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Archive for the ‘Liver & Digestive Diseases Research’ Category

Larry H. Bernstein, MD, FCAP, Curator

http://pharmaceuticalinnovation/6/7/2014/Omega-3 fatty acids, depleting the source, and protein insufficiency in renal disease

 

This article is concerned only with updating the importance of key nutrients for maintenance of health. Nutritional losses are associated with memory loss, impaired immunity, and loss of lean body mass.

 

Low levels of omega-3 fatty acids may cause memory problems

Disease and ConditionsGeneral Diet • Tags: Alzheimer’s diseaseAmerican Academy of NeurologyDocosahexaenoic acidMagnetic resonance imagingNeurologyOmega-3 fatty acid, United States Environmental Protection AgencyUniversity of California Los Angeles

09 Mar 2012

 

ST. PAUL, Minn. – A diet lacking in omega-3 fatty acids, nutrients commonly found in fish, may cause your brain to age faster and lose some of its memory and thinking abilities, according to a study published in the February 28, 2012, print issue of Neurology®, the medical journal of the American Academy of Neurology. Omega-3 fatty acids include the nutrients called docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA).

salmon dinner

salmon dinner

 

 

 

 

 

 

 

 

 

“People with lower blood levels of omega-3 fatty acids had lower brain volumes that were equivalent to about two years of structural brain aging,” said study author Zaldy S. Tan, MD, MPH, of the Easton Center for Alzheimer’s Disease Research and the Division of Geriatrics, University of California at Los Angeles.

For the study, 1,575 people with an average age of 67 and free of dementia underwent MRI brain scans. They were also given tests that measured mental function, body mass and the omega-3 fatty acid levels in their red blood cells.

The researchers found that people whose DHA levels were among the bottom 25 percent of the participants had lower brain volume compared to people who had higher DHA levels. Similarly, participants with levels of all omega-3 fatty acids in the bottom 25 percent also scored lower on tests of visual memory and executive function, such as problem solving and multi-tasking and abstract thinking.

Related articles

 

Mechanisms of muscle wasting in chronic kidney disease.

Xiaonan H WangWilliam E Mitch

Nature Reviews Nephrology (Impact Factor: 7.94). 07/2014; DOI: 10.1038/nrneph.2014.112

Source: PubMed

ABSTRACT In patients with chronic kidney disease (CKD), loss of cellular proteins increases the risks of morbidity and mortality. Persistence of muscle protein catabolism in CKD results in striking losses of muscle proteins as whole-body protein turnover is great; even small but persistent imbalances between protein synthesis and degradation cause substantial protein loss. No reliable methods to prevent CKD-induced muscle wasting currently exist, but mechanisms that control cellular protein turnover have been identified, suggesting that therapeutic strategies will be developed to suppress or block protein loss. Catabolic pathways that cause protein wasting include activation of the ubiquitin-proteasome system (UPS), caspase-3, lysosomes and myostatin (a negative regulator of skeletal muscle growth). These pathways can be initiated by complications associated with CKD, such as metabolic acidosis, defective insulin signalling, inflammation, increased angiotensin II levels, abnormal appetite regulation and impaired microRNA responses. Inflammation stimulates cellular signalling pathways that activate myostatin, which accelerates UPS-mediated catabolism. Blocking this pathway can prevent loss of muscle proteins. Myostatin inhibition could yield new therapeutic directions for blocking muscle protein wasting in CKD or disorders associated with its complications.

 

We’re Fishing the Oceans Dry. It’s Time to Reconsider Fish Farms.

Food and Agriculture Organization of the United Nations -State of World Fisheries and Aquaculture  2014

Food and Agriculture Organization of the United Nations -State of World Fisheries and Aquaculture 2014

 

 

 

 

 

 

 

 

 

 

 

 

Aquaculture has gotten much greener, with American innovators leading the way.

— Text by Maddie Oatman; video by Brett Brownell

| Wed Jul. 2, 2014 6:00 AM EDT    MotherJones.com

 

When I meet Kenny Belov mid-morning at San Francisco’s Fisherman’s Wharf, the boats that would normally be out at sea chasing salmon sit tethered to their docks. The steady breeze coursing through the bay belies choppier conditions farther out—so rough that the local fishermen threw in the towel for the fifth morning in a row. Belov scans the horizon as he explains this, feet away from the warehouse of his sustainable seafood company, TwoXSea. Because his business hinges on what local fishermen can bring in, he’s used to coping with wild fish shortages.

If we continue to fish at the current pace, some scientists predict we’ll be facing oceans devoid of edible marine creatures by 2050.

But unlike these fishermen, Belov has a stash of treasure in his warehouse, as he soon shows me: a golf-cart-size container of plump trout, their glossy bodies still taut from rigor mortis. The night before, Belov drove north to Humboldt to help “chill kill” the fish by submerging them live into barrels of slushy ice water. Belov can count on shipments of these McFarland Springs trout every week—because he helped grow them himself on a farm.

For many consumers, aquaculture lost its appeal after unappetizing news spread about commercial fish farms—like fish feed’s pressure on wild resources, overflowing waste, toxic buildup in the water, and displacement of natural species. But consider this: Our appetite for seafood continues to rise. Globally, we’ve hungered for 3.2 percent more seafood every year for the last five decades, double the rate of our population. Yet more than four-fifths of the world’s wild fisheries are overexploited or fully exploited (yielding the most fish possible with no expected room for growth). Only 3 percent of stocks are considered underexploited—meaning they have any significant room for expansion. If we continue to fish at the current pace, some scientists predict we’ll be facing oceans devoid of edible marine creatures by 2050.

Aquaculture could come to the rescue. The Food and Agriculture Organization of the United Nations predicts that farmed fish will soon surpass wild-caught; by 2030, aquaculture may produce more than 60 percent of fish we consume as food.

Food and Agriculture Organization of the United Nations “State of World Fisheries and Aquaculture” 2014 report

One of the most pressing concerns about aquaculture, though, is that many farmed fish are raised on a diet of 15 million tons a year of smaller bait fish—species like anchovies and menhaden. These bait—also known as forage fish—are ground up and converted into a substance called fishmeal. It takes roughly five pounds of them to produce one pound of farmed salmon. Bait fish are also used for nonfood products like pet food, makeup, farm animal feed, and fish oil supplements.

Forage fish are a “finite resource that’s been fully utilized.”

It may appear as though the ocean enjoys endless schools of these tiny fish, but they too have been mismanaged, and their populations are prone to collapse. They’re a “finite resource that’s been fully utilized,” says Mike Rust of NOAA’s fisheries arm. Which is disturbing, considering that researchers like those at Oceana argue that forage fish may play an outsize role in maintaining the ocean’s ecological balance, including by contributing to the abundance of bigger predatory fish.

And that’s where Belov’s trout come in: Though he swears no one can taste the difference, his fish are vegetarians. That means those five pounds of forage fish can rest easy at sea. It also means that the trout don’t consume some of the other rendered animal proteins in normal fishmeal pellets: bone meal, feather meal, blood meal, and chicken byproducts.

Belov and McFarland Springs’ owner David McFarland were inspired to switch to vegetarian feed in part by Rick Barrows, a USDA researcher. About six years ago, recounts Barrows, several USDA studies confirmed that fish rely on nutrients—vitamins, minerals, fatty acids, and protein—rather than fishmeal or fish oil, to thrive. If those nutrients could be found in other products, including purely plant-based substances, then aquaculture might not be so dependent on feeding fish other smaller fish.

Barrows and team began to test about 50 potential materials a year, and now have a database of 140 that anyone can browse through online. Belov was one of their first commercial partners. The plant-based food fed to McFarland Springs’ trout consists of a hearty blend of marine algae, freshwater micro algae, vitamins, minerals, flax, flax oil, corn, and nut waste. The resulting complete protein means the trout’s omega 3s are high and their omega 6s are low—a ratio that’s said to enhance anti-inflammatory properties. And “they don’t have the concentration of heavy metals that come from the bait fish,” Belov says. I took one of his rosy fillets home and turned it into trout lox; find the recipe here.

McFarland Springs manages the trout’s waste by funneling it out into a natural sagebrush pasture where it composts the soil.

Belov’s fish feed includes California nuts that are too broken or disfigured to be sold.

Barrows thinks region-specific material for this type of feed offers the most potential. For instance, his team learned that around 5 percent of California nuts can’t be sold because they’re broken or disfigured. They realized they could repurpose excess nut parts for the trout feed; the nut bits helped round out the complete protein. Lately, Barrows has become especially excited about turning barley surplus from the beer industry—which comes at a cheap price in Montana, where he’s based—into a feed-grade concentrate for trout feed.

“You can get just as much growth rate out of fishmeal-free feeds as fishmeal,” says Barrows. And his lab has proven as much with eight different fish species: cobia, Florida pompano, coho salmon, Atlantic salmon, walleye, yellowtail, and White seabass.

But the price difference still stands in the way for many fish farmers. Belov pays slightly more than $1/pound for his plant-based feed, whereas fishmeal pellets average around $0.71/pound. He sells his trout for $6.95/pound, about a dollar more than conventional. But he’s well positioned in the affluent Bay Area, and he usually sells out of his McFarland Springs trout well before the end of each week. As innovation continues in the realm of plant-based feeds, he’s hopeful, along with Barrows, that the price of the pellets will continue to drop.

Here in the United States, we consume plenty of farmed fish already, but only 5 percent of it is sourced domestically. “If we didn’t import so much farmed seafood,” implored Four Fish author Paul Greenberg in a recent New York Times op-ed, “we might develop a viable, sustainable aquaculture sector of our own.” It doesn’t just boil down to economics: The locations we generally export from, like China and South Asia, don’t have near the stringent environmental and health regulations as the US. “Growing more seafood at home would help with trade deficit, but also we could control the safety more,” says Barrows.

Though our current aquaculture sector is relatively tiny, US farmers are in a better position to innovate, because we have a sophisticated animal nutrition research center and feed sector, says NOAA’s Rust. “We’re the leading technical country in the world on feed.”

Belov wasn’t always open to aquaculture, and he still feels that fish—such as some salmon—with healthy wild fisheries attached to them should never be farmed. That way, environmentally responsible fishermen can stay in business. His long-term strategy for sustainable seafood? Draw from the “amazing [wild] fisheries that exist, and then you backfill with intelligent aquaculture, and yes, you can feed the planet with sustainable marine products.” Which may take more work, but as he puts it, “We depleted the ocean. It wasn’t anybody else’s fault. So it’s our job to fix it.”

 

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Prologue to Cancer – e-book Volume One – Where are we in this journey?

Prologue to Cancer – e-book Volume One – Where are we in this journey?

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

Article ID #128: Prologue to Cancer – e-book Volume One – Where are we in this journey? Published on 4/13/2014

WordCloud Image Produced by Adam Tubman

Consulting Reviewer and Contributor:  Jose Eduardo de Salles Roselino, MD

 

LH Bernstein

LH Bernstein

Jose Eduardo de Salles Roselino

LES Roselino

 

 

This is a preface to the fourth in the ebook series of Leaders in Pharmaceutical Intelligence, a collaboration of experienced doctorate medical and pharmaceutical professionals.  The topic is of great current interest, and it entails a significant part of current medical expenditure by a group of neoplastic diseases that may develop at different periods in life, and have come to supercede infections or even eventuate in infectious disease as an end of life event.  The articles presented are a collection of the most up-to-date accounts of the state of a now rapidly emerging field of medical research that has benefitted enormously by progress in immunodiagnostics,  radiodiagnostics, imaging, predictive analytics, genomic and proteomic discovery subsequent to the completion of the Human Genome Project, advances in analytic methods in qPCR, gene sequencing, genome mapping, signaling pathways, exome identification, identification of therapeutic targets in inhibitors, activators, initiators in the progression of cell metabolism, carcinogenesis, cell movement, and metastatic potential.  This story is very complicated because we are engaged in trying to evoke from what we would like to be similar clinical events, dissimilar events in their expression and classification, whether they are within the same or different anatomic class.  Thus, we are faced with constructing an objective evidence-based understanding requiring integration of several disciplinary approaches to see a clear picture.  The failure to do so creates a high risk of failure in biopharmaceutical development.

