated ion channels.
RyR and Ca+ release from SR

RyR and Ca+ release from SR

An example of an ion allowed into the cell during a ligand-gated ion channel opening is Ca2+;

  • it acts as a second messenger
  • initiating signal transduction cascades and
  • altering the physiology of the responding cell.

This results in amplification of the synapse response between synaptic cells

  • by remodelling the dendritic spines involved in the synapse.

In eukaryotic cells, most intracellular proteins activated by a ligand/receptor interaction possess an enzymatic activity; examples include tyrosine kinase and phosphatases. Some of them create second messengers such as cyclic AMP and IP3,

cAMP

cAMP

Inositol_1,4,5-trisphosphate.svg

Inositol_1,4,5-trisphosphate.svg

  • the latter controlling the release of intracellular calcium stores into the cytoplasm.

Many adaptor proteins and enzymes activated as part of signal transduction possess specialized protein domains that bind to specific secondary messenger molecules. For example,

  • calcium ions bind to the EF hand domains of calmodulin,
  • allowing it to bind and activate calmodulin-dependent kinase.
calcium movement and RyR2 receptor

calcium movement and RyR2 receptor

PIP3 and other phosphoinositides do the same thing to the Pleckstrin homology domains of proteins such as the kinase protein AKT.

Signals can be generated within organelles, such as chloroplasts and mitochondria, modulating the nuclear
gene expression in a process called retrograde signaling.

Recently, integrative genomics approaches, in which correlation analysis has been applied on transcript and metabolite profiling data of Arabidopsis thaliana, revealed the identification of metabolites which are putatively acting as mediators of nuclear gene expression.

http://fpls.com/unraveling_retrograde_signaling_pathways:_finding_candidate_signaling_molecules_via_metabolomics_and_systems_biology_driven_approaches

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Nutrients 2014, 6, 3245-3258; http://dx.doi.org:/10.3390/nu6083245

Omega-3 (ω-3) fatty acids are one of the two main families of long chain polyunsaturated fatty acids (PUFA). The main omega-3 fatty acids in the mammalian body are

  • α-linolenic acid (ALA), docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA).

Central nervous tissues of vertebrates are characterized by a high concentration of omega-3 fatty acids. Moreover, in the human brain,

  • DHA is considered as the main structural omega-3 fatty acid, which comprises about 40% of the PUFAs in total.

DHA deficiency may be the cause of many disorders such as depression, inability to concentrate, excessive mood swings, anxiety, cardiovascular disease, type 2 diabetes, dry skin and so on.

On the other hand,

  • zinc is the most abundant trace metal in the human brain.

There are many scientific studies linking zinc, especially

  • excess amounts of free zinc, to cellular death.

Neurodegenerative diseases, such as Alzheimer’s disease, are characterized by altered zinc metabolism. Both animal model studies and human cell culture studies have shown a possible link between

  • omega-3 fatty acids, zinc transporter levels and
  • free zinc availability at cellular levels.

Many other studies have also suggested a possible

  • omega-3 and zinc effect on neurodegeneration and cellular death.

Therefore, in this review, we will examine

  • the effect of omega-3 fatty acids on zinc transporters and
  • the importance of free zinc for human neuronal cells.

Moreover, we will evaluate the collective understanding of

  • mechanism(s) for the interaction of these elements in neuronal research and their
  • significance for the diagnosis and treatment of neurodegeneration.

Epidemiological studies have linked high intake of fish and shellfish as part of the daily diet to

  • reduction of the incidence and/or severity of Alzheimer’s disease (AD) and senile mental decline in

Omega-3 fatty acids are one of the two main families of a broader group of fatty acids referred to as polyunsaturated fatty acids (PUFAs). The other main family of PUFAs encompasses the omega-6 fatty acids. In general, PUFAs are essential in many biochemical events, especially in early post-natal development processes such as

  • cellular differentiation,
  • photoreceptor membrane biogenesis and
  • active synaptogenesis.

Despite the significance of these

two families, mammals cannot synthesize PUFA de novo, so they must be ingested from dietary sources. Though belonging to the same family, both

  • omega-3 and omega-6 fatty acids are metabolically and functionally distinct and have
  • opposing physiological effects. In the human body,
  • high concentrations of omega-6 fatty acids are known to increase the formation of prostaglandins and
  • thereby increase inflammatory processes [10].

the reverse process can be seen with increased omega-3 fatty acids in the body.

Many other factors, such as

  1. thromboxane A2 (TXA2),
  2. leukotriene
  3. B4 (LTB4),
  4. IL-1,
  5. IL-6,
  6. tumor necrosis factor (TNF) and
  7. C-reactive protein,

which are implicated in various health conditions, have been shown to be increased with high omega-6 fatty acids but decreased with omega-3 fatty acids in the human body.

Dietary fatty acids have been identified as protective factors in coronary heart disease, and PUFA levels are known to play a critical role in

  • immune responses,
  • gene expression and
  • intercellular communications.

omega-3 fatty acids are known to be vital in

  • the prevention of fatal ventricular arrhythmias, and
  • are also known to reduce thrombus formation propensity by decreasing platelet aggregation, blood viscosity and fibrinogen levels

.Since omega-3 fatty acids are prevalent in the nervous system, it seems logical that a deficiency may result in neuronal problems, and this is indeed what has been identified and reported.

The main

In another study conducted with individuals of 65 years of age or older (n = 6158), it was found that

  • only high fish consumption, but
  • not dietary omega-3 acid intake,
  • had a protective effect on cognitive decline

In 2005, based on a meta-analysis of the available epidemiology and preclinical studies, clinical trials were conducted to assess the effects of omega-3 fatty acids on cognitive protection. Four of the trials completed have shown

a protective effect of omega-3 fatty acids only among those with mild cognitive impairment conditions.

A  trial of subjects with mild memory complaints demonstrated

  • an improvement with 900 mg of DHA.

We review key findings on

  • the effect of the omega-3 fatty acid DHA on zinc transporters and the
  • importance of free zinc to human neuronal cells.

DHA is the most abundant fatty acid in neural membranes, imparting appropriate

  • fluidity and other properties,

and is thus considered as the most important fatty acid in neuronal studies. DHA is well conserved throughout the mammalian species despite their dietary differences. It is mainly concentrated

  • in membrane phospholipids at synapses and
  • in retinal photoreceptors and
  • also in the testis and sperm.

In adult rats’ brain, DHA comprises approximately

  • 17% of the total fatty acid weight, and
  • in the retina it is as high as 33%.

DHA is believed to have played a major role in the evolution of the modern human –

  • in particular the well-developed brain.

Premature babies fed on DHA-rich formula show improvements in vocabulary and motor performance.

Analysis of human cadaver brains have shown that

  • people with AD have less DHA in their frontal lobe
  • and hippocampus compared with unaffected individuals

Furthermore, studies in mice have increased support for the

  • protective role of omega-3 fatty acids.

Mice administrated with a dietary intake of DHA showed

  • an increase in DHA levels in the hippocampus.

Errors in memory were decreased in these mice and they demonstrated

  • reduced peroxide and free radical levels,
  • suggesting a role in antioxidant defense.

Another study conducted with a Tg2576 mouse model of AD demonstrated that dietary

  • DHA supplementation had a protective effect against reduction in
  • drebrin (actin associated protein), elevated oxidation, and to some extent, apoptosis via
  • decreased caspase activity.

 

Zinc

Zinc is a trace element, which is indispensable for life, and it is the second most abundant trace element in the body. It is known to be related to

  • growth,
  • development,
  • differentiation,
  • immune response,
  • receptor activity,
  • DNA synthesis,
  • gene expression,
  • neuro-transmission,
  • enzymatic catalysis,
  • hormonal storage and release,
  • tissue repair,
  • memory,
  • the visual process

and many other cellular functions. Moreover, the indispensability of zinc to the body can be discussed in many other aspects,  as

  • a component of over 300 different enzymes
  • an integral component of a metallothioneins
  • a gene regulatory protein.

Approximately 3% of all proteins contain

  • zinc binding motifs .

The broad biological functionality of zinc is thought to be due to its stable chemical and physical properties. Zinc is considered to have three different functions in enzymes;

  1. catalytic,
  2. coactive and

Indeed, it is the only metal found in all six different subclasses

of enzymes. The essential nature of zinc to the human body can be clearly displayed by studying the wide range of pathological effects of zinc deficiency. Anorexia, embryonic and post-natal growth retardation, alopecia, skin lesions, difficulties in wound healing, increased hemorrhage tendency and severe reproductive abnormalities, emotional instability, irritability and depression are just some of the detrimental effects of zinc deficiency.

Proper development and function of the central nervous system (CNS) is highly dependent on zinc levels. In the mammalian organs, zinc is mainly concentrated in the brain at around 150 μm. However, free zinc in the mammalian brain is calculated to be around 10 to 20 nm and the rest exists in either protein-, enzyme- or nucleotide bound form. The brain and zinc relationship is thought to be mediated

  • through glutamate receptors, and
  • it inhibits excitatory and inhibitory receptors.

Vesicular localization of zinc in pre-synaptic terminals is a characteristic feature of brain-localized zinc, and

  • its release is dependent on neural activity.

Retardation of the growth and development of CNS tissues have been linked to low zinc levels. Peripheral neuropathy, spina bifida, hydrocephalus, anencephalus, epilepsy and Pick’s disease have been linked to zinc deficiency. However, the body cannot tolerate excessive amounts of zinc.

The relationship between zinc and neurodegeneration, specifically AD, has been interpreted in several ways. One study has proposed that β-amyloid has a greater propensity to

  • form insoluble amyloid in the presence of
  • high physiological levels of zinc.

Insoluble amyloid is thought to

  • aggregate to form plaques,

which is a main pathological feature of AD. Further studies have shown that

  • chelation of zinc ions can deform and disaggregate plaques.

In AD, the most prominent injuries are found in

  • hippocampal pyramidal neurons, acetylcholine-containing neurons in the basal forebrain, and in
  • somatostatin-containing neurons in the forebrain.

All of these neurons are known to favor

  • rapid and direct entry of zinc in high concentration
  • leaving neurons frequently exposed to high dosages of zinc.

This is thought to promote neuronal cell damage through oxidative stress and mitochondrial dysfunction. Excessive levels of zinc are also capable of

  • inhibiting Ca2+ and Na+ voltage gated channels
  • and up-regulating the cellular levels of reactive oxygen species (ROS).

High levels of zinc are found in Alzheimer’s brains indicating a possible zinc related neurodegeneration. A study conducted with mouse neuronal cells has shown that even a 24-h exposure to high levels of zinc (40 μm) is sufficient to degenerate cells.

If the human diet is deficient in zinc, the body

  • efficiently conserves zinc at the tissue level by compensating other cellular mechanisms

to delay the dietary deficiency effects of zinc. These include reduction of cellular growth rate and zinc excretion levels, and

  • redistribution of available zinc to more zinc dependent cells or organs.

A novel method of measuring metallothionein (MT) levels was introduced as a biomarker for the

  • assessment of the zinc status of individuals and populations.

In humans, erythrocyte metallothionein (E-MT) levels may be considered as an indicator of zinc depletion and repletion, as E-MT levels are sensitive to dietary zinc intake. It should be noted here that MT plays an important role in zinc homeostasis by acting

  • as a target for zinc ion binding and thus
  • assisting in the trafficking of zinc ions through the cell,
  • which may be similar to that of zinc transporters

Zinc Transporters

Deficient or excess amounts of zinc in the body can be catastrophic to the integrity of cellular biochemical and biological systems. The gastrointestinal system controls the absorption, excretion and the distribution of zinc, although the hydrophilic and high-charge molecular characteristics of zinc are not favorable for passive diffusion across the cell membranes. Zinc movement is known to occur

  • via intermembrane proteins and zinc transporter (ZnT) proteins

These transporters are mainly categorized under two metal transporter families; Zip (ZRT, IRT like proteins) and CDF/ZnT (Cation Diffusion Facilitator), also known as SLC (Solute Linked Carrier) gene families: Zip (SLC-39) and ZnT (SLC-30). More than 20 zinc transporters have been identified and characterized over the last two decades (14 Zips and 8 ZnTs).

Members of the SLC39 family have been identified as the putative facilitators of zinc influx into the cytosol, either from the extracellular environment or from intracellular compartments (Figure 1).

The identification of this transporter family was a result of gene sequencing of known Zip1 protein transporters in plants, yeast and human cells. In contrast to the SLC39 family, the SLC30 family facilitates the opposite process, namely zinc efflux from the cytosol to the extracellular environment or into luminal compartments such as secretory granules, endosomes and synaptic vesicles; thus decreasing intracellular zinc availability (Figure 1). ZnT3 is the most important in the brain where

  • it is responsible for the transport of zinc into the synaptic vesicles of
  • glutamatergic neurons in the hippocampus and neocortex,

Figure 1: Subcellular localization and direction of transport of the zinc transporter families, ZnT and ZIP. Arrows show the direction of zinc mobilization for the ZnT (green) and ZIP (red) proteins. A net gain in cytosolic zinc is achieved by the transportation of zinc from the extracellular region and organelles such as the endoplasmic reticulum (ER) and Golgi apparatus by the ZIP transporters. Cytosolic zinc is mobilized into early secretory compartments such as the ER and Golgi apparatus by the ZnT transporters. Figures were produced using Servier Medical Art, http://www.servier.com/.   http://www.hindawi.com/journals/jnme/2012/173712.fig.001.jpg

Figure 2: Early zinc signaling (EZS) and late zinc signaling (LZS). EZS involves transcription-independent mechanisms where an extracellular stimulus directly induces an increase in zinc levels within several minutes by releasing zinc from intracellular stores (e.g., endoplasmic reticulum). LSZ is induced several hours after an external stimulus and is dependent on transcriptional changes in zinc transporter expression. Components of this figure were produced using Servier Medical Art, http://www.servier.com/ and adapted from Fukada et al. [30].

omega-3 fatty acids in the mammalian body are

  1. α-linolenic acid (ALA),
  2. docosahexenoic acid (DHA) and
  3. eicosapentaenoic acid (EPA).