The chapters that follow cover novel and important research and development in cancer related research, development, diagnostics and treatment, and in balance, present a substantial part of the tumor landscape, with some exceptions.  Will there ever be a unifying concept, as might be hoped for? I certainly can’t see any such prediction on the horizon.  Part of the problem is that disease classification is a human construct to guide us, and so are treatments that have existed and are reexamined for over 2,000 years.  In that time, we have changed, our afflictions have been modified, and our environment has changed with respect to the microorganisms within and around us, viruses, the soil, and radiation exposure, and the impacts of war and starvation, and access to food.  The outline has been given.  Organic and inorganic chemistry combined with physics has given us a new enterprise in biosynthetics that is and will change our world.  But let us keep in mind that this is a human construct, just as drug target development is such a construct, workable with limitations.

What Molecular Biology Gained from Physics

We need greater clarity and completeness in defining the carcinogenetic process.  It is the beginning, but not the end.  But we must first examine the evolution of the scientific structure that leads to our present understanding. This was preceded by the studies of anatomy, physiology, and embryology that had to occur as a first step, which was followed by the researches into bacteriology, fungi, sea urchins and the evolutionary creatures that could be studied having more primary development in scale.  They are still major objects of study, with the expectation that we can derive lessons about comparative mechanisms that have been passed on through the ages and have common features with man.  This became the serious intent of molecular biology, the discipline that turned to find an explanation for genetics, and to carry out controlled experiments modelled on the discipline that already had enormous success in physics, mathematics, and chemistry. In 1900, when Max Planck hypothesized that the frequency of light emitted by the black body depended on the frequency of the oscillator that emitted it, it had important ramifications for chemistry and biology (See Appendix II and Footnote 1, Planck equation, energy and oscillation).  The leading idea is to search below the large-scale observations of classical biology.

The central dogma of molecular biology where genetic material is transcribed into RNA and then translated into protein, provides a starting point, but the construct is undergoing revision in light of emerging novel roles for RNA and signaling pathways.   The term, coined by Warren Weaver (director of Natural Sciences for the Rockefeller Foundation), who observed an emergence of significant change given recent advances in fields such as X-ray crystallography. Molecular biology also plays important role in understanding formations, actions, regulations of various parts of cellswhich can be used efficiently for targeting new drugs, diagnosis of disease, physiology of the Cell. The Nobel Prize in Physiology or Medicine in 1969 was shared by Max Delbrück, Alfred D. Hershey, Salvador E. Luria, whose work with viral replication gave impetus to the field.  Delbruck was a physicist who trained in Copenhagen under Bohr, and specifically committed himself to a rigor in biology, as was in physics.

Dorothy Hodgkin protein crystallography

Dorothy Hodgkin protein crystallography

Rosalind Franlin crystallographer double helix

Rosalind Franlin
crystallographer
double helix

 Max Delbruck         molecular biology

Max Delbruck        
molecular biology

Max Planck

Max Planck Quantum Physics

 

 

 

We then stepped back from classical (descriptive) physiology, with the endless complexity, to molecular biology.  This led us to the genetic code, with a double helix model.  It has recently been found insufficiently explanatory, with the recent construction of triplex and quadruplex models. They have a potential to account for unaccounted for building blocks, such as inosine, and we don’t know whether more than one model holds validity under different conditions .  The other major field of development has been simply unaccounted for in the study of proteomics, especially in protein-protein interactions, and in the energetics of protein conformation, first called to our attention by the work of Jacob, Monod, and Changeux (See Footnote 2).  Proteins are not just rigid structures stamped out by the monotonously simple DNA to RNA to protein concept.  Nothing is ever quite so simple. Just as there are epigenetic events, there are posttranslational events, and yet more.

JPChangeux-150x170

JP Changeux

 

 

 

 

 

 

 

 

The Emergence of Molecular Biology

I now return the discussion to the topic of medicine, the emergence of molecular biology and the need for convergence with biochemistry in the mid-20th century. Jose Eduardo de Salles Roselino recalls “I was previously allowed to make of the conformational energy as made by R Marcus in his Nobel lecture revised (J. of Electroanalytical  Chemistry 438:(1997) p251-259. (See Footnote 1) His description of the energetic coordinates of a landscape of a chemical reaction is only a two-dimensional cut of what in fact is a volcano crater (in three dimensions) (each one varies but the sum of the two is constant. Solvational+vibrational=100% in ordinate) nuclear coordinates in abcissa. In case we could represent it by research methods that allow us to discriminate in one by one degree of different pairs of energy, we would most likely have 360 other similar representations of the same phenomenon. The real representation would take into account all those 360 representations together. In case our methodology was not that fine, for instance it discriminates only differences of minimal 10 degrees in 360 possible, will have 36 partial representations of something that to be perfectly represented will require all 36 being taken together. Can you reconcile it with ATGC?  Yet, when complete genome sequences were presented they were described as though we will know everything about this living being. The most important problems in biology will be viewed by limited vision always and the awareness of this limited is something we should acknowledge and teach it. Therefore, our knowledge is made up of partial representations. If we had the entire genome data for the most intricate biological problems, they are still not amenable to this level of reductionism. But going from general views of signals andsymptoms we could get to the most detailed molecular view and in this case genome provides an anchor.”

“Warburg Effect” describes the preference of glycolysis and lactic acid fermentation rather than oxidative phosphorylation for energy production in cancer cells. Mitochondrial metabolism is an important and necessary component in the functioning and maintenance of the cell, and accumulating evidence suggests that dysfunction of mitochondrial metabolism plays a role in cancer. Progress has demonstrated the mechanisms of the mitochondrial metabolism-to-glycolysis switch in cancer development and how to target this metabolic switch.

 

 

Glycolysis

glycolysis

 

Otto Heinrich Warburg (1883- )

Otto Warburg

435px-Louis_Pasteur,_foto_av_Félix_Nadar_Crisco_edit

Louis Pasteur

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The expression “Pasteur effect” was coined by Warburg when inspired by Pasteur’s findings in yeast cells, when he investigated this metabolic observation (Pasteur effect) in cancer cells. In yeast cells, Pasteur had found that the velocity of sugar used was greatly reduced in presence of oxygen. Not to be confused, in the “Crabtree effect”, the velocity of sugar metabolism was greatly increased, a reversal, when yeast cells were transferred from the aerobic to an anaerobic condition. Thus, the velocity of sugar metabolism of yeast cells was shown to be under metabolic regulatory control in response to change in environmental oxygen conditions in growth. Warburg had to verify whether cancer cells and tissue related normal mammalian cells also have a similar control mechanism. He found that this control was also found in normal cells studied, but was absent in cancer cells. Strikingly, cancer cells continue to have higher anaerobic gycolysis despite the presence of oxygen in their culture media (See Footnote 3).

Taking this a step further, food is digested and supplied to cells In vertebrates mainly in the form of glucose, which is metabolized producing Adenosine Triphosphate (ATP) by two pathways. Glycolysis, occurs via anaerobic metabolism in the cytoplasm, and is of major significance for making ATP quickly, but in a minuscule amount (2 molecules).  In the presence of oxygen, the breakdown process continues in the mitochondria via the Krebs’s cycle coupled with oxidative phosphorylation, which is more efficient for ATP production (36 molecules). Cancer cells seem to depend on glycolysis. In the 1920s, Otto Warburg first proposed that cancer cells show increased levels of glucose consumption and lactate fermentation even in the presence of ample oxygen (known as “Warburg Effect”). Based on this theory, oxidative phosphorylation switches to glycolysis which promotes the proliferation of cancer cells. Many studies have demonstrated glycolysis as the main metabolic pathway in cancer cells.

Albert Szent Gyogy (Warburg’s student) and Otto Meyerhof both studied striated skeletal muscle metabolism invertebrates, and they found those changes observed in yeast by Pasteur. The description of the anaerobic pathway was largely credited to Emden and Meyerhof. Whenever there is increase in muscle work, energy need is above what can be provided by blood supply, the cell metabolism changes from aerobic (where  Acetyl CoA  provides the chemical energy for aerobic production of ATP) to anaerobic metabolism of glucose. In this condition, glucose is obtained directly from its muscle glycogen stores (not from hepatic glycogenolysis).  This is the sole source of chemical energy that is independent of oxygen supplied to the cell. It is a physiological change on muscle metabolism that favors autonomy. It does not depend upon the blood oxygen for aerobic metabolim or blood sources of carbon metabolites borne out from adipose tissue (free fatty acids) or muscle proteins (branched chain amino acids), or vascular delivery of glucose. On that condition, the muscle can perform contraction by its internal source of ATP and uses conversion of pyruvate to lactate in order to regenerate much-needed NAD (by hydride transfer from pyruvate) as a replacement for this mitochondrial function. This regulatory change, keeps glycolysis going at fast rate in order to meet ATP needs of the cell under low yield condition (only two or three ATP for each glucose converted into two lactate molecules). Therefore, it cannot last for long periods of time. This regulatory metabolic change is made in seconds, minutes and therefore happens with the proteins that are already presented in the cell. It does not requires the effect of transcription factors and/or changes in gene expression (See Footnote 1, 2).

In other types mammalian cells, like those from the lens of the eye (86% gycolysis + pentose shunt),  and red blood cells (RBC)[both lacking mitochondria], and also in the deep medullary layer of the kidneys, for lack of mitochondria in the first two cases and normally reduced blood perfusion in the third – A condition required for the counter current mechanism and our ability to concentrate urine also have, permanent higher anaerobic metabolism. In the case of RBC, it includes the ability to produce in a shunt of glycolytic pathway 2,3 diphospho- glycerate that is required to place the hemogloblin macromolecule in an unstable equilibrium between its two forms (R and T – Here presented as simplified accordingly to the model of Monod, Wyman and Changeux. The final model would be even much complex (see for instance, H-W and K review Nature 2007 vol 450: p 964-972 )

Any tissue under a condition of ischemia that is required for some medical procedures (open heart surgery, organ transplants, etc) displays this fast regulatory mechanism (See Footnote 1, 2). A display of these regulatory metabolic changes can be seen in: Cardioplegia: the protection of the myocardium during open heart surgery: a review. D. J. Hearse J. Physiol., Paris, 1980, 76, 751-756 (Fig 1).  The following points are made:

1-       It is a fast regulatory response. Therefore, no genetic mechanism can be taken into account.

2-       It moves from a reversible to an irreversible condition, while the cells are still alive. Death can be seen at the bottom end of the arrow. Therefore, it cannot be reconciled with some of the molecular biology assumptions:

A-       The gene and genes reside inside the heart muscle cells but, in order to preserve intact, the source of coded genetic information that the cell reads and transcribes, DNA must be kept to a minimal of chemical reactivity.

B-       In case sequence determines conformation, activity and function , elevated potassium blood levels could not cause cardiac arrest.

In comparison with those conditions here presented, cancer cells keep the two metabolic options for glucose metabolism at the same time. These cells can use glucose that our body provides to them or adopt temporarily, an independent metabolic form without the usual normal requirement of oxygen (one or another form for ATP generation).  ATP generation is here, an over-simplification of the metabolic status since the carbon flow for building blocks must also be considered and in this case oxidative metabolism of glucose in cancer cells may be viewed as a rich source of organic molecules or building blocks that dividing cells always need.

JES Roselino has conjectured that “most of the Krebs cycle reaction works as ideal reversible thermodynamic systems that can supply any organic molecule that by its absence could prevent cell duplication.” In the vision of Warburg, cancer cells have a defect in Pasteur-effect metabolic control. In case it was functioning normally, it will indicate which metabolic form of glucose metabolism is adequate for each condition. What more? Cancer cells lack differentiated cell function. Any role for transcription factors must be considered as the role of factors that led to the stable phenotypic change of cancer cells. The failure of Pasteur effect must be searched for among the fast regulatory mechanisms that aren’t dependent on gene expression (See Footnote 3).

Extending the thoughts of JES Roselino (Hepatology 1992;16: 1055-1060), reduced blood flow caused by increased hydrostatic pressure in extrahepatic cholestasis decreases mitochondrial function (quoted in Hepatology) and as part of Pasteur effect normal response, increased glycolysis in partial and/or functional anaerobiosis and therefore blocks the gluconeogenic activity of hepatocytes that requires inhibited glycolysis. In this case, a clear energetic link can be perceived between the reduced energetic supply and the ability to perform differentiated hepatic function (gluconeogenesis). In cancer cells, the action of transcription factors that can be viewed as different ensembles of kaleidoscopic pieces (with changing activities as cell conditions change) are clearly linked to the new stable phenotype. In relation to extrahepatic cholestasis mentioned above it must be reckoned that in case a persistent chronic condition is studied a secondary cirrhosis is installed as an example of persistent stable condition, difficult to be reversed and without the requirement for a genetic mutation. (See Footnote 4).

 The Rejection of Complexity

Most of our reasoning about genes was derived from scientific work in microorganisms. These works have provided great advances in biochemistry.

250px-DNA_labeled DNA diagram showing base pairing

double helix

 

hgp_hubris_220x288_72 genome cartoon

Dna triplex pic

Triple helix

 

formation of a triplex DNA structure

formation of triple helix

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1-      The “Gelehrter idea”: No matter what you are doing you will always be better off, in case you have a gene (In chapter 7 Principles of Medical Genetics Gelehrter and Collins Williams & Wilkins 1990).

2-      The idea that everything could be found following one gene one enzyme relationship that works fine for our understanding of the metabolism, in all biological problems.

3-      The idea that everything that explains biochemistry in microorganisms explains also for every living being (J Nirenberg).

4-      The idea that biochemistry may not require that time should be also taken into account. Time must be considered only for genetic and biological evolution studies (S Luria. In Life- The unfinished experiment 1977 C Scribner´s sons NY).

5-      Finally, the idea that everything in biology, could be found in the genome. Since all information in biology goes from DNA through RNA to proteins. Alternatively, are in the DNA, in case the strict line that includes RNA is not included.

This last point can be accepted in case it is considered that ALL GENETIC information is in our DNA. Genetics as part of life and not as its total expression.

For example, when our body is informed that the ambient temperature is too low or alternatively is too high, our body is receiving an information that arrives from our environment. This external information will affect our proteins and eventually, in case of longer periods in a new condition will cause adaptive response that may include conformational changes in transcription factors (proteins) that will also, produce new readings on the DNA. However, it is an information that moves from outside, to proteins and not from DNA to proteins. The last pathway, when transcription factors change its conformation and change DNA reading will follow the dogmatic view as an adaptive response (See Footnotes 1-3).

However, in case, time is taken into account, the first reactions against cold or warmer temperatures will be the ones that happen through change in protein conformation, activities and function before any change in gene expression can be noticed at protein level. These fast changes, in seconds, minutes cannot be explained by changes in gene expression and are strongly linked to what is needed for the maintenance of life.

“It is possible”, says Roselino, “desirable, to explain all these fast biochemical responses to changes in a living being condition as the sound foundation of medical practices without a single mention to DNA. In case a failure in any mechanism necessary to life is found to be genetic in its origin, the genome in context with with this huge set of transcription factors must be taken into account. This is the biochemical line of reasoning that I have learned with Houssay and Leloir. It would be an honor to see it restored in modern terms.”

More on the Mechanism of Metabolic Control

It was important that genomics would play such a large role in medical research for the last 70 years. There is also good reason to rethink the objections of the Nobelists James Watson and Randy Schekman in the past year, whatever discomfort it brings.  Molecular biology has become a tautology, and as a result deranged scientific rigor inside biology.

Crick & Watson with their DNA model, 1953

Eatson and Crick

Randy-Schekman Berkeley

Randy-Schekman Berkeley

 

 

According to JES Roselino, “consider that glycolysis is oscillatory thanks to the kinetic behavior of Phosphofructokinase. Further, by its effect upon Pyruvate kinase through Fructose 1,6 diphosphate oscillatory levels, the inhibition of gluconeogenesis is also oscillatory. When the carbon flow through glycolysis is led to a maximal level gluconeogenesis will be almost completely blocked. The reversal of the Pyruvate kinase step in liver requires two enzymes (Pyruvate carboxylase (maintenance of oxaloacetic levels) + phosphoenolpyruvate carboxykinase (E.C. 4.1.1.32)) and energy requiring reactions that most likely could not as an ensemble, have a fast enough response against pyruvate kinase short period of inhibition during high frequency oscillatory periods of glycolytic flow. Only when glycolysis oscillates at low frequency the opposite reaction could enable gluconeogenic carbon flow.”

In case it can be shown in a rather convincing way, the same reasoning could be applied to understand how simple replicative signals inducing Go to G1 transition in cells, could easily overcome more complex signals required for cell differentiation and differentiated function.

Perhaps the problem of overextension of the equivalence of the DNA and what happens to the organism is also related to the initial reliance on a single cell model to relieve the complexity (which isn’t fully the case).

For instance, consider this fragment:
“Until only recently it was assumed that all proteins take on a clearly defined three-dimensional structure – i.e. they fold in order to be able to assume these functions.”
Cold Spring Harbour Symp. Quant. Biol. 1973  p 187-193 J.C Seidel and J Gergely – Investigation of conformational changes in Spin-Labeled Myosin Model for muscle contraction:
Huxley, A. F. 1971 Proc. Roy. Soc (London) (B) 178:1
Huxley, A.F and R. M. Simmons,1971. Nature 233:633
J.C Haselgrove X ray Evidence for a conformational Change in the Actin-containing filaments…Cold Spring Harbour Symp Quant Biol.1972 v 37: p 341-352

Only a very small sample indicating otherwise. Proteins were held as interacting macromolecules, changing their conformation in regulatory response to changes in the microenvironment (See Footnote 2). DNA was the opposite, non-interacting macromolecules to be as stable as a library must be.

The dogma held that the property of proteins could be read in DNA alone. Consequenly, the few examples quoted above, must be ignored and all people must believe that DNA alone, without environmental factors roles, controls protein amino acid sequence (OK), conformation (not true), activity (not true) and function (not true).

It appeared naively to be correct from the dogma to conclude from interpreting your genome: You have a 50% increased risk of developing the following disease (deterministic statement).  The correct form must be: You belong to a population that has a 50% increase in the risk of….followed by –  what you must do to avoid increase in your personal risk and the care you should take in case you want to have longer healthy life.  Thus, genetics and non-genetic diseases were treated as the same and medical foundations were reinforced by magical considerations (dogmas) in a very profitable way for those involved besides the patient.

 Footnotes:

  1. There is a link of electricity with ions in biology and the oscillatory behavior of some electrical discharges.  In addition, the oscillatory form of electrical discharged may have allowed Planck to relate high energy content with higher frequencies and conversely, low energy content in low frequency oscillatory events.  One may think of high density as an indication of great amount of matter inside a volume in space.  This helps the understanding of Planck’s idea as a high-density-energy in time for a high frequency phenomenon.
  1. Take into account a protein that may have its conformation restricted by an S-S bridge. This protein also, may move to another more flexible conformation in case it is in HS HS condition when the S-S bridge is broken. Consider also that, it takes some time for a protein to move from one conformation for instance, the restricted conformation (S-S) to other conformations. Also, it takes a few seconds or minutes to return to the S-S conformation (This is the Daniel Koshland´s concept of induced fit and relaxation time used by him in order to explain allosteric behavior of monomeric proteins- Monod, Wyman and Changeux requires tetramer or at least, dimer proteins).
  1. In case you have glycolysis oscillating in a frequency much higher than the relaxation time you could lead to the prevalence of high NADH effect leading to high HS /HS condition and at low glycolytic frequency, you could have predominance of S-S condition affecting protein conformation. In case you have predominance of NAD effect upon protein S-S you would get the opposite results.  The enormous effort to display the effect of citrate and over Phosphofructokinase conformation was made by others. Take into account that ATP action as an inhibitor in this case, is a rather unusual one. It is a substrate of the reaction, and together with its action as activator  F1,6 P (or its equivalent F2,6 P) is also unusual. However, it explains oscillatory behaviour of glycolysis. (Goldhammer , A.R, and Paradies: PFK structure and function, Curr. Top Cell Reg 1979; 15:109-141).
  1. The results presented in our Hepatology work must be viewed in the following way: In case the hepatic (oxygenated) blood flow is preserved, the bile secretory cells of liver receive well-oxygenated blood flow (the arterial branches bath secretory cells while the branches originated from portal vein irrigate the hepatocytes.  During extra hepatic cholestasis the low pressure, portal blood flow is reduced and the hepatocytes do not receive enough oxygen required to produce ATP that gluconeogenesis demands. Hepatic artery do not replace this flow since, its branches only join portal blood fluxes after the previous artery pressure  is reduced to a low pressure venous blood – at the point where the formation of hepatic vein is. Otherwise, the flow in the portal vein would be reversed or, from liver to the intestine. It is of no help to take into account possible valves for this reasoning since minimal arterial pressure is well above maximal venous pressure and this difference would keep this valve in permanent close condition. In low portal blood flow condition, the hepatocyte increases pyruvate kinase activity and with increased pyruvate kinase activity Gluconeogenesis is forbidden (See Walsh & Cooper revision quoted in the Hepatology as ref 23). For the hemodynamic considerations, role of artery and veins in hepatic portal system see references 44 and 45 Rappaport and Schneiderman and Rappapaport.

 

 Appendix I.

metabolic pathways

metabolic pathways

Signals Upstream and Targets Downstream of Lin28 in the Lin28 Pathway

Signals Upstream and Targets Downstream of Lin28 in the Lin28 Pathway

 

 

 

 

 

 

 

 

1.  Functional Proteomics Adds to Our Understanding

Ben Schuler’s research group from the Institute of Biochemistry of the University of Zurich has now established that an increase in temperature leads to folded proteins collapsing and becoming smaller. Other environmental factors can trigger the same effect. The crowded environments inside cells lead to the proteins shrinking. As these proteins interact with other molecules in the body and bring other proteins together, understanding of these processes is essential “as they play a major role in many processes in our body, for instance in the onset of cancer”, comments study coordinator Ben Schuler.

Measurements using the “molecular ruler”

“The fact that unfolded proteins shrink at higher temperatures is an indication that cell water does indeed play an important role as to the spatial organisation eventually adopted by the molecules”, comments Schuler with regard to the impact of temperature on protein structure. For their studies the biophysicists use what is known as single-molecule spectroscopy. Small colour probes in the protein enable the observation of changes with an accuracy of more than one millionth of a millimetre. With this “molecular yardstick” it is possible to measure how molecular forces impact protein structure.

With computer simulations the researchers have mimicked the behaviour of disordered proteins. They want to use them in future for more accurate predictions of their properties and functions.

Correcting test tube results

That’s why it’s important, according to Schuler, to monitor the proteins not only in the test tube but also in the organism. “This takes into account the fact that it is very crowded on the molecular level in our body as enormous numbers of biomolecules are crammed into a very small space in our cells”, says Schuler. The biochemists have mimicked this “molecular crowding” and observed that in this environment disordered proteins shrink, too.

Given these results many experiments may have to be revisited as the spatial organisation of the molecules in the organism could differ considerably from that in the test tube according to the biochemist from the University of Zurich. “We have, therefore, developed a theoretical analytical method to predict the effects of molecular crowding.” In a next step the researchers plan to apply these findings to measurements taken directly in living cells.

Explore further: Designer proteins provide new information about the body’s signal processesMore information: Andrea Soranno, Iwo Koenig, Madeleine B. Borgia, Hagen Hofmann, Franziska Zosel, Daniel Nettels, and Benjamin Schuler. Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments. PNAS, March 2014. DOI: 10.1073/pnas.1322611111

 

Effects of Hypoxia on Metabolic Flux

  1. Glucose-6-phosphate dehydrogenase regulation in the hepatopancreas of the anoxia-tolerantmarinemollusc, Littorina littorea

JL Lama , RAV Bell and KB Storey

Glucose-6-phosphate dehydrogenase (G6PDH) gates flux through the pentose phosphate pathway and is key to cellular antioxidant defense due to its role in producing NADPH. Good antioxidant defenses are crucial for anoxia-tolerant organisms that experience wide variations in oxygen availability. The marine mollusc, Littorina littorea, is an intertidal snail that experiences daily bouts of anoxia/hypoxia with the tide cycle and shows multiple metabolic and enzymatic adaptations that support anaerobiosis. This study investigated the kinetic, physical and regulatory properties of G6PDH from hepatopancreas of L. littorea to determine if the enzyme is differentially regulated in response to anoxia, thereby providing altered pentose phosphate pathway functionality under oxygen stress conditions.