In general, seafood is rich in omega-3 fatty acids, more specifically DHA and EPA (Table 1). Thus far, there are nine separate epidemiological studies that suggest a possible link between

  • increased fish consumption and reduced risk of AD
  • and eight out of ten studies have reported a link between higher blood omega-3 levels

DHA and Zinc Homeostasis

Many studies have identified possible associations between DHA levels, zinc homeostasis, neuroprotection and neurodegeneration. Dietary DHA deficiency resulted in

  • increased zinc levels in the hippocampus and
  • elevated expression of the putative zinc transporter, ZnT3, in the rat brain.

Altered zinc metabolism in neuronal cells has been linked to neurodegenerative conditions such as AD. A study conducted with transgenic mice has shown a significant link between ZnT3 transporter levels and cerebral amyloid plaque pathology. When the ZnT3 transporter was silenced in transgenic mice expressing cerebral amyloid plaque pathology,

  • a significant reduction in plaque load
  • and the presence of insoluble amyloid were observed.

In addition to the decrease in plaque load, ZnT3 silenced mice also exhibited a significant

  • reduction in free zinc availability in the hippocampus
  • and cerebral cortex.

Collectively, the findings from this study are very interesting and indicate a clear connection between

  • zinc availability and amyloid plaque formation,

thus indicating a possible link to AD.

DHA supplementation has also been reported to limit the following:

  1. amyloid presence,
  2. synaptic marker loss,
  3. hyper-phosphorylation of Tau,
  4. oxidative damage and
  5. cognitive deficits in transgenic mouse model of AD.

In addition, studies by Stoltenberg, Flinn and colleagues report on the modulation of zinc and the effect in transgenic mouse models of AD. Given that all of these are classic pathological features of AD, and considering the limiting nature of DHA in these processes, it can be argued that DHA is a key candidate in preventing or even curing this debilitating disease.

In order to better understand the possible links and pathways of zinc and DHA with neurodegeneration, we designed a study that incorporates all three of these aspects, to study their effects at the cellular level. In this study, we were able to demonstrate a possible link between omega-3 fatty acid (DHA) concentration, zinc availability and zinc transporter expression levels in cultured human neuronal cells.

When treated with DHA over 48 h, ZnT3 levels were markedly reduced in the human neuroblastoma M17 cell line. Moreover, in the same study, we were able to propose a possible

  • neuroprotective mechanism of DHA,

which we believe is exerted through

  • a reduction in cellular zinc levels (through altering zinc transporter expression levels)
  • that in turn inhibits apoptosis.

DHA supplemented M17 cells also showed a marked depletion of zinc uptake (up to 30%), and

  • free zinc levels in the cytosol were significantly low compared to the control

This reduction in free zinc availability was specific to DHA; cells treated with EPA had no significant change in free zinc levels (unpublished data). Moreover, DHA-repleted cells had

  • low levels of active caspase-3 and
  • high Bcl-2 levels compared to the control treatment.

These findings are consistent with previous published data and further strengthen the possible

  • correlation between zinc, DHA and neurodegeneration.

On the other hand, recent studies using ZnT3 knockout (ZnT3KO) mice have shown the importance of

  • ZnT3 in memory and AD pathology.

For example, Sindreu and colleagues have used ZnT3KO mice to establish the important role of

  • ZnT3 in zinc homeostasis that modulates presynaptic MAPK signaling
  • required for hippocampus-dependent memory

Results from these studies indicate a possible zinc-transporter-expression-level-dependent mechanism for DHA neuroprotection.

Read Full Post »

Complex Models of Signaling: Therapeutic Implications

Complex Models of Signaling: Therapeutic Implications

Curator: Larry H. Bernstein, MD, FCAP

Updated 6/24/2019

Fishy Business: Effect of Omega-3 Fatty Acids on Zinc Transporters and Free Zinc Availability in Human Neuronal Cells

Damitha De Mel and Cenk Suphioglu *

NeuroAllergy Research Laboratory (NARL), School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Waurn Ponds, Victoria, Australia.

Nutrients 2014, 6, 3245-3258; http://dx.doi.org:/10.3390/nu6083245

Omega-3 (ω-3) fatty acids are one of the two main families of long chain polyunsaturated fatty acids (PUFA). The main omega-3 fatty acids in the mammalian body are

  • α-linolenic acid (ALA), docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA).

Central nervous tissues of vertebrates are characterized by a high concentration of omega-3 fatty acids. Moreover, in the human brain,

  • DHA is considered as the main structural omega-3 fatty acid, which comprises about 40% of the PUFAs in total.

DHA deficiency may be the cause of many disorders such as depression, inability to concentrate, excessive mood swings, anxiety, cardiovascular disease, type 2 diabetes, dry skin and so on.

On the other hand,

  • zinc is the most abundant trace metal in the human brain.

There are many scientific studies linking zinc, especially

  • excess amounts of free zinc, to cellular death.

Neurodegenerative diseases, such as Alzheimer’s disease, are characterized by altered zinc metabolism. Both animal model studies and human cell culture studies have shown a possible link between

  • omega-3 fatty acids, zinc transporter levels and
  • free zinc availability at cellular levels.

Many other studies have also suggested a possible

  • omega-3 and zinc effect on neurodegeneration and cellular death.

Therefore, in this review, we will examine

  • the effect of omega-3 fatty acids on zinc transporters and
  • the importance of free zinc for human neuronal cells.

Moreover, we will evaluate the collective understanding of

  • mechanism(s) for the interaction of these elements in neuronal research and their
  • significance for the diagnosis and treatment of neurodegeneration.

Epidemiological studies have linked high intake of fish and shellfish as part of the daily diet to

  • reduction of the incidence and/or severity of Alzheimer’s disease (AD) and senile mental decline in

Omega-3 fatty acids are one of the two main families of a broader group of fatty acids referred to as polyunsaturated fatty acids (PUFAs). The other main family of PUFAs encompasses the omega-6 fatty acids. In general, PUFAs are essential in many biochemical events, especially in early post-natal development processes such as

  • cellular differentiation,
  • photoreceptor membrane biogenesis and
  • active synaptogenesis.

Despite the significance of these

two families, mammals cannot synthesize PUFA de novo, so they must be ingested from dietary sources. Though belonging to the same family, both

  • omega-3 and omega-6 fatty acids are metabolically and functionally distinct and have
  • opposing physiological effects. In the human body,
  • high concentrations of omega-6 fatty acids are known to increase the formation of prostaglandins and
  • thereby increase inflammatory processes [10].

the reverse process can be seen with increased omega-3 fatty acids in the body.

Many other factors, such as

  1. thromboxane A2 (TXA2),
  2. leukotriene
  3. B4 (LTB4),
  4. IL-1,
  5. IL-6,
  6. tumor necrosis factor (TNF) and
  7. C-reactive protein,

which are implicated in various health conditions, have been shown to be increased with high omega-6 fatty acids but decreased with omega-3 fatty acids in the human body.

Dietary fatty acids have been identified as protective factors in coronary heart disease, and PUFA levels are known to play a critical role in

  • immune responses,
  • gene expression and
  • intercellular communications.

omega-3 fatty acids are known to be vital in

  • the prevention of fatal ventricular arrhythmias, and
  • are also known to reduce thrombus formation propensity by decreasing platelet aggregation, blood viscosity and fibrinogen levels

.Since omega-3 fatty acids are prevalent in the nervous system, it seems logical that a deficiency may result in neuronal problems, and this is indeed what has been identified and reported.

The main omega-3 fatty acids in the mammalian body are

  1. α-linolenic acid (ALA),
  2. docosahexenoic acid (DHA) and
  3. eicosapentaenoic acid (EPA).

In general, seafood is rich in omega-3 fatty acids, more specifically DHA and EPA (Table 1). Thus far, there are nine separate epidemiological studies that suggest a possible link between

  • increased fish consumption and reduced risk of AD
  • and eight out of ten studies have reported a link between higher blood omega-3 levels

Table 1. Total percentage of omega-3 fatty acids in common foods and supplements.

Food/Supplement EPA DHA ALA Total %
Fish
SalmonSardine

Anchovy

Halibut

Herring

Mackerel

Tuna

Fresh Bluefin

XX

X

X

X

X

X

X

XX

X

X

X

X

X

X

>50%>50%

>50%

>50%

>50%

>50%

>50%

>50%

Oils/Supplements
Fish oil capsulesCod liver oils

Salmon oil

Sardine oil

XX

X

X

XX

X

X

>50%>50%

>50%

>50%

Black currant oilCanola oil Mustard seed oils

Soybean oil

Walnut oil

Wheat germ oil

XX

X

X

X

X

10%–50%10%–50%

10%–50%

10%–50%

10%–50%

10%–50%

Seeds and other foods
Flaxseeds/LinseedsSpinach

Wheat germ Human milk

Peanut butter

Soybeans

Olive oil

Walnuts

XX

X

X

X

X

X

X

>50%>50%

10%–50%

10%–50%

<10%

<10%

<10%

<10%

 

Table adopted from Maclean C.H. et al. [18].

In another study conducted with individuals of 65 years of age or older (n = 6158), it was found that

  • only high fish consumption, but
  • not dietary omega-3 acid intake,
  • had a protective effect on cognitive decline

In 2005, based on a meta-analysis of the available epidemiology and preclinical studies, clinical trials were conducted to assess the effects of omega-3 fatty acids on cognitive protection. Four of the trials completed have shown

a protective effect of omega-3 fatty acids only among those with mild cognitive impairment conditions.

A  trial of subjects with mild memory complaints demonstrated

  • an improvement with 900 mg of DHA.

We review key findings on

  • the effect of the omega-3 fatty acid DHA on zinc transporters and the
  • importance of free zinc to human neuronal cells.

DHA is the most abundant fatty acid in neural membranes, imparting appropriate

  • fluidity and other properties,

and is thus considered as the most important fatty acid in neuronal studies. DHA is well conserved throughout the mammalian species despite their dietary differences. It is mainly concentrated

  • in membrane phospholipids at synapses and
  • in retinal photoreceptors and
  • also in the testis and sperm.

In adult rats’ brain, DHA comprises approximately

  • 17% of the total fatty acid weight, and
  • in the retina it is as high as 33%.

DHA is believed to have played a major role in the evolution of the modern human –

  • in particular the well-developed brain.

Premature babies fed on DHA-rich formula show improvements in vocabulary and motor performance.

Analysis of human cadaver brains have shown that

  • people with AD have less DHA in their frontal lobe
  • and hippocampus compared with unaffected individuals

Furthermore, studies in mice have increased support for the

  • protective role of omega-3 fatty acids.

Mice administrated with a dietary intake of DHA showed

  • an increase in DHA levels in the hippocampus.

Errors in memory were decreased in these mice and they demonstrated

  • reduced peroxide and free radical levels,
  • suggesting a role in antioxidant defense.

Another study conducted with a Tg2576 mouse model of AD demonstrated that dietary

  • DHA supplementation had a protective effect against reduction in
  • drebrin (actin associated protein), elevated oxidation, and to some extent, apoptosis via
  • decreased caspase activity.

 

Zinc

Zinc is a trace element, which is indispensable for life, and it is the second most abundant trace element in the body. It is known to be related to

  • growth,
  • development,
  • differentiation,
  • immune response,
  • receptor activity,
  • DNA synthesis,
  • gene expression,
  • neuro-transmission,
  • enzymatic catalysis,
  • hormonal storage and release,
  • tissue repair,
  • memory,
  • the visual process

and many other cellular functions. Moreover, the indispensability of zinc to the body can be discussed in many other aspects,  as

  • a component of over 300 different enzymes
  • an integral component of a metallothioneins
  • a gene regulatory protein.

Approximately 3% of all proteins contain

  • zinc binding motifs .

The broad biological functionality of zinc is thought to be due to its stable chemical and physical properties. Zinc is considered to have three different functions in enzymes;

  1. catalytic,
  2. coactive and

Indeed, it is the only metal found in all six different subclasses

of enzymes. The essential nature of zinc to the human body can be clearly displayed by studying the wide range of pathological effects of zinc deficiency. Anorexia, embryonic and post-natal growth retardation, alopecia, skin lesions, difficulties in wound healing, increased hemorrhage tendency and severe reproductive abnormalities, emotional instability, irritability and depression are just some of the detrimental effects of zinc deficiency.

Proper development and function of the central nervous system (CNS) is highly dependent on zinc levels. In the mammalian organs, zinc is mainly concentrated in the brain at around 150 μm. However, free zinc in the mammalian brain is calculated to be around 10 to 20 nm and the rest exists in either protein-, enzyme- or nucleotide bound form. The brain and zinc relationship is thought to be mediated

  • through glutamate receptors, and
  • it inhibits excitatory and inhibitory receptors.

Vesicular localization of zinc in pre-synaptic terminals is a characteristic feature of brain-localized zinc, and

  • its release is dependent on neural activity.

Retardation of the growth and development of CNS tissues have been linked to low zinc levels. Peripheral neuropathy, spina bifida, hydrocephalus, anencephalus, epilepsy and Pick’s disease have been linked to zinc deficiency. However, the body cannot tolerate excessive amounts of zinc.

The relationship between zinc and neurodegeneration, specifically AD, has been interpreted in several ways. One study has proposed that β-amyloid has a greater propensity to

  • form insoluble amyloid in the presence of
  • high physiological levels of zinc.