Several kinetic properties of G6PDH differed significantly between aerobic and 24 h anoxic conditions; compared with the aerobic state, anoxic G6PDH (assayed at pH 8) showed a 38% decrease in K G6P and enhanced inhibition by urea, whereas in pH 6 assays Km NADP and maximal activity changed significantly.

All these data indicated that the aerobic and anoxic forms of G6PDH were the high and low phosphate forms, respectively, and that phosphorylation state was modulated in response to selected endogenous protein kinases (PKA or PKG) and protein phosphatases (PP1 or PP2C). Anoxia-induced changes in the phosphorylation state of G6PDH may facilitate sustained or increased production of NADPH to enhance antioxidant defense during long term anaerobiosis and/or during the transition back to aerobic conditions when the reintroduction of oxygen causes a rapid increase in oxidative stress.

Lama et al.  Peer J 2013.   http://dx.doi.org/10.7717/peerj.21

 

  1. Structural Basis for Isoform-Selective Inhibition in Nitric Oxide Synthase

    TL. Poulos and H Li

In the cardiovascular system, the important signaling molecule nitric oxide synthase (NOS) converts L-arginine into L-citrulline and releases nitric oxide (NO). NO produced by endothelial NOS (eNOS) relaxes smooth muscle which controls vascular tone and blood pressure. Neuronal NOS (nNOS) produces NO in the brain, where it influences a variety of neural functions such as neural transmitter release. NO can also support the immune system, serving as a cytotoxic agent during infections. Even with all of these important functions, NO is a free radical and, when overproduced, it can cause tissue damage. This mechanism can operate in many neurodegenerative diseases, and as a result the development of drugs targeting nNOS is a desirable therapeutic goal.

However, the active sites of all three human isoforms are very similar, and designing inhibitors specific for nNOS is a challenging problem. It is critically important, for example, not to inhibit eNOS owing to its central role in controlling blood pressure. In this Account, we summarize our efforts in collaboration with Rick Silverman at Northwestern University to develop drug candidates that specifically target NOS using crystallography, computational chemistry, and organic synthesis. As a result, we have developed aminopyridine compounds that are 3800-fold more selective for nNOS than eNOS, some of which show excellent neuroprotective effects in animal models. Our group has solved approximately 130 NOS-inhibitor crystal structures which have provided the structural basis for our design efforts. Initial crystal structures of nNOS and eNOS bound to selective dipeptide inhibitors showed that a single amino acid difference (Asp in nNOS and Asn in eNOS) results in much tighter binding to nNOS. The NOS active site is open and rigid, which produces few large structural changes when inhibitors bind. However, we have found that relatively small changes in the active site and inhibitor chirality can account for large differences in isoform-selectivity. For example, we expected that the aminopyridine group on our inhibitors would form a hydrogen bond with a conserved Glu inside the NOS active site. Instead, in one group of inhibitors, the aminopyridine group extends outside of the active site where it interacts with a heme propionate. For this orientation to occur, a conserved Tyr side chain must swing out of the way. This unanticipated observation taught us about the importance of inhibitor chirality and active site dynamics. We also successfully used computational methods to gain insights into the contribution of the state of protonation of the inhibitors to their selectivity. Employing the lessons learned from the aminopyridine inhibitors, the Silverman lab designed and synthesized symmetric double-headed inhibitors with an aminopyridine at each end, taking advantage of their ability to make contacts both inside and outside of the active site. Crystal structures provided yet another unexpected surprise. Two of the double-headed inhibitor molecules bound to each enzyme subunit, and one molecule participated in the generation of a novel Zn site that required some side chains to adopt alternate conformations. Therefore, in addition to achieving our specific goal, the development of nNOS selective compounds, we have learned how subtle differences in and structure can control proteinligand interactions and often in unexpected ways.

 

300px-Nitric_Oxide_Synthase

Nitric oxide synthase

arginine-NO-citulline cycle

arginine-NO-citulline cycle

active site of eNOS (PDB_1P6L) and nNOS (PDB_1P6H).

active site of eNOS (PDB_1P6L) and nNOS (PDB_1P6H).

 

 

NO - muscle, vasculature, mitochondria

NO – muscle, vasculature, mitochondria

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure:  (A) Structure of one of the early dipeptide lead compounds, 1, that exhibits excellentisoform selectivity. (B, C) show the crystal structures of the dipeptide inhibitor 1 in the active site of eNOS (PDB: 1P6L) and nNOS (PDB: 1P6H). In nNOS, the inhibitor “curls” which enables the inhibitor R-amino group to interact with both Glu592 and Asp597. In eNOS, Asn368 is the homologue to nNOS Asp597.

Accounts in Chem Res 2013; 46(2): 390-98.

  1. Jamming a Protein Signal

Interfering with a single cancer-promoting protein and its receptor can open this resistance mechanism by initiating autophagy of the affected cells,  according to researchers at The University of Texas MD Anderson Cancer Center  in the journal Cell Reports.  According to Dr. Anil Sood and Yunfei Wen, lead and first authors, blocking  prolactin, a potent growth factor for ovarian cancer, sets off downstream events that result in cell by autophagy, the process  recycles damaged organelles and proteins for new use by the cell through the phagolysozome. This in turn, provides a clinical rationale for blocking prolactin and its receptor to initiate sustained autophagy as an alternative strategy for treating cancers.

Steep reductions in tumor weight

Prolactin (PRL) is a hormone previously implicated in ovarian, endometrial and other cancer development andprogression. When PRL binds to its cell membrane receptor, PRLR, activation of cancer-promoting cell signaling pathways follows.  A variant of normal prolactin called G129R blocks the reaction between prolactin and its receptor. Sood and colleagues treated mice that had two different lines of human ovarian cancer, both expressing the prolactin receptor, with G129R. Tumor weights fell by 50 percent for mice with either type of ovarian cancer after 28 days of treatment with G129R, and adding the taxane-based chemotherapy agent paclitaxel cut tumor weight by 90 percent. They surmise that higher doses of G129R may result in even greater therapeutic benefit.

 

3D experiments show death by autophagy

 

[video width=”1280″ height=”720″ mp4=”http://pharmaceuticalintelligence.com/wp-content/uploads/2014/04/1741-7007-11-65-s1-macromolecular-juggling-by-ubiquitylation-enzymes1.mp4″][/video]

 

Next the team used the prolactin-mimicking peptide to treat cultures of cancer spheroids which sharply reduced their numbers, and blocked the activation of JAK2 and STAT signaling pathways.

Protein analysis of the treated spheroids showed increased presence of autophagy factors and genomic analysis revealed increased expression of a number of genes involved in autophagy progression and cell death.  Then a series of experiments using fluorescence and electron microscopy showed that the cytosol of treated cells had large numbers of cavities caused by autophagy.

The team also connected the G129R-induced autophagy to the activity of PEA-15, a known cancer inhibitor. Analysis of tumor samples from 32 ovarian cancer patients showed that tumors express higher levels of the prolactin receptor and lower levels of phosphorylated PEA-15 than normal ovarian tissue. However, patients with low levels of the prolactin receptor and higher PEA-15 had longer overall survival than those with high PRLR and low PEA-15.

Source: MD Anderson Cancer Center

 

  1. Chemists’ Work with Small Peptide Chains of Enzymes

Korendovych and his team designed seven simple peptides, each containing seven amino acids. They then allowed the molecules of each peptide to self-assemble, or spontaneously clump together, to form amyloids. (Zinc, a metal with catalytic properties, was introduced to speed up the reaction.) What they found was that four of the seven peptides catalyzed the hydrolysis of molecules known as esters, compounds that react with water to produce water and acids—a feat not uncommon among certain enzymes.

“It was the first time that a peptide this small self-assembled to produce an enzyme-like catalyst,” says Korendovych. “Each enzyme has to be an exact fit for its respective substrate,” he says, referring to the molecule with which an enzyme reacts. “Even after millions of years, nature is still testing all the possible combinations of enzymes to determine which ones can catalyze metabolic reactions. Our results make an argument for the design of self-assembling nanostructured catalysts.”

Source: Syracuse University

Here are three articles emphasizing the value of combinatorial analysis, which can be formed from genomic, clinical, and proteomic data sets.

 

  1. Comparative analysis of differential network modularity in tissue specific normal and cancer protein interaction networks

    F Islam , M Hoque , RS Banik , S Roy , SS Sumi, et al.

As most biological networks show modular properties, the analysis of differential modularity between normal and cancer protein interaction networks can be a good way to understand cancer more significantly. Two aspects of biological network modularity e.g. detection of molecular complexes (potential modules or clusters) and identification of crucial nodes forming the overlapping modules have been considered in this regard.

The computational analysis of previously published protein interaction networks (PINs) has been conducted to identify the molecular complexes and crucial nodes of the networks. Protein molecules involved in ten major cancer signal transduction pathways were used to construct the networks based on expression data of five tissues e.g. bone, breast, colon, kidney and liver in both normal and cancer conditions.

Cancer PINs show higher level of clustering (formation of molecular complexes) than the normal ones. In contrast, lower level modular overlapping is found in cancer PINs than the normal ones. Thus a proposition can be made regarding the formation of some giant nodes in the cancer networks with very high degree and resulting in reduced overlapping among the network modules though the predicted molecular complex numbers are higher in cancer conditions.

Islam et al. Journal of Clinical Bioinformatics 2013, 3:19-32

  1. A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis

    Wanting Liu , Yonghong Peng and Desmond J. Tobin
    PeerJ 1:e49;        http://dx.doi.org/10.7717/peerj.49

Here we present an integrated microarray analysis framework, based on a genome-wide relative significance (GWRS) and genome-wide global significance (GWGS) model. When applied to five microarray datasets on melanoma published between 2000 and 2011, this method revealed a new signature of 200 genes. When these were linked to so-called ‘melanoma driver’ genes involved in MAPK, Ca2+, and WNT signaling pathways we were able to produce a new 12-gene diagnostic biomarker signature for melanoma (i.e., EGFR, FGFR2, FGFR3, IL8, PTPRF, TNC, CXCL13, COL11A1, CHP2, SHC4, PPP2R2C, andWNT4).We have begun to experimentally validate a subset of these genes involved inMAPK signaling at the protein level, including CXCL13, COL11A1, PTPRF and SHC4 and found these to be overexpressed inmetastatic and primarymelanoma cells in vitro and in situ compared to melanocytes cultured from healthy skin epidermis and normal healthy human skin.

 

catalytic amyloid forming particle

catalytic amyloid forming particle

 

 

 

 

 

 

 

        8.    PanelomiX: A threshold-based algorithm to create panels of biomarkers

X Robin , N Turck , A Hainard , N Tiberti, et al.
               Translational Proteomics 2013.    http://dx.doi.org/10.1016/j.trprot.2013.04.003

The PanelomiX toolbox combines biomarkers and evaluates the performance of panels to classify patients better than singlemarkers or other classifiers. The ICBTalgorithm proved to be an efficient classifier, the results of which can easily be interpreted.

Here are two current examples of the immense role played by signaling pathways in carcinogenic mechanisms and in treatment targeting, which is also confounded by acquired resistance.

 

  1. Triple-Negative Breast Cancer

  1. epidermal growth factor receptor (EGFR or ErbB1) and
  2. high activity of the phosphatidylinositol 3-kinase (PI3K)–Akt pathway

are both targeted in triple-negative breast cancer (TNBC).

  • activation of another EGFR family member [human epidermal growth factor receptor 3 (HER3) (or ErbB3)] may limit the antitumor effects of these drugs.

This study found that TNBC cell lines cultured with the EGFR or HER3 ligand EGF or heregulin, respectively, and treated with either an Akt inhibitor (GDC-0068) or a PI3K inhibitor (GDC-0941) had increased abundance and phosphorylation of HER3.

The phosphorylation of HER3 and EGFR in response to these treatments

  1. was reduced by the addition of a dual EGFR and HER3 inhibitor (MEHD7945A).
  2. MEHD7945A also decreased the phosphorylation (and activation) of EGFR and HER3 and
  3. the phosphorylation of downstream targets that occurred in response to the combination of EGFR ligands and PI3K-Akt pathway inhibitors.

In culture, inhibition of the PI3K-Akt pathway combined with either MEHD7945A or knockdown of HER3

  1. decreased cell proliferation compared with inhibition of the PI3K-Akt pathway alone.
  2. Combining either GDC-0068 or GDC-0941 with MEHD7945A inhibited the growth of xenografts derived from TNBC cell lines or from TNBC patient tumors, and
  3. this combination treatment was also more effective than combining either GDC-0068 or GDC-0941 with cetuximab, an EGFR-targeted antibody.
  4. After therapy with EGFR-targeted antibodies, some patients had residual tumors with increased HER3 abundance and EGFR/HER3 dimerization (an activating interaction).

Thus, we propose that concomitant blockade of EGFR, HER3, and the PI3K-Akt pathway in TNBC should be investigated in the clinical setting.

Reference: Antagonism of EGFR and HER3 Enhances the Response to Inhibitors of the PI3K-Akt Pathway in Triple-Negative Breast Cancer. JJ Tao, P Castel, N Radosevic-Robin, M Elkabets, et al.  Sci. Signal., 25 March 2014;
7(318), p. ra29   http://dx.doi.org/10.1126/scisignal.2005125

 

                  10.   Metastasis in RAS Mutant or Inhibitor-Resistant Melanoma Cells

The protein kinase BRAF is mutated in about 40% of melanomas, and BRAF inhibitors improve progression-free and overall survival in these patients. However, after a relatively short period of disease control, most patients develop resistance because of reactivation of the RAF–ERK (extracellular signal–regulated kinase) pathway, mediated in many cases by mutations in RAS. We found that BRAF inhibition induces invasion and metastasis in RAS mutant melanoma cells through a mechanism mediated by the reactivation of the MEK (mitogen-activated protein kinase kinase)–ERK pathway.

Reference: BRAF Inhibitors Induce Metastasis in RAS Mutant or Inhibitor-Resistant Melanoma Cells by Reactivating MEK and ERK Signaling. B Sanchez-Laorden, A Viros, MR Girotti, M Pedersen, G Saturno, et al., Sci. Signal., 25 March 2014;  7(318), p. ra30  http://dx.doi.org/10.1126/scisignal.2004815

Appendix II.

The world of physics in the twentieth century saw the end of determinism established by Newton. This is characterized by discrete laws that describe natural observations. These are in gravity and in eletricity. In an early phase of investigation, an era of galvanic or voltaic electricity represented a revolutionary break from the historical focus on frictional electricity. Alessandro Voltadiscovered that chemical reactions could be used to create positively charged anodes and negatively charged cathodes.  In 1790, Prof. Luigi Alyisio Galvani of Bologna, while conducting experiments on “animal electricity“, noticed the twitching of a frog’s legs in the presence of an electric machine. He observed that a frog’s muscle, suspended on an iron balustrade by a copper hook passing through its dorsal column, underwent lively convulsions without any extraneous cause, the electric machine being at this time absent.  Volta communicated a description of his pile to the Royal Society of London and shortly thereafter Nicholson and Cavendish (1780) produced the decomposition of water by means of the electric current, using Volta’s pile as the source of electromotive force.

Siméon Denis Poisson attacked the difficult problem of induced magnetization, and his results provided  a first approximation. His innovation required the application of mathematics to physics.  His memoirs on the theory of electricity and magnetism created a new branch of mathematical physics.  The discovery of electromagnetic induction was made almost simultaneously and independently by Michael Faraday and Joseph Henry. Michael Faraday, the successor of Humphry Davy, began his epoch-making research relating to electric and electromagnetic induction in 1831. In his investigations of the peculiar manner in which iron filings arrange themselves on a cardboard or glass in proximity to the poles of a magnet, Faraday conceived the idea of magnetic “lines of force” extending from pole to pole of the magnet and along which the filings tend to place themselves. On the discovery being made that magnetic effects accompany the passage of an electric current in a wire, it was also assumed that similar magnetic lines of force whirled around the wire. He also posited that iron, nickel, cobalt, manganese, chromium, etc., are paramagnetic (attracted by magnetism), whilst other substances, such as bismuth, phosphorus, antimony, zinc, etc., are repelled by magnetism or are diamagnetic.

Around the mid-19th century, Fleeming Jenkin‘s work on ‘ Electricity and Magnetism ‘ and Clerk Maxwell’s ‘ Treatise on Electricity and Magnetism ‘ were published. About 1850 Kirchhoff published his laws relating to branched or divided circuits. He also showed mathematically that according to the then prevailing electrodynamic theory, electricity would be propagated along a perfectly conducting wire with the velocity of light. Herman Helmholtz investigated the effects of induction on the strength of a current and deduced mathematical equations, which experiment confirmed. In 1853 Sir William Thomson (later Lord Kelvin) predicted as a result of mathematical calculations the oscillatory nature of the electric discharge of a condenser circuit.  Joseph Henry, in 1842 discerned  the oscillatory nature of the Leyden jardischarge.

In 1864 James Clerk Maxwell announced his electromagnetic theory of light, which was perhaps the greatest single step in the world’s knowledge of electricity. Maxwell had studied and commented on the field of electricity and magnetism as early as 1855/6 when On Faraday’s lines of force was read to the Cambridge Philosophical Society. The paper presented a simplified model of Faraday’s work, and how the two phenomena were related. He reduced all of the current knowledge into a linked set of differential equations with 20 equations in 20 variables. This work was later published as On Physical Lines of Force in1861. In order to determine the force which is acting on any part of the machine we must find its momentum, and then calculate the rate at which this momentum is being changed. This rate of change will give us the force. The method of calculation which it is necessary to employ was first given by Lagrange, and afterwards developed, with some modifications, by Hamilton’s equations. Now Maxwell logically showed how these methods of calculation could be applied to the electro-magnetic field. The energy of a dynamical systemis partly kinetic, partly potential. Maxwell supposes that the magnetic energy of the field is kinetic energy, the electric energy potential.  Around 1862, while lecturing at King’s College, Maxwell calculated that the speed of propagation of an electromagnetic field is approximately that of the speed of light.   Maxwell’s electromagnetic theory of light obviously involved the existence of electric waves in free space, and his followers set themselves the task of experimentally demonstrating the truth of the theory. By 1871, he presented the Remarks on the mathematical classification of physical quantities.

A Wave-Particle Dilemma at the Century End

In 1896 J.J. Thomson performed experiments indicating that cathode rays really were particles, found an accurate value for their charge-to-mass ratio e/m, and found that e/m was independent of cathode material. He made good estimates of both the charge e and the mass m, finding that cathode ray particles, which he called “corpuscles”, had perhaps one thousandth of the mass of the least massive ion known (hydrogen). He further showed that the negatively charged particles produced by radioactive materials, by heated materials, and by illuminated materials, were universal.  In the late 19th century, the Michelson–Morley experiment was performed by Albert Michelson and Edward Morley at what is now Case Western Reserve University. It is generally considered to be the evidence against the theory of a luminiferous aether. The experiment has also been referred to as “the kicking-off point for the theoretical aspects of the Second Scientific Revolution.” Primarily for this work, Albert Michelson was awarded theNobel Prize in 1907.

Wave–particle duality is a theory that proposes that all matter exhibits the properties of not only particles, which have mass, but also waves, which transfer energy. A central concept of quantum mechanics, this duality addresses the inability of classical concepts like “particle” and “wave” to fully describe the behavior of quantum-scale objects. Standard interpretations of quantum mechanics explain this paradox as a fundamental property of the universe, while alternative interpretations explain the duality as an emergent, second-order consequence of various limitations of the observer. This treatment focuses on explaining the behavior from the perspective of the widely used Copenhagen interpretation, in which wave–particle duality serves as one aspect of the concept of complementarity, that one can view phenomena in one way or in another, but not both simultaneously.  Through the work of Max PlanckAlbert EinsteinLouis de BroglieArthur Compton, Niels Bohr, and many others, current scientific theory holds that all particles also have a wave nature (and vice versa).

Beginning in 1670 and progressing over three decades, Isaac Newton argued that the perfectly straight lines of reflection demonstrated light’s particle nature, but Newton’s contemporaries Robert Hooke and Christiaan Huygens—and later Augustin-Jean Fresnel—mathematically refined the wave viewpoint, showing that if light traveled at different speeds in different, refraction could be easily explained. The resulting Huygens–Fresnel principle was supported by Thomas Young‘s discovery of double-slit interference, the beginning of the end for the particle light camp.  The final blow against corpuscular theory came when James Clerk Maxwell discovered that he could combine four simple equations, along with a slight modification to describe self-propagating waves of oscillating electric and magnetic fields. When the propagation speed of these electromagnetic waves was calculated, the speed of light fell out. While the 19th century had seen the success of the wave theory at describing light, it had also witnessed the rise of the atomic theory at describing matter.

Matter and Light

In 1789, Antoine Lavoisier secured chemistry by introducing rigor and precision into his laboratory techniques. By discovering diatomic gases, Avogadro completed the basic atomic theory, allowing the correct molecular formulae of most known compounds—as well as the correct weights of atoms—to be deduced and categorized in a consistent manner. The final stroke in classical atomic theory came when Dimitri Mendeleev saw an order in recurring chemical properties, and created a table presenting the elements in unprecedented order and symmetry.   Chemistry was now an atomic science.

Black-body radiation, the emission of electromagnetic energy due to an object’s heat, could not be explained from classical arguments alone. The equipartition theorem of classical mechanics, the basis of all classical thermodynamic theories, stated that an object’s energy is partitioned equally among the object’s vibrational modes. This worked well when describing thermal objects, whose vibrational modes were defined as the speeds of their constituent atoms, and the speed distribution derived from egalitarian partitioning of these vibrational modes closely matched experimental results. Speeds much higher than the average speed were suppressed by the fact that kinetic energy is quadratic—doubling the speed requires four times the energy—thus the number of atoms occupying high energy modes (high speeds) quickly drops off. Since light was known to be waves of electromagnetism, physicists hoped to describe this emission via classical laws. This became known as the black body problem. The Rayleigh–Jeans law which, while correctly predicting the intensity of long wavelength emissions, predicted infinite total energy as the intensity diverges to infinity for short wavelengths.

The solution arrived in 1900 when Max Planck hypothesized that the frequency of light emitted by the black body depended on the frequency of the oscillator that emitted it, and the energy of these oscillators increased linearly with frequency (according to his constant h, where E = hν). By demanding that high-frequency light must be emitted by an oscillator of equal frequency, and further requiring that this oscillator occupy higher energy than one of a lesser frequency, Planck avoided any catastrophe; giving an equal partition to high-frequency oscillators produced successively fewer oscillators and less emitted light. And as in the Maxwell–Boltzmann distribution, the low-frequency, low-energy oscillators were suppressed by the onslaught of thermal jiggling from higher energy oscillators, which necessarily increased their energy and frequency. Planck had intentionally created an atomic theory of the black body, but had unintentionally generated an atomic theory of light, where the black body never generates quanta of light at a given frequency with energy less than .

In 1905 Albert Einstein took Planck’s black body model in itself and saw a wonderful solution to another outstanding problem of the day: the photoelectric effect, the phenomenon where electrons are emitted from atoms when they absorb energy from light.   Only by increasing the frequency of the light, and thus increasing the energy of the photons, can one eject electrons with higher energy. Thus, using Planck’s constant h to determine the energy of the photons based upon their frequency, the energy of ejected electrons should also increase linearly with frequency; the gradient of the line being Planck’s constant. These results were not confirmed until 1915, when Robert Andrews Millikan, produced experimental results in perfect accord with Einstein’s predictions. While  the energy of ejected electrons reflected Planck’s constant, the existence of photons was not explicitly proven until the discovery of the photon antibunching effect  When Einstein received his Nobel Prizein 1921, it was  for the photoelectric effect, the suggestion of quantized light. Einstein’s “light quanta” represented the quintessential example of wave–particle duality. Electromagnetic radiation propagates following  linear wave equations, but can only be emitted or absorbed as discrete elements, thus acting as a wave and a particle simultaneously.

Radioactivity Changes the Scientific Landscape

The turn of the century also features radioactivity, which later came to the forefront of the activities of World War II, the Manhattan Project, the discovery of the chain reaction, and later – Hiroshima and Nagasaki.