Insoluble amyloid is thought to

  • aggregate to form plaques,

which is a main pathological feature of AD. Further studies have shown that

  • chelation of zinc ions can deform and disaggregate plaques.

In AD, the most prominent injuries are found in

  • hippocampal pyramidal neurons, acetylcholine-containing neurons in the basal forebrain, and in
  • somatostatin-containing neurons in the forebrain.

All of these neurons are known to favor

  • rapid and direct entry of zinc in high concentration
  • leaving neurons frequently exposed to high dosages of zinc.

This is thought to promote neuronal cell damage through oxidative stress and mitochondrial dysfunction. Excessive levels of zinc are also capable of

  • inhibiting Ca2+ and Na+ voltage gated channels
  • and up-regulating the cellular levels of reactive oxygen species (ROS).

High levels of zinc are found in Alzheimer’s brains indicating a possible zinc related neurodegeneration. A study conducted with mouse neuronal cells has shown that even a 24-h exposure to high levels of zinc (40 μm) is sufficient to degenerate cells.

If the human diet is deficient in zinc, the body

  • efficiently conserves zinc at the tissue level by compensating other cellular mechanisms

to delay the dietary deficiency effects of zinc. These include reduction of cellular growth rate and zinc excretion levels, and

  • redistribution of available zinc to more zinc dependent cells or organs.

A novel method of measuring metallothionein (MT) levels was introduced as a biomarker for the

  • assessment of the zinc status of individuals and populations.

In humans, erythrocyte metallothionein (E-MT) levels may be considered as an indicator of zinc depletion and repletion, as E-MT levels are sensitive to dietary zinc intake. It should be noted here that MT plays an important role in zinc homeostasis by acting

  • as a target for zinc ion binding and thus
  • assisting in the trafficking of zinc ions through the cell,
  • which may be similar to that of zinc transporters

Zinc Transporters

Deficient or excess amounts of zinc in the body can be catastrophic to the integrity of cellular biochemical and biological systems. The gastrointestinal system controls the absorption, excretion and the distribution of zinc, although the hydrophilic and high-charge molecular characteristics of zinc are not favorable for passive diffusion across the cell membranes. Zinc movement is known to occur

  • via intermembrane proteins and zinc transporter (ZnT) proteins

These transporters are mainly categorized under two metal transporter families; Zip (ZRT, IRT like proteins) and CDF/ZnT (Cation Diffusion Facilitator), also known as SLC (Solute Linked Carrier) gene families: Zip (SLC-39) and ZnT (SLC-30). More than 20 zinc transporters have been identified and characterized over the last two decades (14 Zips and 8 ZnTs).

Members of the SLC39 family have been identified as the putative facilitators of zinc influx into the cytosol, either from the extracellular environment or from intracellular compartments (Figure 1).

The identification of this transporter family was a result of gene sequencing of known Zip1 protein transporters in plants, yeast and human cells. In contrast to the SLC39 family, the SLC30 family facilitates the opposite process, namely zinc efflux from the cytosol to the extracellular environment or into luminal compartments such as secretory granules, endosomes and synaptic vesicles; thus decreasing intracellular zinc availability (Figure 1). ZnT3 is the most important in the brain where

  • it is responsible for the transport of zinc into the synaptic vesicles of
  • glutamatergic neurons in the hippocampus and neocortex,

 

Figure 1. Putative cellular localization of some of the different human zinc transporters (i.e., Zip1- Zip4 and ZnT1- ZnT7). Arrows indicate the direction of zinc passage by the appropriate putative zinc transporters in a generalized human cell. Although there are fourteen Zips and eight ZnTs known so far, only the main zinc transporters are illustrated in this figure for clarity and brevity.

Figure 1: Subcellular localization and direction of transport of the zinc transporter families, ZnT and ZIP. Arrows show the direction of zinc mobilization for the ZnT (green) and ZIP (red) proteins. A net gain in cytosolic zinc is achieved by the transportation of zinc from the extracellular region and organelles such as the endoplasmic reticulum (ER) and Golgi apparatus by the ZIP transporters. Cytosolic zinc is mobilized into early secretory compartments such as the ER and Golgi apparatus by the ZnT transporters. Figures were produced using Servier Medical Art, http://www.servier.com/.   http://www.hindawi.com/journals/jnme/2012/173712.fig.001.jpg

zinc transporters

zinc transporters

 

 

Early zinc signaling (EZS) and late zinc signaling (LZS)

Early zinc signaling (EZS) and late zinc signaling (LZS)

http://www.hindawi.com/journals/jnme/2012/floats/173712/thumbnails/173712.fig.002_th.jpg

 

Figure 2: Early zinc signaling (EZS) and late zinc signaling (LZS). EZS involves transcription-independent mechanisms where an extracellular stimulus directly induces an increase in zinc levels within several minutes by releasing zinc from intracellular stores (e.g., endoplasmic reticulum). LSZ is induced several hours after an external stimulus and is dependent on transcriptional changes in zinc transporter expression. Components of this figure were produced using Servier Medical Art, http://www.servier.com/ and adapted from Fukada et al. [30].

 

DHA and Zinc Homeostasis

Many studies have identified possible associations between DHA levels, zinc homeostasis, neuroprotection and neurodegeneration. Dietary DHA deficiency resulted in

  • increased zinc levels in the hippocampus and
  • elevated expression of the putative zinc transporter, ZnT3, in the rat brain.

Altered zinc metabolism in neuronal cells has been linked to neurodegenerative conditions such as AD. A study conducted with transgenic mice has shown a significant link between ZnT3 transporter levels and cerebral amyloid plaque pathology. When the ZnT3 transporter was silenced in transgenic mice expressing cerebral amyloid plaque pathology,

  • a significant reduction in plaque load
  • and the presence of insoluble amyloid were observed.

In addition to the decrease in plaque load, ZnT3 silenced mice also exhibited a significant

  • reduction in free zinc availability in the hippocampus
  • and cerebral cortex.

Collectively, the findings from this study are very interesting and indicate a clear connection between

  • zinc availability and amyloid plaque formation,

thus indicating a possible link to AD.

DHA supplementation has also been reported to limit the following:

  1. amyloid presence,
  2. synaptic marker loss,
  3. hyper-phosphorylation of Tau,
  4. oxidative damage and
  5. cognitive deficits in transgenic mouse model of AD.

In addition, studies by Stoltenberg, Flinn and colleagues report on the modulation of zinc and the effect in transgenic mouse models of AD. Given that all of these are classic pathological features of AD, and considering the limiting nature of DHA in these processes, it can be argued that DHA is a key candidate in preventing or even curing this debilitating disease.

In order to better understand the possible links and pathways of zinc and DHA with neurodegeneration, we designed a study that incorporates all three of these aspects, to study their effects at the cellular level. In this study, we were able to demonstrate a possible link between omega-3 fatty acid (DHA) concentration, zinc availability and zinc transporter expression levels in cultured human neuronal cells.

When treated with DHA over 48 h, ZnT3 levels were markedly reduced in the human neuroblastoma M17 cell line. Moreover, in the same study, we were able to propose a possible

  • neuroprotective mechanism of DHA,

which we believe is exerted through

  • a reduction in cellular zinc levels (through altering zinc transporter expression levels)
  • that in turn inhibits apoptosis.

DHA supplemented M17 cells also showed a marked depletion of zinc uptake (up to 30%), and

  • free zinc levels in the cytosol were significantly low compared to the control

This reduction in free zinc availability was specific to DHA; cells treated with EPA had no significant change in free zinc levels (unpublished data). Moreover, DHA-repleted cells had

  • low levels of active caspase-3 and
  • high Bcl-2 levels compared to the control treatment.

These findings are consistent with previous published data and further strengthen the possible

  • correlation between zinc, DHA and neurodegeneration.

On the other hand, recent studies using ZnT3 knockout (ZnT3KO) mice have shown the importance of

  • ZnT3 in memory and AD pathology.

For example, Sindreu and colleagues have used ZnT3KO mice to establish the important role of

  • ZnT3 in zinc homeostasis that modulates presynaptic MAPK signaling
  • required for hippocampus-dependent memory

Results from these studies indicate a possible zinc-transporter-expression-level-dependent mechanism for DHA neuroprotection.

Collectively from these studies, the following possible mechanism can be proposed (Figure 2).

possible benefits of DHA in neuroprotection through reduction of ZnT3 transporter

possible benefits of DHA in neuroprotection through reduction of ZnT3 transporter

 

Figure 2. Proposed neuroprotection mechanism of docosahexaenoic acid (DHA) in reference to synaptic zinc. Schematic diagram showing possible benefits of DHA in neuroprotection through reduction of ZnT3 transporter expression levels in human neuronal cells, which results in a reduction of zinc flux and thus lowering zinc concentrations in neuronal synaptic vesicles, and therefore contributing to a lower incidence of neurodegenerative diseases (ND), such as Alzheimer’s disease (AD).

More recent data from our research group have also shown a link between the expression levels of histone H3 and H4 proteins in human neuronal cells in relation to DHA and zinc. Following DHA treatment, both H3 and H4 levels were up-regulated. In contrast, zinc treatment resulted in a down-regulation of histone levels. Both zinc and DHA have shown opposing effects on histone post-translational modifications, indicating a possible distinctive epigenetic pattern. Upon treatment with zinc, M17 cells displayed an increase in histone deacetylase (HDACs) and a reduction in histone acetylation. Conversely, with DHA treatment, HDAC levels were significantly reduced and the acetylation of histones was up-regulated. These findings also support a possible interaction between DHA and zinc availability.

Conclusions

It is possible to safely claim that there is more than one potential pathway by which DHA and zinc interact at a cellular level, at least in cultured human neuronal cells. Significance and importance of both DHA and zinc in neuronal survival is attested by the presence of these multiple mechanisms.
Most of these reported studies were conducted using human neuroblastoma cells, or similar cell types, due to the lack of live mature human neuronal cells. Thus, the results may differ from results achieved under actual human physiological conditions due to the structural and functional differences between these cells and mature human neurons. Therefore, an alternative approach that can mimic the human neuronal cells more effectively would be advantageous.

Sphingosine-1-phosphate signaling as a therapeutic target          

E Giannoudaki, DJ Swan, JA Kirby, S Ali

Applied Immunobiology and Transplantation Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK

Cell Health and Cytoskeleton 2012; 4: 63–72

S1P is a 379Da member of the lysophospholipid family. It is the direct metabolite of sphingosine through the action of two sphingosine kinases, SphK1 and SphK2. The main metabolic pathway starts with the hydrolysis of sphingomyelin, a membrane sphingolipid, into ceramide by the enzyme sphingomyelinase and the subsequent production of sphingosine by ceramidase (Figure 1). Ceramide can also be produced de novo in the endoplasmic reticulum (ER) from serine and palmitoyl coenzyme A through multiple intermediates. S1P production is regulated by various S1P-specific and general lipid phosphatases, as well as S1P lyase, which irreversibly degrades S1P into phosphoethanolamine and hexadecanal. The balance between intracellular S1P and its metabolite ceramide can determine cellular fate. Ceramide promotes apoptosis, while S1P suppresses cell death and promotes cell survival. This creates an S1P ceramide “rheostat” inside the cells. S1P lyase expression in tissue is higher than it is in erythrocytes and platelets, the main “suppliers” of S1P in blood. This causes a tissue–blood gradient of S1P, which is important in many S1P-mediated responses, like the lymphocyte egress from lymphoid organs.

S1P signaling overview

S1P is produced inside cells; however, it can also be found extracellularly, in a variety of different tissues. It is abundant in the blood, at concentrations of 0.4–1.5 μM, where it is mainly secreted by erythrocytes and platelets. Blood S1P can be found separately, but mainly it exists in complexes with high-density lipoprotein (HDL) (∼60%).  Many of the cardioprotective effects of HDL are hypothesized to involve S1P. Before 1996, S1P was thought to act mainly intracellularly as a second messenger. However, the identification of several GPCRs that bind S1P led to the initiation of many studies on

  • extracellular S1P signaling through those receptors.

There are five receptors that have been identified currently. These can be coupled with different G-proteins. Assuming that each receptor coupling with a G protein has a slightly different function, one can recognize the complexity of S1P receptor signaling.

S1P as a second messenger

S1P is involved in many cellular processes through its GPCR signaling; studies demonstrate that S1P also acts at an intracellular level. Intracellular S1P plays a role in maintaining the balance of cell survival signal toward apoptotic signals, creating a

  • cell “rheostat” between S1P and its precursor ceramide.

Important evidence that S1P can act intracellularly as a second messenger came from yeast (Saccharomyces cerevisiae) and plant (Arabidopsis thaliana) cells. Yeast cells do not express any S1P receptors, although they can be affected by S1P during heat-shock responses. Similarly, Arabidopsis has only one GPCR-like protein, termed “GCR1,” which does not bind S1P, although S1P regulates stomata closure during drought.

Sphingosine-1-phosphate

Sphingosine-1-phosphate

In mammals, the sphingosine kinases have been found to localize in different cell compartments, being responsible for the accumulation of S1P in those compartments to give intracellular signals. In mitochondria, for instance,

  • S1P was recently found to interact with prohibitin 2,

a conserved protein that maintains mitochondria assembly and function. According to the same study,

SphK2 is the major producer of S1P in mitochondria and the knockout of its gene can cause

  • disruption of mitochondrial respiration and cytochrome c oxidase function.

SphK2 is also present in the nucleus of many cells and has been implicated to cause cell cycle arrest, and it causes S1P accumulation in the nucleus. It seems that nuclear S1P is affiliated with the histone deacetylases HDAC1 and HDAC2,

  • inhibiting their activity, thus having an indirect effect in epigenetic regulation of gene expression.

In the ER, SphK2 has been identified to translocate during stress, and promote apoptosis. It seems that S1P has specific targets in the ER that cause apoptosis, probably through calcium mobilization signals.