Marie Curie

Marie Curie

 

 

 

Marie Skłodowska-Curie was a Polish and naturalized-French physicist and chemist who conducted pioneering research on radioactivity. She was the first woman to win a Nobel Prize, the only woman to win in two fields, and the only person to win in multiple sciences. She was also the first woman to become a professor at the University of Paris, and in 1995 became the first woman to be entombed on her own merits in the Panthéon in Paris. She shared the 1903 Nobel Prize in Physics with her husband Pierre Curie and with physicist Henri Becquerel. She won the 1911 Nobel Prize in Chemistry.  Her achievements included a theory of radioactivity (a term that she coined, techniques for isolating radioactive isotopes, and the discovery of polonium and radium. She named the first chemical element that she discovered – polonium, which she first isolated in 1898 – after her native country. Under her direction, the world’s first studies were conducted into the treatment of neoplasms using radioactive isotopes. She founded the Curie Institutes in Paris and in Warsaw, which remain major centres of medical research today. During World War I, she established the first military field radiological centres.  Curie died in 1934 due to aplastic anemia brought on by exposure to radiation – mainly, it seems, during her World War I service in mobile X-ray units created by her.

 

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Genomics and Medicine: The Physician’s View

Genomics and Medicine: The Physician’s View

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

 

Genomics has had a rapid growth of research into variability of human genetics in both healthy populations in the study of population migration, and in the study of genetic sequence alterations that may increase the risk of expressed human disease.  This is the case for cardiology, cancer, inflammtory conditions, and gastrointestinal diseases. For the most part, genomics research in the last decade has shed light on potential therapeutic targets, but the identification of drug toxicities in late phase trials has been associated with a 70 percent failure rate in bringing new drugs to the market.   Despite good technologies for investigative studies, initial work is carried out on animals and then the transferrability of the work from a “model” to man has to be assured.  That is the first issue of concern.

Secondly, there is a well considered reluctance on the part of experienced and well prepared physicians to be “early” adopters to newly introduced drugs, with the apprehension that unidentified clinical problems can be expected to be unmasked.  It is, however, easier to consider when a new drug belongs to an established class of medications, and it has removed known adverse effects.  In this case, the adverse effects are known side effects, but not necessarily serious drug reactions that would preclude use.

A third consideration is the cost of drug development, and the cost of development is passed on to the healthcare organization in the purchasing cost. We can rest assured that the Pharmacy and Therapeutics Review Committee will not cease meeting on a regular schedule anytime soon.  Further, how do the drug failures become embedded in the cost of the pharmaceutical budget passed on to the recipient.  Historically, insurance is an actuarial discipline.  But in the lifetime of an individual, they are bound to see a physician for acute or chronic medical attention.  Only the timing cannot be predicted.  As a result, dealing with the valid introduction of new medications is a big concern for both the public and the private insurer.

How does this compute for the physician provider.  The practice of medicine is not quickly adaptive, as the physician’s primary concern is to do no harm.   Genomics testing is not widely available, and it is for the most part not definitive for diagnostic purposes as things stand today.  It may provide assessment of risk, or of survival expectation.  The physician uses a step by step assessment, using the patient and family history, a focused physical exam, laboratory and radiology, proceeding to other more specialized exams.  Much of the laboratory testing is based on the appearance in the circulation of changes in blood chemistry of the nature of electrolytes, circulating cells in the blood and of the blood forming organ, proteins, urea and uric acid.  They are not exquisitely sensitive, but they might be sufficient for their abnormal concentrations appearing at the time the patient presents with a complaint. What tests are ordered is determioned by a need for relevant information to make a medical decision.

The relevant questions are:

1. acuity of symptoms and signs.
2. actions to be taken.
3. tests that are needed to clarify the examination findings.

once a provisional diagnosis is obtained, referrals, additional testing, and medication orders are provided based on the assessment.

Where does genetic testing fit into this? At this point, it will only be used

  1. to confirm a restricted list of diagnoses that have a high association with the condition, and
  2. only with the participation of a medical geneticist, when
  3. profiling the patient and other members of the family is required.

10d0de1 Vitruvian Man by Leonardo da Vinci

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Stabilizers that prevent Transthyretin-mediated Cardiomyocyte Amyloidotic Toxicity

Reporter and curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/12-2-2013/larryhbern/Stabilizers that prevent transthyretin-mediated cardiomyocyte amyloidotic toxicity

Transthyretin is a small protein with a half-life of < 48 hours, synthesized by the liver, and a major transport protein for thyroxin.  There are 80 variants known, and some variants that occur in the Portuguese, a small section of Japan, Sweden, and Brazil, are associated will primary amyloidosis, the only cure for which is liver transplantation.  It causes fibrillary inclusions in the heart, but also affects the autonomic nervous system.  Some of the major work on this has been done for many years in the laboratory of   Jeffery W. Kelly, at the Skaggs Institute for Chemical Biology, the Scripps Research Institute.  A recent publication is of considerable interest.

Potent Kinetic Stabilizers that Prevent Transthyretin-mediated Cardiomyocyte Proteotoxicity

 Mamoun M. Alhamadsheh1,6,7, Stephen Connelly2,7, Ahryon Cho1, Natàlia Reixach3, Evan T. Powers3,4,5, Dorothy W. Pan1, Ian A. Wilson2,5, Jeffery W. Kelly3,4,5, and Isabella A. Graef1,*
Sci Transl Med. Author manuscript; available in PMC 2012 August 24.
1Department of Pathology, Stanford University Medical School, Stanford, California, USA
2Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
3Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
4Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
5The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
6Department of Pharmaceutics & Medicinal Chemistry, University of the Pacific, Stockton, California, USA

Abstract

The V122I mutation that alters the stability of transthyretin (TTR) affects 3–4% of African Americans and leads to amyloidogenesis and development of cardiomyopathy. In addition, 10–15% of individuals over the age of 65 develop senile systemic amyloidosis (SSA) and cardiac
TTR deposits due to wild-type TTR amyloidogenesis. As no approved therapies for TTR amyloid cardiomyopathy are available, the development of drugs that prevent amyloid-mediated cardiotoxicity is desired. To this aim, we developed a fluorescence polarization-based HTS screen,
which identified several new chemical scaffolds targeting TTR. These novel compounds were potent kinetic stabilizers of TTR and
  • prevented tetramer dissociation,
  • unfolding and aggregation of both wild type and the most common cardiomyopathy-associated TTR mutant, V122I-TTR.
High-resolution co-crystal structures and characterization of the binding energetics revealed how these diverse structures bound to tetrameric TTR. Our study also showed that these compounds effectively inhibited the proteotoxicity of V122I-TTR towards human cardiomyocytes.
Several of these ligands stabilized TTR in human serum more effectively than diflunisal, which is one of the best known inhibitors of TTR aggregation, and may be promising leads for the treatment and/or prevention of TTR-mediated cardiomyopathy.

Author Contributions:

M.M.A. designed and performed most experiments, S.C. performed crystallographic structure determination, A.C peformed the serum TTR stabilization. N.R. performed the cell-based assays.   E.T.P. analyzed the ITC data. D.W.P. helped with probe synthesis. I.A.W. supervised the crystallographic work. J.W.K. supervised the work, S.C., N.R., I.A.W. and J.W.K. edited the paper. I.A.G supervised the work, M.M.A. and I.A.G prepared the manuscript.

 INTRODUCTION

The misassembly of soluble proteins into toxic amyloid aggregates underlies a large number of human degenerative diseases (1–3). TTR is one of more than 30 human amyloidogenic proteins whose misassembly can cause
  • a variety of degenerative gain-of-toxic-function diseases.
TTR is a tetrameric protein (54 kDa), secreted from the liver into the blood where, using orthogonal sites,
  • it transports thyroxine (T4) and
  • holo-retinol binding protein (4).
However, 99% of the TTR T4 binding sites remain unoccupied in humans
  • owing to the presence of two other T4 transport proteins in blood (3).
Familial TTR amyloid diseases, which are associated with one of more than 80 mutations in the TTR gene, include
  • the systemic neuropathies (familial amyloid polyneuropathy [FAP]),
  • cardiomyopathies (familial amyloid cardiomyopathy [FAC]), and
  • central nervous system amyloidoses (CNSA) (5–8).
Cardiac amyloidosis is most commonly caused by
  • deposition of immunoglobulin light chains or
  • TTR in the cardiac interstitium and conducting system.
It is a chronic and progressive condition, which can lead to arrhythmias, biventricular heart failure, and death (8–10). Two types of TTR-associated amyloid cardiomyopathies are clinically important.
  1. Wild-type (WT) TTR aggregation underlies the development of senile systemic amyloidosis (SSA). Cardiac TTR deposits can be found in 10 to 15% of the population over the age of 65 at autopsy (10,11). Many of these patients are asymptomatic, but there is little doubt that SSA is an underdiagnosed disease.
  2. In addition, a number of TTR mutations, including V122I, lead to amyloidogenesis and familial amyloid cardiomyopathy (FAC) (12–15). Population studies show that the V122I mutation is found in 3–4% of African Americans (~1.3 million people) and contributes to the increased prevalence of heart failure among this population segment (14,15).

The mutant TTR allele behaves as an autosomal dominant allele with age-dependent penetrance and

  • the frequency of cardiac amyloidosis from TTR in African-American individuals above age 60 is four times that seen in Caucasian-Americans of comparable age.
All of the TTR mutations associated with familial amyloidosis decrease tetramer stability, and
  • some decrease the kinetic barrier for tetramer dissociation (3, 16).
  • The latter is important because tetramer dissociation is the rate-limiting step in the TTR amyloidogenesis cascade (3).

Kinetic stabilization of the native, tetrameric structure of TTR by

  • interallelic trans suppression (incorporation of mutant subunits that raise the dissociative transition state energy) prevents
    1. post-secretory dissociation and aggregation, as well as the related disease 
    2. familial amyloid polyneuropathy (FAP), by slowing TTR tetramer dissociation (17).
Occupancy of the TTR T4 binding sites with rationally designed small molecules is known to stabilize the native tetrameric state of TTR over the dissociative transition state,
  • raising the kinetic barrier,
  • imposing kinetic stabilization on the tetramer and
  • preventing amyloidogenesis (3, 16, 18).
Previous studies have focused on rational ligand design and as a result
  • most of the TTR stabilizers reported to date are halogenated biaryl analogues of T4,
  • many resembling non-steroidal anti-inflammatory drugs (NSAIDs).
Some of these compounds, such as the NSAID diflunisal, which is currently tested in clinical trials in FAP patients for its efficacy to ameliorate
  • peripheral neuropathy resulting from TTR deposition, (19) have anti-inflammatory activity (20, 21).
The pharmacological effects of NSAIDs are due to inhibition of cyclo-oxygenase (COX) enzymes (22). Inhibition of COX-1 can produce side effects such as
  • gastrointestinal irritation, leading to ulcers and bleeding (23).
Inhibition of COX-2 has been associated with an
  • increased risk of severe cardiovascular events, including heart failure,
  • particularly in patients with preexisting cardiorenal dysfunction (20, 21, 24, 25).
Therefore, heart and kidney impairment are exclusion criteria for participation of patients in the diflunisal clinical trials to treat TTR-mediated FAP (19). Genomic variations can
  • increase the sensitivity of individuals to adverse side effects of NSAIDs.
Serum concentrations of NSAIDs depend on CYP2C9 and/or CYP2C8 activity. CYP2C9 polymorphism might play a significant role in the profile of adverse side effects of NSAID and alleles that affect the activity of CYP2C9 are found at different frequency in subjects of Caucasian, African or Asian descent (26, 27). Hence, the long-term therapy with drugs that have inhibitory effect on COX activity to prevent TTR aggregation is especially problematic in patients who suffer from TTR-mediated cardiomyopathy. The design and development of drugs to treat/prevent FAC or SSA thus presents the challenge
  1. not only to find compounds with a greater variety of chemical scaffolds that accomplish stabilization, but
  2. do so without the adverse side effects due to inhibition of COX activity.
 For these reasons, the development of a rapid and robust screen for compounds that bind to and stabilize TTR could be useful. To date, no high-throughput screening (HTS) methodology is available for the discovery of TTR ligands (28,29). Therefore, we developed a versatile
  • fluorescence polarization (FP) based HTS assay that can detect
  • binding of small molecules to the T4 binding pocket of TTR under physiological conditions.

RESULTS

Design and synthesis of the TTR FP probe

FP is used to study molecular interactions by monitoring changes in the apparent size of a fluorescently labeled molecule. Binding is measured by an increase in the FP signal, which is proportional to the decrease in the rate of tumbling of a fluorescent ligand upon association with macromolecules such as proteins (Fig. 1A). To synthesize a fluorescent TTR ligand 1, we initially started with the NSAID diflunisal analogue 2 (Fig. 1B) (30). The product of attaching a linker to 2, compound 3, had very low binding affinity to TTR (Kd1 >3290 nM, fig. S1A and fig. S1B).
The crystal structure of the diclofenac analog 4 showed that
  • the phenolic hydroxyl flanked by the two chlorine atoms is oriented out of the binding pocket into the solvent (31).
  • We reasoned that attaching a PEG amine linker to the phenol group of 4 would generate compound 5 which would bind to TTR (Fig. 1B and fig. S1C)

5 was coupled to fluorescein isothiocyanate (FITC) to produce the FITC-coupled TTR FP probe (1, Fig. 1B). The binding characteristics of the probe (Kd1 = 13 nM and Kd2 = 100 nM) were assessed with ITC (Fig. 2A).

Evaluation of the FP assay

The binding of 1 to TTR was evaluated to test its suitability for the FP assay with a standard saturation binding experiment. A fixed concentration of probe 1 (0.1 μM) was incubated with increasing concentrations of TTR (0.005 μM to 10 μM) and the formation of 1•TTR complex was quantified by the increase in FP signal (excitation λ 485 nm, emission λ 525 nm) relative to the concentration of TTR (Fig. 2B). The fluorescence polarization increased with the concentration of TTR until saturation was reached. A large dynamic range (70 – 330 mP) was measured for the assay. To validate the FP assay, we tested known TTR binders in a displacement assay (for detailed information see Supplemental Material). Compound 2 (Kapp = 231 nM, R2 = 0.997), Thyroxine (T4) (Kapp = 186 nM, R2 = 0.998) and diclofenac (Kapp = 4660 nM, R2 = 0.999) decreased the FP signal in a dose- dependent  manner  (Fig. 2C,  fig. S2B and S2C). The FP assay is a competitive displacement assay and therefore it provides apparent binding constants (Kapp). However, these apparent binding constants correlate well with the data obtained by ITC which measures direct interactions in solution and gives an actual (Kd) value.

 Adaptation of the FP assay for HTS

Next, we optimized the FP assay for HTS and screened a ~130,000 small molecule library for compounds that displaced probe 1 from the T4 binding sites of TTR. The FP assay was performed in 384-well plates with low concentrations of probe 1 (1.5 nM) and TTR (50 nM) in a 10  μL assay volume.  Detergent (0.01% Triton X-100) was added to the assay buffer to avoid false positive hits from aggregation of the small molecules. The assay demonstrated robust performance, with a, large dynamic range (~70–230 mP) and a Z′ factor (32, 33) in the range of 0.57–0.78 (fig. S3A and S3B).

Hits were defined as compounds, which resulted in at least 50% decrease in FP and demonstrated relative fluorescence between 70 and 130%. Many fluorescence quenchers and enhancers, which have less than 70% and greater than 130% total fluorescence relative to a control (compound without TTR), were excluded from the hit list. The excluded compounds have native fluorescence that is similar to fluorescein, which would interfere with the FP measurements and result in false positive hits. Two hundred compounds were designated as positive hits (0.167% hit rate). The top 33 compounds (compounds with lowest FP IC50) were assayed in a 10-point duplicate dose-response FP assay and displayed an IC50 (concentration that resulted in 50% decrease in the FP signal) between 0.277 and 10.957 μM (table S2).

Validation of the HTS hits

The top 33 compounds were retested with the FP assay (table S2) and with surface plasmon resonance (SPR) as another independent biophysical method. Solutions of the 33 hits were passed over immobilized, biotinylated TTR on a streptavidin coated chip. The binding of a small molecule to TTR on the sensor chip produces a SPR response signal (RU). The RU signal after addition of the top 33 compounds was measured and compared to a negative, solvent only, control. All compounds identified by the screen as hits were confirmed as TTR binders using SPR (fig. S4). We also found known TTR binders, such as NSAIDs (diclofenac, meclofenamic acid, and niflumic acid) and isoflavones (apigenin) in our screen (3, 34) (table S2). Among the best ligands (Fig. 2D) were the NSAID, niflumic acid, two catechol-O-methyl-tranferase (COMT) inhibitors, 3,5-dintrocatechol and Ro 41-0960 (35) and a number  of compounds   not previously known to bind to TTR. The chemical structures of these ligands were confirmed by 1H NMR and high-resolution mass spectrometry(HRMS) and the chemical purity was determined to be >95% (fig. S5).

Inhibition of TTR amyloidogenesis by the HTS hits

To test whether the new TTR ligands (7.2 μM) could function as kinetic stabilizers, we measured their ability to inhibit TTR (3.6 μM) amyloidogenesis at 72 hrs at pH 4.4 (fig. S6) (29). All 33 compounds inhibited TTR aggregation (<50% fibril formation, table S2). Of these, 23 were very good (<20% fibril formation) and 11 were excellent (<2% fibril formation) TTR kinetic stabilizers (Fig. 3A). All of the potent TTR stabilizers, except niflumic acid, and the two COMT inhibitors 3,5-dintrocatechol and Ro 41-0960, were chemical entities with no previously reported biological activity. Since occupancy of only
one T4 binding site within TTR is sufficient for kinetic stabilization of the tetramer (3), we tested the most potent ligands at substoichiometric concentrations (2.4 fold molar excess of TTR relative to ligand) in a kinetic aggregation assay monitored over 5 days (Fig. 3B). Under these conditions ligands 7, 14, 15 and Ro 41-0960 dramatically slowed fibril formation and outperformed the known TTR stabilizer, diclofenac, which blocked only ~55% of TTR aggregation.

Evaluating the TTR ligands for COX-1 enzymatic inhibition and binding to thyroid hormone receptor

A successful clinical candidate against TTR amyloid cardiomyopathy should have minimal off-target toxicity due to the potential need for life-long use of these drugs. Specifically, the TTR ligands should exhibit minimal binding to COX and the nuclear thyroid hormone receptor (THR). Inhibition of COX is contraindicated for treating FAC patients, since COX inhibition can not only lead to renal dysfunction and blood pressure elevation, but may precipitate heart failure in vulnerable individuals (20, 21, 24, 25). Therefore, the most potent TTR ligands were evaluated for their ability to inhibit COX-1 activity, as well as, for binding to THR, in comparison with the NSAID niflumic acid. Although niflumic acid exhibited substantial (94%) COX-1 inhibition, three of the 12 new compounds evaluated (7, 6 and 10) displayed less than 1% inhibition of COX-1. Only one ligand (compound 8) showed significant (58%) and two compounds (6 and 10) minor (5%) binding to THR (Fig. 3C).

Characterization of the binding energetics to TTR

Many reported TTR ligands, including T4, bind TTR with negative cooperativity, which appears to arise from subtle conformational changes in TTR upon ligand binding to the first T4 site (3, 16, 36). We used ITC to determine the binding constants and to evaluate cooperativity between the two TTR T4 sites (Fig. 2A, Fig. 4A, Fig. 4B and fig. S1 and fig. S7). The ITC data for compounds 1, 7, 14, and Ro 41-0906 binding to TTR were fit to a two-site binding model and show that these potent ligands bind TTR with low nanomolar affinity. The dissociation constants for these ligands indicated that they bound TTR with negative cooperativity (table S3). Analysis of the free energies associated with ligand binding to TTR indicates that binding was driven both by burial of the hydrophobic ligand in the TTR binding site (which leads to the favorable binding entropies) and specific ligand-TTR interactions (which leads to the favorable binding enthalpies) (Fig. 2A, Fig. 4A, Fig.4B, and fig. S7B) (37). The binding of compounds 7 (Kd1 = 58 nM and Kd2 = 500 nM) and 14 (Kd1 = 26 nM and Kd2 = 1800 nM) to TTR did not cause major conformational changes to the TTR tetramer structure (Fig. 5).
Remainder of document is found at publication site, including Figures.
SOURCE

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Transthyretin and Lean Body Mass in Stable and Stressed State

Curator: Larry H Bernstein, MD, FCAP

Chapter 20
Plasma Transthyretin Reflects the Fluctuations
of Lean Body Mass in Health and Disease
Yves Ingenbleek
Abstract

Transthyretin (TTR) is a 55-kDa protein secreted mainly by the choroid plexus and the liver. Whereas its intracerebral production appears as a stable secretory process allowing even distribution of intrathecal thyroid hormones, its hepatic synthesis is influenced by nutritional and inflammatory circumstances working concomitantly. Both morbid conditions are governed by distinct pathogenic mechanisms leading to the reduction in size of lean body mass (LBM). The liver production of TTR integrates the dietary and stressful components of any disease spectrum, explaining why it is the sole plasma protein whose evolutionary patterns closely follow the shape outlined by LBM fluctuations. Serial measurement of TTR therefore provides unequalled information on the alterations affecting overall protein nutritional status. Recent advances in TTR physiopathology emphasize the detecting power and preventive role played by the protein in hyperhomocysteinemic states, acquired metabolic disorders currently ascribed to dietary restriction in water-soluble vitamins. Sulfur (S)-deficiency is proposed as an additional causal factor in the sizeable proportion of hyperhomocysteinemic patients characterized by adequate vitamin intake but experiencing varying degrees of nitrogen (N)-depletion. Owing to the fact that N and S coexist in plant and animal tissues within tightly related concentrations, decreasing LBM as an effect of dietary shortage and/or excessive hypercatabolic losses induces proportionate S-losses. Regardless of water-soluble vitamin status, elevation of homocysteine plasma levels is negatively correlated with LBM reduction and declining TTR plasma levels. These findings occur as the result of impaired cystathionine-b-synthase activity, an enzyme initiating the transsulfuration pathway and whose suppression promotes the upstream accumulation and remethylation of homocysteine molecules. Under conditions of N- and S-deficiencies,the maintenance of methionine homeostasis indicates high metabolic priority.
Y. Ingenbleek
Laboratory of Nutrition, University Louis Pasteur Strasbourg
e-mail: yves.ingenbleek@wanadoo.fr
S.J. Richardson and V. Cody (eds.), Recent Advances in Transthyretin Evolution, 329
Structure and Biological Functions,
DOI: 10.1007/978‐3‐642‐00646‐3_20, # Springer‐Verlag Berlin Heidelberg 2009

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Liver Toxicity halts Clinical Trial of IAP Antagonist for Advanced Solid Tumors

Curator: Stephen J. Williams, Ph.D.

UPDATED 8/12/2022

Athough not related to IAP Antagonists this update does report 2 deaths from IDILI or idiosynchratic drug induced liver injury from a gene therapy trial using an AAV (adeno associated virus) targeting the disease spinal muscular atrophy.  Please see below after reading about IDILI.

 

A recent press release on FierceBiotech reported the FDA had put a halt on a phase 1 study for advanced refractory solid tumors and lymphomas of Curis Inc. oral inhibitor of apoptosis (IAP) antagonist CUDC-427.  The FDA placed the trial on partial clinical hold following reports of a death of a patient from severe liver failure.  The single-agent, dose escalation Phase 1 study was designed to determine the maximum tolerated dose and recommended doses for a Phase 2 trial. The press release can be found at:

http://www.fiercebiotech.com/press-releases/curis-reports-third-quarter-2013-financial-results-and-provides-cudc-427-de.

According to the report one patient with breast cancer that had metastasized to liver, lungs, bone, and ovaries developed severe hepatotoxicity as evidenced by elevated serum transaminase activities (AST and ALT) and hyper-billirubinemia.  Serum liver enzyme activities did not attenuate upon discontinuation of CUDC-427.  This was unlike prior experience to the CUDC-427 drug, in which decreased hepatic function was reversed upon drug discontinuation.  The patient died from liver failure one month after discontinuation of CUDC-427.

It was noted that no other patient had experienced such a serious, irreversible liver dysfunction.