Sphingosine 1-phosphate (S1P) is a small bioactive lipid molecule that is involved in several processes both intracellularly and extracellularly. It acts intracellularly

  • to promote the survival and growth of the cell,

through its interaction with molecules in different compartments of the cell.

It can also exist at high concentrations extracellularly, in the blood plasma and lymph. This causes an S1P gradient important for cell migration. S1P signals through five G protein-coupled receptors, S1PR1–S1PR5, whose expression varies in different types of cells and tissue. S1P signaling can be involved in physiological and pathophysiological conditions of the cardiovascular, nervous, and immune systems and diseases such as ischemia/reperfusion injury, autoimmunity, and cancer. In this review, we discuss how it can be used to discover novel therapeutic targets.

The involvement of S1P signaling in disease

In a mouse model of myocardial ischemia-reperfusion injury (IRI), S1P and its carrier, HDL, can help protect myocardial tissue and decrease the infarct size. It seems they reduce cardiomyocyte apoptosis and neutrophil recruitment to the ischemic tissue and may decrease leukocyte adhesion to the endothelium. This effect appears to be S1PR3 mediated, since in S1PR3 knockout mice it is alleviated.

Ischemia activates SphK1, which is then translocated to the plasma membrane. This leads to an increase of intracellular S1P, helping to promote cardiomyocyte survival against apoptosis, induced by ceramide. SphK1 knockout mice cannot be preconditioned against IRI, whereas SphK1 gene induction in the heart protects it from IRI. Interestingly, a recent study shows SphK2 may also play a role, since its knockout reduces the cardioprotective effects of preconditioning. Further, administration of S1P or sphingosine during reperfusion results in better recovery and attenuation of damage to cardiomyocytes. As with preconditioning, SphK1 deficiency also affects post-conditioning of mouse hearts after ischemia reperfusion (IR).

S1P does not only protect the heart from IRI. During intestinal IR, multiple organs can be damaged, including the lungs. S1P treatment of mice during intestinal IR seems to have a protective effect on lung injury, probably due to suppression of iNOS-induced nitric oxide generation. In renal IRI, SphK1 seems to be important, since its deficiency increased the damage in kidney tissue, whereas the lentiviral overexpression of the SphK1 gene protected from injury. Another study suggests that, after IRI, apoptotic renal cells release S1P, which recruits macrophages through S1PR3 activation and might contribute to kidney regeneration and restoration of renal epithelium. However, SphK2 is negatively implicated in hepatic IRI, its inhibition helping protect hepatocytes and restoring mitochondrial function.

Further studies are implicating S1P signaling or sphingosine kinases in several kinds of cancer as well as autoimmune diseases.

Figure 2 FTY720-P causes retention of T cells in the lymph nodes.

Notes: C57BL/6 mice were injected with BALB/c splenocytes in the footpad to create an allogenic response then treated with FTY720-P or vehicle every day on days 2 to 5. On day 6, the popliteal lymph nodes were removed. Popliteal node-derived cells were mixed with BALB/c splenocytes in interferon gamma (IFN-γ) cultured enzyme-linked immunosorbent spot reactions. Bars represent the mean number of IFN-γ spot-forming cells per 1000 popliteal node-derived cells, from six mice treated with vehicle and seven with FTY720-P. **P , 0.01.  (not shown)

Fingolimod (INN, trade name Gilenya, Novartis) is an immunomodulating drug, approved for treating multiple sclerosis. It has reduced the rate of relapses in relapsing-remitting multiple sclerosis by over half. Fingolimod is a sphingosine-1-phosphate receptor modulator, which sequesters lymphocytes in lymph nodes, preventing them from contributing to an autoimmune reaction.

Fingolimod3Dan

Fingolimod3Dan

 

http://upload.wikimedia.org/wikipedia/commons/thumb/4/48/Fingolimod3Dan.gif/200px-Fingolimod3Dan.gif

The S1P antagonist FTY720 has been approved by the US Food and Drug Administration to be used as a drug against multiple sclerosis (MS). FTY720 is in fact a prodrug, since it is phosphorylated in vivo by SphK2 into FTY720-P, an S1P structural analog, which can activate S1PR1, 3, 4, and 5. FTY720-P binding to S1PR1 causes internalization of the receptor, as does S1P – but instead of recycling it back to the cell surface, it promotes its ubiquitination and degradation at the proteasome. This has a direct effect on lymphocyte trafficking through the lymph nodes, since it relies on S1PR1 signaling and S1P gradient (Figure 2). In MS, it stops migrating lymphocytes into the brain, but it may also have direct effects on the CNS through neuroprotection. FTY720 can pass the blood–brain barrier and it could be phosphorylated by local sphingosine kinases to act through S1PR1 and S1PR3 receptors that are mainly expressed in the CNS. In MS lesions, astrocytes upregulate those two receptors and it has been shown that FTY720-P treatment in vitro inhibits astrocyte production of inflammatory cytokines. A recent study confirms the importance of S1PR3 signaling on activated astrocytes, as well as SphK1, that are upregulated and promote the secretion of the potentially neuroprotective cytokine CXCL-1.

There are several studies implicating the intracellular S1P ceramide rheostat to cancer cell survival or apoptosis and resistance to chemotherapy or irradiation in vitro. Studies with SphK1 inhibition in pancreatic, prostate cancers, and leukemia, show increased ceramide/S1P ratio and induction of apoptosis. However, S1P receptor signaling plays conflicting roles in cancer cell migration and metastasis.

Modulation of S1P signaling: therapeutic potential

S1P signaling can be involved in many pathophysiological conditions. This means that we could look for therapeutic targets in all the molecules taking part in S1P signaling and production, most importantly the S1P receptors and the sphingosine kinases. S1P agonists and antagonists could also be used to modulate S1P signaling during pathological conditions.

S1P can have direct effects on the cardiovascular system. During IRI, intracellular S1P can protect the cardiomyocytes and promote their survival. Pre- or post-conditioning of the heart with S1P could be used as a treatment, but upregulation of sphingosine kinases could also increase intracellular S1P bioavailability. S1P could also have effects on endothelial cells and neutrophil trafficking. Vascular endothelial cells mainly express S1PR1 and S1PR3; only a few types express S1PR2. S1PR1 and S1PR3 activation on these cells has been shown to enhance their chemotactic migration, probably through direct phosphorylation of S1PR1 by Akt, in a phosphatidylinositol 3-kinase and Rac1-dependent signaling pathway. Moreover, it stimulates endothelial cell proliferation through an ERK pathway. S1PR2 activation, however, inhibits endothelial cell migration, morphogenesis, and angiogenesis, most likely through Rho-dependent inhibition of Rac signaling pathway, as Inoki et al showed in mouse cells with the use of S1PR1 and S1PR3 specific antagonists.

Regarding permeability of the vascular endothelium and endothelial barrier integrity, S1P receptors can have different effects. S1PR1 activation enhances endothelial barrier integrity by stimulation of cellular adhesion and upregulation of adhesion molecules. However, S1PR2 and S1PR3 have been shown to have barrier-disrupting effects in vitro, and vascular permeability increasing effects in vivo. All the effects S1P can have on vascular endothelium and smooth muscle cells suggest that activation of S1PR2, not S1PR1 and S1PR3, signaling, perhaps with the use of S1PR2 specific agonists, could be used therapeutically to inhibit angiogenesis and disrupt vasculature, suppressing tumor growth and progression.

An important aspect of S1P signaling that is being already therapeutically targeted, but could be further investigated, is immune cell trafficking. Attempts have already been made to regulate lymphocyte cell migration with the use of the drug FTY720, whose phosphorylated form can inhibit the cells S1PR1-dependent egress from the lymph nodes, causing lymphopenia. FTY720 is used as an immunosuppressant for MS but is also being investigated for other autoimmune conditions and for transplantation. Unfortunately, Phase II and III clinical trials for the prevention of kidney graft rejection have not shown an advantage over standard therapies. Moreover, FTY720 can have some adverse cardiac effects, such as bradycardia. However, there are other S1PR1 antagonists that could be considered instead, including KRP-203, AUY954, and SEW2871. KRP-203 in particular has been shown to prolong rat skin and heart allograft survival and attenuate chronic rejection without causing bradycardia, especially when combined with other immunomodulators.

There are studies that argue S1P pretreatment has a negative effect on neutrophil chemotaxis toward the chemokine CXCL-8 (interleukin-8) or the potent chemoattractant formyl-methionyl-leucyl-phenylalanine. S1P pretreatment might also inhibit trans-endothelial migration of neutrophils, without affecting their adhesion to the endothelium. S1P effects on neutrophil migration toward CXCL-8 might be the result of S1PRs cross-linking with the CXCL-8 receptors in neutrophils, CXCR-1 and CXCR-2. Indeed, there is evidence suggesting S1PR4 and S1PR3 form heterodimers with CXCR-1 in neutrophils. Another indication that S1P plays a role in neutrophil trafficking is a recent paper on S1P lyase deficiency, a deficiency that impairs neutrophil migration from blood to tissue in knockout mice.

S1P lyase and S1PRs in neutrophils may be new therapeutic targets against IRI and inflammatory conditions in general. Consistent with these results, another study has shown that inhibition of S1P lyase can have a protective effect on the heart after IRI and this effect is alleviated when pretreated with an S1PR1 and S1PR3 antagonist. Inhibition was achieved with a US Food and Drug Administration-approved food additive, 2-acetyl-4-tetrahydroxybutylimidazole, providing a possible new drug perspective. Another S1P lyase inhibitor, LX2931, a synthetic analog of 2-acetyl-4-tetrahydroxybutylimidazole, has been shown to cause peripheral lymphopenia when administered in mice, providing a potential treatment for autoimmune diseases and prevention of graft rejection in transplantation. This molecule is currently under Phase II clinical trials in rheumatoid arthritis patients.

S1P signaling research has the potential to discover novel therapeutic targets. S1P signaling is involved in many physiological and pathological processes. However, the complexity of S1P signaling makes it necessary to consider every possible pathway, either through its GPCRs, or intracellularly, with S1P as a second messenger. Where the activation of one S1P receptor may lead to the desired outcome, the simultaneous activation of another S1P receptor may lead to the opposite outcome. Thus, if we are to target a specific signaling pathway, we might need specific agonists for S1P receptors to activate one S1P receptor pathway, while, at the same time, we might need to inhibit another through S1P receptor antagonists.

Evidence of sphingolipid signaling in cancer

Biologically active lipids are important cellular signaling molecules and play a role in cell communication and cancer cell proliferation, and cancer stem cell biology.  A recent study in ovarian cancer cell lines shows that exogenous sphingosine 1 phosphate (SIP1) or overexpression of the sphingosine kinase (SPHK1) increases ovarian cancer cell proliferation, invasion and contributes to cancer stem cell like phenotype.  The diabetes drug metformin was shown to be an inhibitor of SPHK1 and reduce ovarian cancer tumor growth.

 2019 Apr;17(4):870-881. doi: 10.1158/1541-7786.MCR-18-0409. Epub 2019 Jan 17.

SPHK1 Is a Novel Target of Metformin in Ovarian Cancer.

Abstract

The role of phospholipid signaling in ovarian cancer is poorly understood. Sphingosine-1-phosphate (S1P) is a bioactive metabolite of sphingosine that has been associated with tumor progression through enhanced cell proliferation and motility. Similarly, sphingosine kinases (SPHK), which catalyze the formation of S1P and thus regulate the sphingolipid rheostat, have been reported to promote tumor growth in a variety of cancers. The findings reported here show that exogenous S1P or overexpression of SPHK1 increased proliferation, migration, invasion, and stem-like phenotypes in ovarian cancer cell lines. Likewise, overexpression of SPHK1 markedly enhanced tumor growth in a xenograft model of ovarian cancer, which was associated with elevation of key markers of proliferation and stemness. The diabetes drug, metformin, has been shown to have anticancer effects. Here, we found that ovarian cancer patients taking metformin had significantly reduced serum S1P levels, a finding that was recapitulated when ovarian cancer cells were treated with metformin and analyzed by lipidomics. These findings suggested that in cancer the sphingolipid rheostat may be a novel metabolic target of metformin. In support of this, metformin blocked hypoxia-induced SPHK1, which was associated with inhibited nuclear translocation and transcriptional activity of hypoxia-inducible factors (HIF1α and HIF2α). Further, ovarian cancer cells with high SPHK1 were found to be highly sensitive to the cytotoxic effects of metformin, whereas ovarian cancer cells with low SPHK1 were resistant. Together, the findings reported here show that hypoxia-induced SPHK1 expression and downstream S1P signaling promote ovarian cancer progression and that tumors with high expression of SPHK1 or S1P levels might have increased sensitivity to the cytotoxic effects of metformin. IMPLICATIONS: Metformin targets sphingolipid metabolism through inhibiting SPHK1, thereby impeding ovarian cancer cell migration, proliferation, and self-renewal.

Nrf2:INrf2(Keap1) Signaling in Oxidative Stress

James W. Kaspar, Suresh K. Niture, and Anil K. Jaiswal*

Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD

Free Radic Biol Med. 2009 Nov 1; 47(9): 1304–1309. http://dx.doi.org:/10.1016/j.freeradbiomed.2009.07.035

Nrf2:INrf2(Keap1) are cellular sensors of chemical and radiation induced oxidative and electrophilic stress. Nrf2 is a nuclear transcription factor that

  • controls the expression and coordinated induction of a battery of defensive genes encoding detoxifying enzymes and antioxidant proteins.

This is a mechanism of critical importance for cellular protection and cell survival. Nrf2 is retained in the cytoplasm by an inhibitor INrf2. INrf2 functions as an adapter for

  • Cul3/Rbx1 mediated degradation of Nrf2.
  • In response to oxidative/electrophilic stress,
  • Nrf2 is switched on and then off by distinct

early and delayed mechanisms.

Oxidative/electrophilic modification of INrf2cysteine151 and/or PKC phosphorylation of Nrf2serine40 results in the escape or release of Nrf2 from INrf2. Nrf2 is stabilized and translocates to the nucleus, forms heterodimers with unknown proteins, and binds antioxidant response element (ARE) that leads to coordinated activation of gene expression. It takes less than fifteen minutes from the time of exposure

  • to switch on nuclear import of Nrf2.

This is followed by activation of a delayed mechanism that controls

  • switching off of Nrf2 activation of gene expression.

GSK3β phosphorylates Fyn at unknown threonine residue(s) leading to

  • nuclear localization of Fyn.

Fyn phosphorylates Nrf2tyrosine568 resulting in

  • nuclear export of Nrf2,
  • binding with INrf2 and
  • degradation of Nrf2.

The switching on and off of Nrf2 protects cells against free radical damage, prevents apoptosis and promotes cell survival.

NPRA-mediated suppression of AngII-induced ROS production contributes to the antiproliferative effects of B-type natriuretic peptide in VSMC

Pan Gao, De-Hui Qian, Wei Li,  Lan Huang
Mol Cell Biochem (2009) 324:165–172

http://dx.doi.org/10.1007/s11010-008-9995-y

Excessive proliferation of vascular smooth cells (VSMCs) plays a critical role in the pathogenesis of diverse vascular disorders, and inhibition of VSMCs proliferation has been proved to be beneficial to these diseases.

In this study, we investigated the antiproliferative effect of

  • B-type natriuretic peptide (BNP), a natriuretic peptide with potent antioxidant capacity,

on rat aortic VSMCs, and the possible mechanisms involved. The results indicate that

  • BNP potently inhibited Angiotensin II (AngII)-induced VSMCs proliferation,

as evaluated by [3H]-thymidine incorporation assay. Consistently, BNP significantly decreased

  • AngII-induced intracellular reactive oxygen species (ROS)
  • and NAD(P)H oxidase activity.

8-Br-cGMP, a cGMP analog,

  • mimicked these effects.

To confirm its mechanism, siRNA of natriuretic peptide receptor-A(NRPA) strategy technology was used

  • to block cGMP production in VSMCs, and
  • siNPRA attenuated the inhibitory effects of BNP in VSMCs.

Taken together, these results indicate that

  • BNP was capable of inhibiting VSMCs proliferation by
  • NPRA/cGMP pathway,

which might be associated with

  • the suppression of ROS production.

These results might be related, at least partly, to the anti-oxidant property of BNP.

Cellular prion protein is required for neuritogenesis: fine-tuning of multiple signaling pathways involved in focal adhesions and actin cytoskeleton dynamics

A Alleaume-Butaux, C Dakowski, M Pietri, S Mouillet-Richard, Jean-Marie Launay, O Kellermann, B Schneider

1INSERM, UMR-S 747, 2Paris Descartes University, Sorbonne Paris, 3Public Hospital of Paris, Department of Biochemistry, Paris, France; 4Pharma Research Department, Hoffmann La Roche Ltd, Basel, Switzerland

Cell Health and Cytoskeleton 2013; 5: 1–12

Neuritogenesis is a complex morphological phenomena accompanying neuronal differentiation. Neuritogenesis relies on the initial breakage of the rather spherical symmetry of neuroblasts and the formation of buds emerging from the postmitotic neuronal soma. Buds then evolve into neurites, which later convert into an axon or dendrites. At the distal tip of neurites, the growth cone integrates extracellular signals and guides the neurite to its target. The acquisition of neuronal polarity depends on deep modifications of the neuroblast cytoskeleton characterized by the remodeling and activation of focal adhesions (FAs) and localized destabilization of the actin network in the neuronal sphere.Actin instability in unpolarized neurons allows neurite sprouting, ie, the protrusion of microtubules, and subsequent neurite outgrowth. Once the neurite is formed, actin microfilaments recover their stability and exert a sheathed action on neurites, a dynamic process necessary for the maintenance and integrity of neurites.

A combination of extrinsic and intrinsic cues pilots the architectural and functional changes in FAs and the actin network along neuritogenesis. This process includes neurotrophic factors (nerve growth factor, brain derived neurotrophic factor, neurotrophin, ciliary neurotrophic factor, glial derived neurotrophic factor) and their receptors, protein components of the extracellular matrix (ECM) (laminin, vitronectin, fibronectin), plasma membrane integrins and neural cell adhesion molecules (NCAM), and intracellular molecular protagonists such as small G proteins (RhoA, Rac, Cdc42) and their downstream targets.

Neuritogenesis is a dynamic phenomenon associated with neuronal differentiation that allows a rather spherical neuronal stem cell to develop dendrites and axon, a prerequisite for the integration and transmission of signals. The acquisition of neuronal polarity occurs in three steps:

(1) neurite sprouting, which consists of the formation of buds emerging from the postmitotic neuronal soma;

(2) neurite outgrowth, which represents the conversion of buds into neurites, their elongation and evolution into axon or dendrites; and

(3) the stability and plasticity of neuronal polarity.

In neuronal stem cells, remodeling and activation of focal adhesions (FAs) associated with deep modifications of the actin cytoskeleton is a prerequisite for neurite sprouting and subsequent neurite outgrowth. A multiple set of growth factors and interactors located in the extracellular matrix and the plasma membrane orchestrate neuritogenesis

  • by acting on intracellular signaling effectors,
  • notably small G proteins such as RhoA, Rac, and Cdc42,
  • which are involved in actin turnover and the dynamics of FAs.

The cellular prion protein (PrPC), a glycosylphosphatidylinositol

  • (GPI)-anchored membrane protein

mainly known for its role in a group of fatal

  • neurodegenerative diseases,

has emerged as a central player in neuritogenesis.

Here, we review the contribution of PrPC to neuronal polarization and detail the current knowledge on the

  • signaling pathways fine-tuned by PrPC
  • to promote neurite sprouting, outgrowth, and maintenance.

We emphasize that PrPC-dependent neurite sprouting is a process in which PrPC

  • governs the dynamics of FAs and the actin cytoskeleton
  • via β1 integrin signaling.

The presence of PrPC is necessary to render neuronal stem cells

  • competent to respond to neuronal inducers and
  • to develop neurites.

In differentiating neurons, PrPC exerts

  • a facilitator role towards neurite elongation.

This function relies on the interaction of PrPC with a set of diverse partners such as

  1. elements of the extracellular matrix,
  2. plasma membrane receptors,
  3. adhesion molecules, and
  4. soluble factors that control actin cytoskeleton turnover through Rho-GTPase signaling.

Once neurons have reached their terminal stage of differentiation and acquired their polarized morphology, PrPC also

  • takes part in the maintenance of neurites.

By acting on tissue nonspecific alkaline phosphatase, or

  • matrix metalloproteinase type 9,

PrPC stabilizes interactions between

  • neurites and the extracellular matrix.

Keywords: prion, neuronal differentiation

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Integrins, Cadherins, Signaling and the Cytoskeleton

Curator: Larry H. Bernstein, MD, FCAP 

 

We have reviewed the cytoskeleton, cytoskeleton pores and ionic translocation under lipids. We shall now look at this again, with specific attention to proteins, transporters and signaling.

Integrins and extracellular matrix in mechanotransduction

Lindsay Ramage
Queen’s Medical Research Institute, University of Edinburgh,

Edinburgh, UK
Cell Health and Cytoskeleton 2012; 4: 1–9

https://s3.amazonaws.com/academia.edu.documents/37116869/CHC-21829-integrins-and-extracellular-matrix-in-mechanotransduction_122311.pdf?response-content-disposition=inline%3B%20filename%3DCell_Health_and_Cytoskeleton_Integrins_a.pdf&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWOWYYGZ2Y53UL3A%2F20191231%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20191231T021009Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&X-Amz-Signature=b376084e0e1c31c399ee7fe96eb81b1b65d3346d647192e9ebeff96f577e117d

Integrins are a family of cell surface receptors which

  • mediate cell–matrix and cell–cell adhesions.

Among other functions they provide an important

  • mechanical link between the cells external and intracellular environments while
  • the adhesions that they form also have critical roles in cellular signal-transduction.

Cell–matrix contacts occur at zones in the cell surface where

  • adhesion receptors cluster and when activated
  • the receptors bind to ligands in the extracellular matrix.

The extracellular matrix surrounds the cells of tissues and forms the

  • structural support of tissue which is particularly important in connective tissues.

Cells attach to the extracellular matrix through

  • specific cell-surface receptors and molecules
  • including integrins and transmembrane proteoglycans.

Integrins work alongside other proteins such as

  • cadherins,
  • immunoglobulin superfamily
  • cell adhesion molecules,
  • selectins, and
  • syndecans

to mediate

  • cell–cell and
  • cell–matrix interactions and communication.

Activation of adhesion receptors triggers the formation of matrix contacts in which

  • bound matrix components,
  • adhesion receptors,
  • and associated intracellular cytoskeletal and signaling molecules

form large functional, localized multiprotein complexes.

Cell–matrix contacts are important in a variety of different cell and

tissue properties including

  1. embryonic development,
  2. inflammatory responses,
  3. wound healing,
  4. and adult tissue homeostasis.

This review summarizes the roles and functions of integrins and extracellular matrix proteins in mechanotransduction.

Integrins are a family of αβ heterodimeric receptors which act as

  • cell adhesion molecules
  • connecting the ECM to the actin cytoskeleton.

The actin cytoskeleton is involved in the regulation of

  1. cell motility,
  2. cell polarity,
  3. cell growth, and
  4. cell survival.

The integrin family consists of around 25 members which are composed of differing

  • combinations of α and β subunits.

The combination of αβ subunits determines

  • binding specificity and
  • signaling properties.

In mammals around 19 α and eight β subunits have been characterized.

Both α and β integrin subunits contain two separate tails, which

  • penetrate the plasma membrane and possess small cytoplasmic domains which facilitate
  • the signaling functions of the receptor.

There is some evidence that the β subunit is the principal

site for

  • binding of cytoskeletal and signaling molecules,

whereas the α subunit has a regulatory role. The integrin

tails

  • link the ECM to the actin cytoskeleton within the cell and with cytoplasmic proteins,

such as talin, tensin, and filamin. The extracellular domains of integrin receptors bind the ECM ligands.

The ECM is a complex mixture of matrix molecules, including -glycoproteins, collagens, laminins, glycosaminoglycans, proteoglycans,
and nonmatrix proteins, – including growth factors.
These can be categorized as insoluble molecules within the ECM, soluble molecules, and/or matrix-associated biochemicals, such as systemic hormones or growth factors and cytokines that act locally.

The integrin receptor formed from the binding of α and β subunits is shaped like a globular head supported by two rod-like legs (Figure 1). Most of the contact between the two subunits occurs in the head region, with the intracellular tails of the subunits forming the legs of the receptor.6 Integrin recognition of ligands is not constitutive but is regulated by alteration of integrin affinity for ligand binding. For integrin binding to ligands to occur the integrin must be primed and activated, both of which involve conformational changes to the receptor.

The integrins are composed of well-defined domains used for protein–protein interactions. The α-I domains of α integrin subunits comprise the ligand binding sites. X-ray crystallography has identified an α-I domain within the β subunit and a β propeller domain within the α subunit which complex to form the ligand-binding head of the integrin.

The use of activating and conformation-specific antibodies also suggests that the β chain is extended in the active integrin. It has since been identified that the hybrid domain in the β chain is critical for integrin activation, and a swing-out movement of this leg activates integrins.

http://www.ks.uiuc.edu/Publications/Stories/tcbg_ytt/pdfs/dbp6.pdf

DBP6: Integrin

Integrin

Integrin

Integrin.large

Integrin.large

Linking integrin conformation to function

Figure  Integrin binding to extracellular matrix (ECM). Conformational changes to integrin structure and clustering of subunits which allow enhanced function of the receptor.

integrin coupled to F-actin via linker

integrin coupled to F-actin via linker

http://dx.dio.org:/integrin-coupled-to-f-actin-via-linker-nrm3896-f4.jpg

Integrin extracellular binding activity is regulated from inside the cell and binding to the ECM induces signals that are transmitted into the cell.15 This bidirectional signaling requires

  • dynamic,
  • spatially, and
  • temporally regulated formation and
  • disassembly of multiprotein complexes that
    form around the short cytoplasmic tails of integrins.

Ligand binding to integrin family members leads to clustering of integrin molecules in the plasma membrane and recruitment of actin filaments and intracellular signaling molecules to the cytoplasmic domain of the integrins. This forms focal adhesion complexes which are able to maintain

  • not only adhesion to the ECM
  • but are involved in complex signaling pathways

which include establishing

  1. cell polarity,
  2. directed cell migration, and
  3. maintaining cell growth and survival.

Initial activation through integrin adhesion to matrix recruits up to around 50 diverse signaling molecules

  • to assemble the focal adhesion complex
  • which is capable of responding to environmental stimuli efficiently.

Mapping of the integrin

  • adhesome binding and signaling interactions

identified a network of 156 components linked together which can be modified by 690 interactions.

The binding of the adaptor protein talin to the β subunit cytoplasmic tail is known to have a key role in integrin activation. This is thought to occur through the disruption of

  • inhibitory interactions between α and β subunit cytoplasmic tails.

Talin also binds

  • to actin and to cytoskeletal and signaling proteins.

This allows talin to directly link activated integrins

to signaling events and the cytoskeleton.

 

Genetic programming occurs with the binding of integrins to the ECM

Signal transduction pathway activation arising from integrin-

ECM binding results in changes in gene expression of cells

and leads to alterations in cell and tissue function. Various

different effects can arise depending on the

  1. cell type,
  2. matrix composition, and
  3. integrins activated.

One way in which integrin expression is important in genetic programming is in the fate and differentiation of stem cells.
Osteoblast differentiation occurs through ECM interactions

with specific integrins

  • to initiate intracellular signaling pathways leading to osteoblast-specific gene expression
  • disruption of interactions between integrins and collagen;
  • fibronectin blocks osteoblast differentiation and

Disruption of α2 integrin prevents osteoblast differentiation, and activation of the transcription factor

  • osteoblast-specific factor 2/core-binding factor α1.

It was found that the ECM-integrin interaction induces osteoblast-specific factor 2/core-binding factor α1 to

  • increase its activity as a transcriptional enhancer
  • rather than increasing protein levels.

It was also found that modification of α2 integrin alters

  • induction of the osteocalcin promoter;
  • inhibition of α2 prevents activation of the osteocalcin promoter,
  • overexpression enhanced osteocalcin promoter activity.

It has been suggested that integrin-type I collagen interaction is necessary for the phosphorylation and activation of osteoblast-specific transcription factors present in committed osteoprogenitor cells.

A variety of growth factors and cytokines have been shown to be important in the regulation of integrin expression and function in chondrocytes. Mechanotransduction in chondrocytes occurs through several different receptors and ion channels including integrins. During osteoarthritis the expression of integrins by chondrocytes is altered, resulting in different cellular transduction pathways which contribute to tissue pathology.

In normal adult cartilage, chondrocytes express α1β1, α10β1 (collagen receptors), α5β1, and αvβ5 (fibronectin) receptors. During mechanical loading/stimulation of chondrocytes there is an influx of ions across the cell membrane resulting from activation of mechanosensitive ion channels which can be inhibited by subunit-specific anti-integrin blocking antibodies or RGD peptides. Using these strategies it was identified that α5β1 integrin is a major mechanoreceptor in articular chondrocyte responses to mechanical loading/stimulation.

Osteoarthritic chondrocytes show a depolarization response to 0.33 Hz stimulation in contrast to the hyperpolarization response of normal chondrocytes. The mechanotransduction pathway in chondrocytes derived from normal and osteoarthritic cartilage both involve recognition of the mechanical stimulus by integrin receptors resulting in the activation of integrin signaling pathways leading to the generation of a cytokine loop. Normal and osteoarthritic chondrocytes show differences at multiple stages of the mechanotransduction cascade (Figure 3). Early events are similar; α5β1 integrin and stretch activated ion channels are activated and result in rapid tyrosine phosphorylation events. The actin cytoskeleton is required for the integrin-dependent Mechanotransduction leading to changes in membrane potential in normal but not osteoarthritic chondrocytes.

Cell–matrix interactions are essential for maintaining the integrity of tissues. An intact matrix is essential for cell survival and proliferation and to allow efficient mechanotransduction and tissue homeostasis. Cell–matrix interactions have been extensively studied in many tissues and this knowledge is being used to develop strategies to treat pathology. This is particularly important in tissues subject to abnormal mechanical loading, such as musculoskeletal tissues. Integrin-ECM interactions are being used to enhance tissue repair mechanisms in these tissues through differentiation of progenitor cells for in vitro and in vivo use. Knowledge of how signaling cascades are differentially regulated in response to physiological and pathological external stimuli (including ECM availability and mechanical loading/stimulation) will enable future strategies to be developed to prevent and treat the progression of pathology associated with integrin-ECM interactions.

Cellular adaptation to mechanical stress: role of integrins, Rho, cytoskeletal tension and mechanosensitive ion channels

  1. Matthews, DR. Overby, R Mannix and DE. Ingber
    1Vascular Biology Program, Departments of Pathology and Surgery, Children’s Hospital, and 2Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA J Cell Sci 2006; 119: 508-518. http://dx.doi.org:/10.1242/jcs.02760

To understand how cells sense and adapt to mechanical stress, we applied tensional forces to magnetic microbeads bound to cell-surface integrin receptors and measured changes in bead isplacement with sub-micrometer resolution using optical microscopy. Cells exhibited four types of mechanical responses: (1) an immediate viscoelastic response;

(2) early adaptive behavior characterized by pulse-to-pulse attenuation in response to oscillatory forces;

(3) later adaptive cell stiffening with sustained (>15 second) static stresses; and

(4) a large-scale repositioning response with prolonged (>1 minute) stress.

Importantly, these adaptation responses differed biochemically. The immediate and early responses were affected by

  • chemically dissipating cytoskeletal prestress (isometric tension), whereas
  • the later adaptive response was not.

The repositioning response was prevented by

  • inhibiting tension through interference with Rho signaling,

similar to the case of the immediate and early responses, but it was also prevented by

  • blocking mechanosensitive ion channels or
  • by inhibiting Src tyrosine kinases.

All adaptive responses were suppressed by cooling cells to 4°C to slow biochemical remodeling. Thus, cells use multiple mechanisms to sense and respond to static and dynamic changes in the level of mechanical stress applied to integrins.

Microtubule-Stimulated ADP Release, ATP Binding, and Force Generation In Transport Kinesins

J Atherton, I Farabella, I-Mei Yu, SS Rosenfeld, A Houdusse, M Topf, CA Moores

1Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, United Kingdom; 2Structural Motility, Institut Curie, Centre National de la Recherche Scientifique, Paris, France; 3Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
eLife 2014;3:e03680. http://dx.doi.org:/10.7554/eLife.03680

Kinesins are a large family of microtubule (MT)-based motors that play important roles in many cellular activities including

  • mitosis,
  • motility, and
  • intracellular transport

Their involvement in a range of pathological processes also highlights their significance as therapeutic targets and the importance of understanding the molecular basis of their function They are defined by their motor domains that contain both the microtubule (MT) and ATP binding sites. Three ATP binding motifs—the P-loop, switch I, switch II–are highly conserved among kinesins, myosin motors, and small GTPases. They share a conserved mode of MT binding such that MT binding, ATP binding, and hydrolysis are functionally coupled for efficient MT-based work.

The interior of a cell is a hive of activity, filled with proteins and other items moving from one location to another. A network of filaments called microtubules forms tracks along which so-called motor proteins carry these items. Kinesins are one group of motor proteins, and a typical kinesin protein has one end (called the ‘motor domain’) that can attach itself to the microtubules.

The other end links to the cargo being carried, and a ‘neck’ connects the two. When two of these proteins work together, flexible regions of the neck allow the two motor domains to move past one another, which enable the kinesin to essentially walk along a microtubule in a stepwise manner.

Atherton et al. use a technique called cryo-electron microscopy to study—in more detail than previously seen—the structure of the motor domains of two types of kinesin called kinesin-1 and kinesin-3. Images were taken at different stages of the cycle used by the motor domains to extract the energy from ATP molecules. Although the two kinesins have been thought to move along the microtubule tracks in different ways, Atherton et al. find that the core mechanism used by their motor domains is the same.

When a motor domain binds to the microtubule, its shape changes, first stimulating release of the breakdown products of ATP from the previous cycle. This release makes room for a new ATP molecule to bind. The structural changes caused by ATP binding are relatively small but produce larger changes in the flexible neck region that enable individual motor domains within a kinesin pair to co-ordinate their movement and move in a consistent direction. This mechanism involves tight coupling between track binding and fuel usage and makes kinesins highly efficient motors.

A number of kinesins drive long distance transport of cellular cargo with dimerisation allowing them to take multiple 8 nm ATP-driven steps toward MT plus ends. Their processivity depends on communication between the two motor domains, which is achieved via the neck linker that connects each motor domain to the dimer-forming coiled-coil

Kinesins are a superfamily of microtubule-based

  • ATP-powered motors, important for multiple, essential cellular functions.

How microtubule binding stimulates their ATPase and controls force generation is not understood. To address this fundamental question, we visualized microtubule-bound kinesin-1 and kinesin-3 motor domains at multiple steps in their ATPase cycles—including their nucleotide-free states—at ∼7 Å resolution using cryo-electron microscopy.

All our reconstructions have, as their asymmetric unit, a triangle-shaped motor domain bound to an αβ-tubulin dimer within the MT lattice (Figure 1). The structural comparisons below are made with respect to the MT surface, which, at the resolution of our structures (∼7 Å, Table 1), is the same (CCC > 0.98 for all). As is well established across the superfamily, the major and largely invariant point of contact between kinesin motor domains and the MT is helix-α4, which lies at the tubulin intradimer interface (Figure 1C, Kikkawa et al., 2001).

However, multiple conformational changes are seen throughout the rest of each domain in response to bound nucleotide (Figure 1D). Below, we describe the conformational changes in functionally important regions of each motor domain starting with the nucleotide-binding site, from which all other conformational changes emanate.

The nucleotide-binding site (Figure 2) has three major elements: (1) the P-loop (brown) is visible in all our reconstructions;

(2) loop9 (yellow, contains switch I) undergoes major conformational changes through the ATPase cycle; and

(3) loop11 (red, contains switch II) that connects strand-β7 to helix-α4,

the conformation and flexibility of which is determined by MT binding and motor nucleotide state.

Movement and extension of helix-α6 controls neck linker docking

the N-terminus of helix-α6 is closely associated with elements of the nucleotide binding site suggesting that its conformation alters in response to different nucleotide states. In addition, because the orientation of helix-α6 with respect to helix-α4 controls neck linker docking and because helix-α4 is held against the MT during the ATPase cycle,

  • conformational changes in helix-α6 control movement of the neck linker.

Mechanical amplification and force generation involves conformational changes across the motor domain

A key conformational change in the motor domain following Mg-ATP binding is peeling of the central β-sheet from the C-terminus of helix-α4 increasing their separation (Figure 3—figure supplement 2); this is required to accommodate rotation of helix-α6 and consequent neck linker docking (Figure 3B–E).

Peeling of the central β-sheet has previously been proposed to arise from tilting of the entire motor domain relative to static MT contacts, pivoting around helix-α4 (the so-called ‘seesaw’ model; Sindelar, 2011). Specifically, this model predicts that the major difference in the motor before and after Mg-ATP binding would be the orientation of the motor domain with respect to helix-α4.

Kinesin mechanochemistry and the extent of mechanistic conservation within the motor superfamily are open questions, critical to explain how MT binding, and ATP binding and hydrolysis drive motor activity. Our structural characterisation of two transport motors now allows us to propose a model that describes the roles of mechanochemical elements that together drive conserved MT-based motor function.

Model of conserved MT-bound kinesin mechanochemistry. Loop11/N-terminus of helix-α4 is flexible in ADP-bound kinesin in solution, the neck linker is also flexible while loop9 chelates ADP. MT binding is sensed by loop11/helix-α4 N-terminus, biasing them towards more ordered conformations.

We propose that this favours crosstalk between loop11 and loop9, stimulating ADP release. In the NN conformation, both loop11 and loop9 are well ordered and primed to favour ATP binding, while helix-α6—which is required for mechanical amplification–is closely associated with the MT on the other side of the motor domain. ATP binding draws loop11 and loop9 closer together; causing

(1) tilting of most of the motor domain not contacting the MT towards the nucleotide-binding site,

(2) rotation, translation, and extension of helix-α6 which we propose contributes to force generation, and

(3) allows neck linker docking and biases movement of the 2nd head towards the MT plus end.

In both motors, microtubule binding promotes

  • ordered conformations of conserved loops that
  • stimulate ADP release,
  • enhance microtubule affinity and
  • prime the catalytic site for ATP binding.

ATP binding causes only small shifts of these nucleotide-coordinating loops but induces

  • large conformational changes elsewhere that
  • allow force generation and
  • neck linker docking towards the microtubule plus end.

Family-specific differences across the kinesin–microtubule interface account for the

  • distinctive properties of each motor.

Our data thus provide evidence for a

conserved ATP-driven

  • mechanism for kinesins and
  • reveal the critical mechanistic contribution of the microtubule interface.

Phosphorylation at endothelial cell–cell junctions: Implications for VE-cadherin function

I Timmerman, PL Hordijk, JD van Buul

Cell Health and Cytoskeleton 2010; 2: 23–31
Endothelial cell–cell junctions are strictly regulated in order to

  • control the barrier function of endothelium.

Vascular endothelial (VE)-cadherin is one of the proteins that is crucial in this process. It has been reported that

  • phosphorylation events control the function of VE-cadherin.

This review summarizes the role of VE-cadherin phosphorylation in the regulation of endothelial cell–cell junctions and highlights how this affects vascular permeability and leukocyte extravasation.

The vascular endothelium is the inner lining of blood vessels and

  • forms a physical barrier between the vessel lumen and surrounding tissue;
  • controlling the extravasation of fluids,
  • plasma proteins and leukocytes.

Changes in the permeability of the endothelium are tightly regulated. Under basal physiological conditions, there is a continuous transfer of substances across the capillary beds. In addition the endothelium can mediate inducible,

  • transient hyperpermeability
  • in response to stimulation with inflammatory mediators,
  • which takes place primarily in postcapillary venules.

However, when severe, inflammation may result in dysfunction of the endothelial barrier in various parts of the vascular tree, including large veins, arterioles and capillaries. Dysregulated permeability is observed in various pathological conditions, such as tumor-induced angiogenesis, cerebrovascular accident and atherosclerosis.

Two fundamentally different pathways regulate endothelial permeability,

  • the transcellular and paracellular pathways.

Solutes and cells can pass through the body of endothelial cells via the transcellular pathway, which includes

  • vesicular transport systems, fenestrae, and biochemical transporters.

The paracellular route is controlled by

  • the coordinated opening and closing of endothelial junctions and
  • thereby regulates traffic across the intercellular spaces between endothelial cells.

Endothelial cells are connected by

  • tight, gap and
  • adherens junctions,

of which the latter, and particularly the adherens junction component,

  • vascular endothelial (VE)-cadherin,
  • are of central importance for the initiation and stabilization of cell–cell contacts.

Although multiple adhesion molecules are localized at endothelial junctions, blocking the adhesive function of VE-cadherin using antibodies is sufficient to disrupt endothelial junctions and to increase endothelial monolayer permeability both in vitro and in vivo. Like other cadherins, VE-cadherin mediates adhesion via homophilic, calcium-dependent interactions.

This cell–cell adhesion

  • is strengthened by binding of cytoplasmic proteins, the catenins,
  • to the C-terminus of VE-cadherin.

VE-cadherin can directly bind β-catenin and plakoglobin, which

  • both associate with the actin binding protein α-catenin.

Initially, α-catenin was thought to directly anchor cadherins to the actin cytoskeleton, but recently it became clear that

  • α-catenin cannot bind to both β-catenin and actin simultaneously.

Data using purified proteins show that

  • monomeric α-catenin binds strongly to cadherin-bound β-catenin;
  • in contrast to the dimer which has a higher affinity for actin filaments,
  • indicating that α-catenin might function as a molecular switch regulating cadherin-mediated cell–cell adhesion and actin assembly.

Thus, interactions between the cadherin complex and the actin cytoskeleton are more complex than previously thought. Recently, Takeichi and colleagues reported that

  • the actin binding protein EPLIN (epithelial protein lost in neoplasm)
  • can associate with α-catenin and thereby
  • link the E-cadherin–catenin complex to the actin cytoskeleton.

Although this study was performed in epithelial cells,

  • an EPLIN-like molecule might serve as
  • a bridge between the cadherin–catenin complex and
  • the actin cytoskeleton in endothelial cells.

Next to β-catenin and plakoglobin, p120-catenin also binds directly to the intracellular tail of VE-cadherin.

Numerous lines of evidence indicate that

  • p120-catenin promotes VE-cadherin surface expression and stability at the plasma membrane.

Different models are proposed that describe how p120-catenin regulates cadherin membrane dynamics, including the hypothesis

  • that p120-catenin functions as a ‘cap’ that prevents the interaction of VE-cadherin
  • with the endocytic membrane trafficking machinery.

In addition, p120-catenin might regulate VE-cadherin internalization through interactions with small GTPases. Cytoplasmic p120-catenin, which is not bound to VE-cadherin, has been shown to

  • decrease RhoA activity,
  • elevate active Rac1 and Cdc42, and thereby is thought
  • to regulate actin cytoskeleton organization and membrane trafficking.

The intact cadherin-catenin complex is required for proper functioning of the adherens junction. Mutant forms of VE-cadherin which

  • lack either the β-catenin, plakoglobin or p120 binding regions reduce the strength of cell–cell adhesion.

Moreover, our own results showed that

  • interfering with the interaction between α-catenin and β-catenin,
  • using a cell-permeable peptide which encodes the binding site in α-catenin for β-catenin,
  • resulted in an increased permeability of the endothelial monolayer.

Several mechanisms may be involved in the regulation of the organization and function of the cadherin–catenin complex, including endocytosis of the complex, VE-cadherin cleavage and actin cytoskeleton reorganization. The remainder of this review primarily focuses on the

  • role of tyrosine phosphorylation in the control of VE-cadherin-mediated cell–cell adhesion.

Regulation of the adhesive function of VE-cadherin by tyrosine phosphorylation

It is a widely accepted concept that tyrosine phosphorylation of components of the VE–cadherin-catenin complex

  • Correlates with the weakening of cell–cell adhesion.

One of the first reports that supported this idea showed that the level of phosphorylation of VE-cadherin was

  • high in loosely confluent endothelial cells, but
  • low in tightly confluent monolayers,

when intercellular junctions are stabilized.

In addition, several conditions that induce tyrosine phosphorylation

of adherens junction components, like

  • v-Src transformation
  • and inhibition of phosphatase activity by pervanadate,

have been shown to shift cell–cell adhesion from a strong to a weak state. More physiologically relevant;

permeability-increasing agents such as

  • histamine,
  • tumor necrosis factor-α (TNF-α),
  • thrombin,
  • platelet-activating factor (PAF) and
  • vascular endothelial growth factor (VEGF)

increase tyrosine phosphorylation of various components of the cadherin–catenin complex.

A general idea has emerged that

  • tyrosine phosphorylation of the VE-cadherin complex
  • leads to the uncoupling of VE-cadherin from the actin cytoskeleton
  • through dissociation of catenins from the cadherin.

However, tyrosine phosphorylation of VE-cadherin is required for efficient transmigration of leukocytes.

This suggests that VE-cadherin-mediated cell–cell contacts

  1. are not just pushed open by the migrating leukocytes, but play
  2. a more active role in the transmigration process.

A schematic overview of leukocyte adhesion-induced signals leading to VE-cadherin phosphorylation

Regulation of the integrity of endothelial cell–cell contacts by phosphorylation of VE-cadherin

Regulation of the integrity of endothelial cell–cell contacts by phosphorylation of VE-cadherin

Regulation of the integrity of endothelial cell–cell contacts by phosphorylation of VE-cadherin.

Notes: A) Permeability-inducing agents such as thrombin, histamine and VEGF, induce tyrosine phosphorylation (pY) of VE-cadherin and the associated catenins. Although the specific consequences of catenin tyrosine phosphorylation in endothelial cells are still unknown, VE-cadherin tyrosine phosphorylation results in opening of the cell–cell junctions (indicated by arrows) and enhanced vascular permeability. How tyrosine phosphorylation affects VE-cadherin adhesiveness is not yet well understood; disrupted binding of catenins, which link the cadherin to the actin cytoskeleton, may be involved. VEGF induces phosphorylation of VE-cadherin at specific residues, Y658 and Y731, which have been reported to regulate p120-catenin and β-catenin binding, respectively. Moreover, VEGF stimulation results in serine phosphorylation (pSer) of VE-cadherin, specifically at residue S665, which leads to its endocytosis. B) Adhesion of leukocytes to endothelial cells via ICAM-1 increases endothelial permeability by inducing phosphorylation of VE-cadherin on tyrosine residues. Essential mediators, such as the kinases Pyk2 and Src, and signaling routes involving reactive oxygen species (ROS) and Rho, have been shown to act downstream of ICAM-1. Different tyrosine residues within the cytoplasmic domain of VE-cadherin are involved in the extravasation of neutrophils and lymphocytes, including Y658 and Y731. (β: β-catenin, α: α-catenin, γ: γ-catenin/plakoglobin).

N-glycosylation status of E-cadherin controls cytoskeletal dynamics through the organization of distinct β-catenin- and γ-catenin-containing AJs

BT Jamal, MN Nita-Lazar, Z Gao, B Amin, J Walker, MA Kukuruzinska
Cell Health and Cytoskeleton 2009; 1: 67–80

N-glycosylation of E-cadherin has been shown to inhibit cell–cell adhesion. Specifically, our recent studies have provided evidence that the reduction of E-cadherin N-glycosylation promoted the recruitment of stabilizing components, vinculin and serine/ threonine protein phosphatase 2A (PP2A), to adherens junctions (AJs) and enhanced the association of AJs with the actin cytoskeleton. Here, we examined the details of how

  • N-glycosylation of E-cadherin affected the molecular organization of AJs and their cytoskeletal interactions.

Using the hypoglycosylated E-cadherin variant, V13, we show that

  • V13/β-catenin complexes preferentially interacted with PP2A and with the microtubule motor protein dynein.

This correlated with dephosphorylation of the microtubule-associated protein tau, suggesting that

  • increased association of PP2A with V13-containing AJs promoted their tethering to microtubules.

On the other hand, V13/γ-catenin complexes associated more with vinculin, suggesting that they

  • mediated the interaction of AJs with the actin cytoskeleton.
  • N-glycosylation driven changes in the molecular organization of AJs were physiologically significant because transfection of V13 into A253 cancer cells, lacking both mature AJs and tight junctions (TJs), promoted the formation of stable AJs and enhanced the function of TJs to a greater extent than wild-type E-cadherin.

These studies provide the first mechanistic insights into how N-glycosylation of E-cadherin drives changes in AJ composition through

  • the assembly of distinct β-catenin- and γ-catenin-containing scaffolds that impact the interaction with different cytoskeletal components.

Cytoskeletal Basis of Ion Channel Function in Cardiac Muscle

Matteo Vatta, and Georgine Faulkner,

1 Departments of Pediatrics (Cardiology), Baylor College of Medicine, Houston, TX 2 Department of Reproductive and Developmental Sciences, University of Trieste, Trieste, Italy
3 Muscular Molecular Biology Unit, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy

Future Cardiol. 2006 July 1; 2(4): 467–476. http://dx.doi.org:/10.2217/14796678.2.4.467

The heart is a force-generating organ that responds to

  • self-generated electrical stimuli from specialized cardiomyocytes.

This function is modulated

  • by sympathetic and parasympathetic activity.

In order to contract and accommodate the repetitive morphological changes induced by the cardiac cycle, cardiomyocytes

  • depend on their highly evolved and specialized cytoskeletal apparatus.

Defects in components of the cytoskeleton, in the long term,

  • affect the ability of the cell to compensate at both functional and structural levels.

In addition to the structural remodeling,

  • the myocardium becomes increasingly susceptible to altered electrical activity leading to arrhythmogenesis.

The development of arrhythmias secondary to structural remodeling defects has been noted, although the detailed molecular mechanisms are still elusive. Here I will review

  • the current knowledge of the molecular and functional relationships between the cytoskeleton and ion channels

and, I will discuss the future impact of new data on molecular cardiology research and clinical practice.

Myocardial dysfunction in the end-stage failing heart is very often associated with increasing

  • susceptibility to ventricular tachycardia (VT) and ventricular fibrillation (VF),

both of which are common causes of sudden cardiac death (SCD).

Among the various forms of HF,

myocardial remodeling due to ischemic cardiomyopathy (ICM) or dilated cardiomyopathy (DCM)

  • is characterized by alterations in baseline ECG,

which includes the

  • prolongation of the QT interval,
  • as well as QT dispersion,
  • ST-segment elevation, and
  • T-wave abnormalities,

especially during exercise. In particular, subjects with

severe left ventricular chamber dilation such as in DCM can have left bundle branch block (LBBB), while right bundle branch block (RBBB) is more characteristic of right ventricular failure.  LBBB and RBBB have both been repeatedly associated with AV block in heart failure.

The impact of volume overload on structural and electro-cardiographic alterations has been noted in cardiomyopathy patients treated with left ventricular assist device (LVAD) therapy, which puts the heart at mechanical rest. In LVAD-treated subjects,

  • QRS- and both QT- and QTc duration decreased,
  • suggesting that QRS- and QT-duration are significantly influenced by mechanical load and
  • that the shortening of the action potential duration contributes to the improved contractile performance after LVAD support.

Despite the increasing use of LVAD supporting either continuous or pulsatile blood flow in patients with severe HF, the benefit of this treatment in dealing with the risk of arrhythmias is still controversial.

Large epidemiological studies, such as the REMATCH study, demonstrated that the

  • employment of LVAD significantly improved survival rate and the quality of life, in comparison to optimal medical management.

An early postoperative period study after cardiac unloading therapy in 17 HF patients showed that in the first two weeks after LVAD implantation,

  • HF was associated with a relatively high incidence of ventricular arrhythmias associated with QTc interval prolongation.

In addition, a recent retrospective study of 100 adult patients with advanced HF, treated with an axial-flow HeartMate LVAD suggested that

  • the rate of new-onset monomorphic ventricular tachycardia (MVT) was increased in LVAD treated patients compared to patients given only medical treatment,

while no effect was observed on the development of polymorphic ventricular tachycardia (PVT)/ventricular fibrillation (VF).

The sarcomere

The myocardium is exposed to severe and continuous biomechanical stress during each contraction-relaxation cycle. When fiber tension remains uncompensated or simply unbalanced,

  • it may represent a trigger for arrhythmogenesis caused by cytoskeletal stretching,
  • which ultimately leads to altered ion channel localization, and subsequent action potential and conduction alterations.

Cytoskeletal proteins not only provide the backbone of the cellular structure, but they also

  • maintain the shape and flexibility of the different sub-cellular compartments, including the
  1. plasma membrane,
  2. the double lipid layer, which defines the boundaries of the cell and where
  • ion channels are mainly localized.

The interaction between the sarcomere, which is the basic for the passive force during diastole and for the restoring force during systole. Titin connects

  • the Z-line to the M-line of the sarcomeric structure
    (Figure 1).

In addition to the strategic

  • localization and mechanical spring function,
  • titin is a length-dependent sensor during
  • stretch and promotes actin-myosin interaction

Titin is stabilized by the cross-linking protein

  • telethonin (T-Cap), which localizes at the Z-line and is also part of titin sensor machinery (Figure 1).

The complex protein interactions in the sarcomere entwine telethonin to other

  • Z-line components through the family of the telethonin-binding proteins of the Z-disc, FATZ, also known as calsarcin and myozenin.

FATZ binds to

  1. calcineurin,
  2. γ-filamin as well as the
  3. spectrin-like repeats (R3–R4) of α-actinin-2,

the major component of the Z-line and a pivotal

  • F-actin cross-linker (Figure 1).contractile unit of striated muscles, and
  • the sarcolemma,

the plasma membrane surrendering the muscle fibers in skeletal muscle and the muscle cell of the cardiomyocyte,

  • determines the mechanical plasticity of the cell, enabling it to complete and re-initiate each contraction-relaxation cycle.

At the level of the sarcomere,

  • actin (thin) and myosin (thick) filaments generate the contractile force,

while other components such as titin, the largest protein known to date, are responsible for

  • the passive force during diastole and for the restoring force during systole, and (titin).
  • the Z-line to the M-line of the sarcomeric structure
    (Figure 1).

In addition to the strategic

  • localization and mechanical spring function,
  • it acts as a length-dependent sensor during stretch and
  • promotes actin-myosin interaction.

Stabilized by the cross-linking protein telethonin (T-Cap),

  • titin localizes at the Z-line and is
  • part of titin sensor machinery

Another cross-linker of α-actinin-2 in the complex Z-line scaffold is

  • the Z-band alternatively spliced PDZ motif protein (ZASP),
  • which has an important role in maintaining Z-disc stability

in skeletal and cardiac muscle (Figure 1).

ZASP contains a PDZ motif at its N-terminus,

  • which interacts with C-terminus of α-actinin-2,
  • and a conserved sequence called the ZASP like motif (ZM)
  • found in the alternatively spliced exons 4 and 6.

It has also been reported

  • to bind to the FATZ (calsarcin) family of Z-disc proteins (Figure 1).

The complex protein interactions in the sarcomere entwine telethonin to other Z-line components through the family of the telethonin-binding proteins of the

  1. Z-disc,
  2. FATZ, also known as calsarcin and
  3. myozenin

FATZ binds to calcineurin,

  1. γ-filamin as well as the
  2. spectrin-like repeats (R3–R4) of α-actinin-2, the major component of the Z-line and a pivotal F-actin cross-linker (Figure 1).
sarcomere structure

sarcomere structure

Figure 1. Sarcomere structure

The diagram illustrates the sarcomeric structure. The Z-line determines the boundaries of the contractile unit, while Titin connects the Z-line to the M-line and acts as a functional spring during contraction/relaxation cycles.

Sarcomeric Proteins and Ion Channels

In addition to systolic dysfunction characteristic of dilated cardiomyopathy (DCM) and diastolic dysfunction featuring hypertrophic cardiomyopathy (HCM), the clinical phenotype of patients with severe cardiomyopathy is very often associated with a high incidence of cardiac arrhythmias. Therefore, besides fiber stretch associated with mechanical and hemodynamic impairment, cytoskeletal alterations due to primary genetic defects or indirectly to alterations in response to cellular injury can potentially

  1. affect ion channel anchoring, and trafficking, as well as
  2. functional regulation by second messenger pathways,
  3. causing an imbalance in cardiac ionic homeostasis that will trigger arrhythmogenesis.

Intense investigation of

  • the sarcomeric actin network,
  • the Z-line structure, and
  • chaperone molecules docking in the plasma membrane,

has shed new light on the molecular basis of

  • cytoskeletal interactions in regulating ion channels.

In 1991, Cantiello et al., demonstrated that

  • although the epithelial sodium channel and F-actin are in close proximity,
  • they do not co-localize.

Actin disruption using cytochalasin D, an agent that interferes with actin polymerization, increased Na+ channel activity in 90% of excised patches tested within 2 min, which indicated that

  • the integrity of the filamentous actin (F-actin) network was essential
  • for the maintenance of normal Na+ channel function.

Later, the group of Dr. Jonathan Makielski demonstrated that

  • actin disruption induced a dramatic reduction in Na+ peak current and
  • slowed current decay without affecting steady-state voltage-dependent availability or recovery from inactivation.

These data were the first to support a role for the cytoskeleton in cardiac arrhythmias.

F-actin is intertwined in a multi-protein complex that includes

  • the composite Z-line structure.

Further, there is a direct binding between

  • the major protein of the Z-line, α-actinin-2 and
  • the voltage-gated K+ channel 1.5 (Kv1.5), (Figure 2).

The latter is expressed in human cardiomyocytes and localizes to

  • the intercalated disk of the cardiomyocyte
  • in association with connexin and N-cadherin.

Maruoka et al. treated HEK293 cells stably expressing Kv1.5 with cytochalasin D, which led to

  • a massive increase in ionic and gating IK+ currents.

This was prevented by pre-incubation with phalloidin, an F-actin stabilizing agent. In addition, the Z-line protein telethonin binds to the cytoplasmic domain of minK, the beta subunit of the potassium channel KCNQ1 (Figure 2).

Molecular interactions between the cytoskeleton and ion channels

Molecular interactions between the cytoskeleton and ion channels

Figure 2. Molecular interactions between the cytoskeleton and ion channels

The figure illustrates the interactions between the ion channels on the sarcolemma, and the sarcomere in cardiac myocytes. Note that the Z-line is connected to the cardiac T-tubules. The diagram illustrates the complex protein-protein interactions that occur between structural components of the cytoskeleton and ion channels. The cytoskeleton is involved in regulating the metabolism of ion channels, modifying their expression, localization, and electrical properties. The cardiac sodium channel Nav1.5 associates with the DGC, while potassium channels such as Kv1.5, associate with the Z-line.

Ion Channel Subunits and Trafficking

Correct localization is essential for ion channel function and this is dependent upon the ability of auxiliary proteins to

  • shuttle ion channels from the cytoplasm to their final destination such as
  • the plasma membrane or other sub-cellular compartments.

In this regard, Kvβ-subunits are

  • cytoplasmic components known to assemble with the α-subunits of voltage-dependent K+ (Kv) channels
  • at their N-terminus to form stable Kvα/β hetero-oligomeric channels.

When Kvβ is co-expressed with Kv1.4 or Kv1.5, it enhances Kv1.x channel trafficking to the cell membrane without changing the overall protein channel content. The regulatory Kvβ subunits, which are also expressed in cardiomyocytes, directly decrease K+ current by

  • accelerating Kv1.x channel inactivation.

Therefore, altered expression or mutations in Kvβ subunits could cause abnormal ion channel transport to the cell surface, thereby increasing the risk of cardiac arrhythmias.

Ion Channel Protein Motifs and Trafficking

Cell membrane trafficking in the Kv1.x family may occur in a Kvβ subunit-independent manner through specific motifs in their C-terminus. Mutagenesis of the final asparagine (N) in the Kv1.2 motif restores the leucine (L) of the Kv1.4 motif

  • re-establishing high expression levels at the plasma membrane in a Kvβ-independent manner

Cytoskeletal Proteins and Ion Channel Trafficking

Until recently, primary arrhythmias such as LQTS have been almost exclusively regarded as ion channelopathies. Other mutations have been identified with regard to channelopathies. However, the conviction that primary mutations in ion channels were solely responsible for

  • the electrical defects associated with arrhythmias

has been shaken by the identification of mutations in the

  • ANK2 gene encoding the cytoskeletal protein ankyrin-B

that is associated with LQTS in animal models and humans.

Ankyrin-B acts as a chaperone protein, which shuttles the cardiac sodium channel from the cytoplasm to the membrane. Immunohistochemical analysis has localized ankyrin-B to the Zlines/T-tubules on the plasma membrane in the myocardium. Mutations in ankyrin-B associated with LQTS

  • alter sodium channel trafficking due to loss of ankyrin-B localization at the Z-line/transverse (T)-tubules.

Reduced levels of ankyrin-B at cardiac Z-lines/T-tubules were associated with the deficiency of ankyrin-B-associated proteins such as Na/K-ATPase, Na/Ca exchanger (NCX) and inositol-1, 4, 5-trisphosphate receptors (InsP3R).

Dystrophin component of the Dystrophin Glycoprotien Complex (DGC)

Synchronized contraction is essential for cardiomyocytes, which are connected to each other via the extracellular matrix (ECM) through the DGC. The N-terminus domain of dystrophin

  • binds F-actin, and connects it to the sarcomere, while
  • the cysteine-rich (CR) C-terminus domain ensures its connection to the sarcolemma (Figure 2).

The central portion of dystrophin, the rod domain, is composed of

  • rigid spectrin-like repeats and four hinge portions (H1–H4) that determine the flexibility of the protein.

Dystrophin possesses another F-actin binding domain in the Rod domain region, between the basic repeats 11- 17 (DysN-R17).

Dystrophin, originally identified as the gene responsible for Duchenne and Becker muscular dystrophies (DMD/BMD), and later for the X-linked form of dilated cardiomyopathy (XLCM), exerts a major function in physical force transmission in striated muscle. In addition to its structural significance, dystrophin and other DGC proteins such as syntrophins are required for the

  • correct localization,
  • clustering and
  • regulation of ion channel function.

Syntrophins have been implicated in ion channel regulation.  Syntrophins contain two pleckstrin homology (PH) domains, a PDZ domain, and a syntrophin-unique (SU) C-terminal region. The interaction between syntrophins and dystrophin occurs at the PH domain distal to the syntrophin N-terminus and through the highly conserved SU domain. Conversely, the PH domain proximal to the N-terminal portion of the protein and the PDZ domain interact with other membrane components such as

  1. phosphatidyl inositol-4, 5-bisphosphate,
  2. neuronal NOS (nNOS),
  3. aquaporin-4,
  4. stress-activated protein kinase-3, and
  5. 5,

thereby linking all these molecules to the dystrophin complex (Figure 2).

Among the five known isoforms of syntrophin, the 59 KDa α1-syntrophin isoform is the most highly represented in human heart, whereas in skeletal muscle it is only present on the

  • sarcolemma of fast type II fibers.

In addition, the skeletal muscle γ2-syntrophin was found at high levels only at the

  • postsynaptic membrane of the neuromuscular junctions.

In addition to syntrophin, other scaffolding proteins such as caveolin-3 (CAV3), which is present in the caveolae, flask-shaped plasma membrane microdomains, are involved

  • in signal transduction and vesicle trafficking in myocytes,
  • modulating cardiac remodeling during heart failure.

CAV3 and α1-syntrophin, localizes at the T-tubule and are part of the DGC. In addition, α1-syntrophin binds Nav1.5, while

  • caveolin-3 binds the Na+/Ca2+ exchanger, Nav1.5 and the L-type Ca2+ channel as well as nNOS and the DGC (Figure 2).

Although ankyrin-B is the only protein found mutated in patients with primary arrhythmias, other proteins such as caveolin-3 and the syntrophins if mutated may alter ion channel function.

Conclusions

It is important to be aware of the enormous variety of clinical presentations that derive from distinct variants in the same pool of genetic factors. Knowledge of these variants could facilitate tailoring the therapy of choice for each patient. In particular, the recent findings of structural and functional links between

  • the cytoskeleton and ion channels

could expand the therapeutic interventions in

  • arrhythmia management in structurally abnormal myocardium, where aberrant binding
  • between cytoskeletal proteins can directly or indirectly alter ion channel function.

Executive Summary

Arrhythmogenesis and myocardial structure

  • Rhythm alterations can develop as a secondary consequence of myocardial structural abnormalities or as a result of a primary defect in the cardiac electric machinery.
  • Until recently, no molecular mechanism has been able to fully explain the occurrence of arrhythmogenesis in heart failure, however genetic defects that are found almost exclusively in ion channel genes account for the majority of primary arrhythmias such as long QT syndromes and Brugada syndrome. The contractile apparatus is linked to ion channels
  • The sarcomere, which represents the contractile unit of the myocardium not only generates the mechanical force necessary to exert the pump function, but also provides localization and anchorage to ion channels.
  • Alpha-actinin-2, and telethonin, two members of the Z-line scaffolding protein complex in the striated muscle associate with the potassium voltage-gated channel alpha subunit Kv1.5 and the beta subunit KCNE1 respectively.
  • Mutations in KCNE1 have previously been associated with the development of arrhythmias in LQTS subjects.
  • Mutations in both alpha-actinin-2, and telethonin were identified in individuals with cardiomyopathy. The primary defect is structural leading to ventricular dysfunction, but the secondary consequence is arrhythmia.

Ion channel trafficking and sub-cellular compartments

  • Ion channel trafficking from the endoplasmic reticulum (ER) to the Golgi complex is an important check-point for regulating the functional channel molecules on the plasma membrane. Several molecules acting as chaperones bind to and shuttle the channel proteins to their final localization on the cell surface
  • Ion channel subunits such as Kvβ enhance Kv1.x ion channel presentation on the sarcolemma. The α subunits of the Kv1.x potassium channels can be shuttled in a Kvβ-independent manner through specific sequence motif at Kv1.x protein level.
  • In addition, cytoskeletal proteins such as ankyrin-G bind Nav1.5 and are involved in the sodium channel trafficking. Another member of the ankyrin family, ankyrin-B was found mutated in patients with LQTS but the pathological mechanism of ankyrin-B mutations is still obscure, although the sodium current intensity is dramatically reduced.

The sarcolemma and ion channels

  • The sarcolemma contains a wide range of ion channels, which are responsible for the electrical propagating force in the myocardium.
  • The DGC is a protein complex, which forms a scaffold for cytoskeletal components and ion channels.
  • Dystrophin is the major component of the DGC and mutations in dystrophin and DGC cause muscular dystrophies and X-linked cardiomyopathies (XLCM) in humans. Cardiomyopathies are associated with arrhythmias
  • Caveolin-3 and syntrophins associate with Nav1.5, and are part of the DGC. Syntrophins can directly modulate Nav1.5 channel function.

Conclusions

  • The role of the cytoskeleton in ion channel function has been hypothesized in the past, but only recently the mechanism underlying the development of arrhythmias in structurally impaired myocardium has become clearer.
  • The recently acknowledged role of the cytoskeleton in ion channel function suggests that genes encoding cytoskeletal proteins should be regarded as potential candidates for variants involved in the susceptibility to arrhythmias, as well as the primary target of genetic mutations in patients with arrhythmogenic syndromes such as LQTS and Brugada syndrome.
  • Studies of genotype-phenotype correlation and and patient risk stratification for mutations in cytoskeletal proteins will help to tailor the therapy and management of patients with arrhythmias.

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