Although any incidence of hepatotoxicity can be cause for concern, the incidence of IDIOSYNCRATIC IRREVERSIBLE HEPATOTOXICITY warrants a higher scrutiny.

Four general concepts can explain toxicity profiles and divergences between individuals:

  1. Toxicogenomics: Small differences in the genetic makeup between individuals (such as polymorphisms (SNP) could result in differences in toxicity profile for a drug.  This ais a serious possibility as only one patient presented with such irreversible liver damage
  2. Toxicodynamics:  The toxicologic effect is an extension of the pharmacologic mechanism of action (or  lack thereof: could there have been alternate signaling pathways activated in this patient or noncanonical mechanism)
  3. Toxicokinetic:  The differences in toxicological response due to differences in absorption, distribution, metabolism, excretion etc. (kinetic parameters)
  4. Idiosyncratic: etiology is unknown; usually a minority of adverse effects

 

Since there is not enough information to investigate toxicogenomic or toxicokinetic mechanisms for this compound, the rest of this post will investigate the possible mechanisms of hepatotoxicity due to IAP antagonists and clues from other clinical trials which might shed light on a mechanism of toxicity (toxicodynamic) or idiosyncratic events.

Therefore this post curates the current understanding of drug-induced liver injury (DILI), especially focusing on a type of liver injury referred to as idiosyncratic drug-induced liver injury (IDILI) in the context of:

  1. Targeted and newer chemotherapies such as IAP antagonists
  2. Current concepts of mechanisms of IDILI including:

i)        Inflammatory responses provoked by presence of disease

ii)      Cellular stresses, provoked by disease, uncovering NONCANONICAL toxicity pathways

iii)    Pharmacogenomics risk factors of IDILI

Eventually this post aims to stimulate the discussion: 

  • Given inflammation, genetic risk factors, and cellular stresses (seen in clinical setting) have been implicated in idiosyncratic drug-induced liver injury from targeted therapies, should preclinical hepatotoxicity studies also be conducted in the presence of the metastatic disease?
  • Does inflammation and cellular stress from clinical disease unmask NONCANONICAL pharmacologic and/or toxicological mechanisms of action?

Classification of types of Cellular Liver injury:  A listing of types of cellular injury is given for review

I.     Hepatic damage after Acute Exposure

A. Cytotoxic (Necrotic):  irreversible cell death characterized by loss of cell membrane integrity, intracellular swelling, nuclear shrinkage (pyknosis) and eventual cytoplasmic breakdown of nuclear DNA (either by a process known as karyolysis or karyorhexus) localized inflammation as a result of release of cellular constituents.  Intracellular ATP levels are commonly seen in necrotic death.  Necrosis, unlike apoptosis, does not require a source of ATP.  A nice review by Yoshihide Tsujimoto describing and showing (by microscopy) the  differences between apoptosis and necrosis can be found here.

B. Cholestatic:  hepatobiliary dysfunction with bile stasis and accumulation of bile salts.  Cholestatic injury can result in lipid (particularly cholesterol) accumulation in cannicular membranes resulting in decreased permeability of the membrane, hyperbillirubinemia and is generally thought to result in metabolic defects.

C. Lipid Peroxidation: free radical generation producing peroxide of cellular lipids, generally resulting in a cytotoxic cell death

II.     Hepatic damage after Chronic Exposure

A. Chirrotic: Chronic morphologic alteration of the liver characterized by the presence of septae of collagen distributed throughout the major portion of the liver; Forms fibrous sheaths altering hepatic blood flow, resulting in a necrotic process with scar tissue; Alteration of hepatic metabolic systems.

B. Carcinogenesis

III. Idiosyncratic Drug Induced Liver Injury

The aforementioned mechanisms of hepatotoxicity are commonly referred to as the “intrinsic” (or end target-organ) toxicity mechanisms.  Idiosyncratic drug-induced liver injury (IDILI) is not well understood but can be separated into allergic and nonallergic reactions.  Although the risk of acute liver failure associated with idiosyncratic hepatotoxins is low (about 1 in ten thousand patients) there are more than 1,000 drugs and herbal products associated with this type of toxic reaction. Idiosyncratic drug induced liver failure usually gets a black box warning from the FDA. Idiosyncratic drug-induced liver injury differs from “intrinsic” toxicity in that IDILI:

  • Happens in a minority of patients (susceptible patients)
  • Not reproducible in animal models
  • Not dose-dependent
  • Variable time of onset
  • Variable liver pathology (not distinctive lesions)
  • Not related to drug’s pharmacologic mechanism of action (trovafloxacin IDILI vs. levofloxacin)

A great review in Perspectives in Pharmacology written by Robert Roth and Patricia Ganey at Michigan State University explains these differences between intrinsic and idiosyncratic drug-induced hepatotoxicity[1] (however authors do note that there are many similarities between the two mechanisms).    It is felt that drug sensitivity (allergic) and inflammatory responses (nonallergic) may contribute to the occurrence of IDILI.  For instance lipopolysaccharide (LPS) form bacteria can potentiate acetaminophen toxicity.  In fact animal models of IDILI have been somewhat successful:

  • co-treatment of rats and mice with nontoxic doses of trovafloxacin (casues IDILI in humans) and LPS resulted in marked hepatotoxicity while no hepatotoxicity seen with levofloxacin plus LPS[2]
  • correlates well with incidence of human IDILI (adapted from a review Inflammatory Stress and Idiosyncratic Hepatotoxicity: Hints from Animal Models (in Pharmacology Reviews)[3].  Idiosyncratic injury damage has been reported for diclofenac, halothane, and sulinac.  These drugs also show hepatotoxicity in the LPS model for IDILI.
  • Roth and Ganey suggest the reason why idiosyncratic hepatotoxicity is not seen  in most acute animal toxicity studies is that, in absence of stress/inflammation  IDILI occurrence is masked by lethality but stress/inflammation shifts increases sensitivity to liver injury at a point before lethality is seen

IDILdosestressrossmantheory

Figure.  Idiosyncratic toxic responses of the liver.    In the absence of stress and/or genetic factors, drug exposure may result in an idiosyncratic liver injury (IDILI) at a point (or dose) beyond the therapeutic range and lethal exposure for that drug.  Preclinical studies, usually conducted at sublethal doses, would not detect DILI .  Stress and/or genetic factors sensitize the liver to toxic effects of the drug (synergism) and DILI is detected at exposure levels closer to therapeutic range.  Note IDILI is not necessarily dose-dependent but cellular stress (like ROS or inflammation) may expose NONCANONICAL mechanisms of drug action or toxicity which result in IDILI. Model adapted from Roth and Ganey.

What Stress factors contribute to IDILI?

Various stresses including inflammation from bacterial, viral infections ,inflammatory cytokines  and stress from reactive oxygen (ROS) have been suggested as mechanisms for IDILI.

  1. Inflammation/Cytokines (also discussed in other sections of this post):  Inflammation has long been associated with human cases of DILI.    Many cytokines and inflammatory mediators have been implicated including TNFα, IL7, TGFβ, and IFNϒ (viral infection) leading some to conclude that serum measurement of cytokines could be a potential biomarker for DILI[4].  In addition, ROS (see below) is generated from inflammation and also considered a risk factor for DILI[5].
  2. Reactive Oxygen (ROS)/Reactive Metabolites: Oxidative stress, either generated from reactive drug metabolites or from mitochondrial sources, has been shown to be involved in apoptotic and necrotic cell death.  Both alterations in the enzymes involved in the generation of and protection from ROS have been implicated in increased risk to DILI including (as discussed further) alterations in mitochondrial superoxide dismutase 2 (SOD2) and glutathione S-transferases.  Both ROS and inflammatory cytokines can promote JNK signaling, which has been implicated in DILI[6].

Dr. Neil Kaplowitz suggested that we:

“develop a unifying hypothesis that involves underlying genetic or acquired mitochondrial abnormalities as a major determinant of susceptibility for a number of drugs that target mitochondria and cause DILI. The mitochondrial hypothesis, implying gradually accumulating and initially silent mitochondrial injury in heteroplasmic cells which reaches a critical threshold and abruptly triggers liver injury, is consistent with the findings that typically idiosyncratic DILI is delayed (by weeks or months), that increasing age and female gender are risk factors and that these drugs are targeted to the liver and clearly exhibit a mitochondrial hazard in vitro and in vivo. New animal models (e.g., the Sod2(+/-) mouse) provide supporting evidence for this concept. However, genetic analyses of DILI patient samples are needed to ultimately provide the proof-of-concept”[7].

Clin Infect Dis. 2004 Mar 38(Supplement 2) S44-8, Figure 1

Clin Infect Dis. 2004 Mar 38(Supplement 2) S44-8, Figure 3

Figures. Mechanisms of Drug-Induced Liver Injury and Factors related to the occurrence of  DILI (used with permission from Oxford Press; reference [7])

To this end, Dr. Brett Howell and other colleagues at the Hamner-UNC Institute for Drug Safety Sciences (IDSS) developed an in-silico model of DILI ( the DILISym™ model)which is based on  depletion of cellular ATP and reactive metabolite formation as indices of DILI.

Have there been Genetic Risk Factors identified for DILI?

Candidate-gene-associated studies (CGAS) have been able to identify several genetic risk factors for DILI including:

  1. Uridine Diphosphate Glucuronosyltransferase 2B7 (UGT2B7): variant increased susceptibility to diclofenac-induced DILI
  2. Adenosine triphosphate-binding cassette C2 (ABCC2) variant ABCC-24CT increased susceptibility to diclofenac-induced DILI
  3. Glutathione S-transferase (GSTT1): patients with a double GSTT1-GSTM1 null genotype had a significant 2.7 fold increased risk of DILI from nonsteroidal anti-inlammatory agents, troglitazone and tacrine.  GSTs are involved in the detoxification of phase 1 metabolites and also protect against cellular ROS.

Although these CGAS confirmed these genetic risk factors,  Stefan Russman suggests a priori genome-wide association studies (GWAS) might provide a more complete picture of genetic risk factors for DILI as CGAS is limited due to

  1. Candidate genes are selected based on current mechanisms and knowledge of DILI so genetic variants with no known knowledge of or mechanistic information would not be detected
  2. Many CGAS rely on analysis of a limited number of SNP and did not consider intronic regions which may control gene expression

A priori GWAS have the advantage of being hypothesis-free, and although they may produce a high number of false-positives, new studies of genetic risk factors of ximelagatran, flucioxaciliin and diclofenac-induced liver injury are using a hybrid approach which combines the whole genome and unbiased benefits of GWAS with the confirmatory and rational design of CGAS[8-10].

Even though idiosyncratic DILI is rare, the severity, unpredictable onset, and unknown etiology and risk factors have prompted investigators such as Stefan Russmann from University Hospital Zurich and Ignazio Grattagliano from University of Bari to suggest:

Identification of risk factors for rare idiosyncratic hepatotoxicity requires special networks that contribute to data collection and subsequent identification of environmental as well as genetic risk factors for clinical cases of idiosyncratic DILI[11].

Therefore, a DILI network project (DILIN) had been developed to collect samples and detailed genetic and clinical data on IDILI cases from multiple medical centers.  The project aims to identify the upstream and downstream genetic risk factors for IDILI[12].  Please see a SlideShare presentation here of the goals of the DILI network project.

Drs Colin Spraggs and Christine Hunt had reviewed possible genetic risk factors of DILI seen with various tyrosine kinase inhibitors (TKIs) including Lapatinib (Tykerb/Tyverb©, a dual inhibitor of  HER2/EGFR heterodimer) and paopanib (Votrient©; a TKI that targets VEGFR1,2,3 and PDGFRs)[13].

From a compilation of studies:

  • Elevation in serum bilirubin during treatment with lapatinib and pazopanib are associated with UGT1A1 polymorphism related to Gilbert’s syndrome (a clinically benign syndrome)
  • Anecdotal evidence shows that polymorphisms of lapatinib and pazopanib metabolizing enzymes may contribute to differences seen in onset of DILI
  • Pazopanib-induced elevations of ALT correlate with HFE variants, suggesting alterations in iron transport may predispose to DILI
  • Strong correlations between lapatinib-induced DILI and class II HLA locus suggest inflammatory stress response important in DILI

Note that these clinical findings were not evident from the preclinical tox studies. According to the European Medicines Agency assessment report for Tykerb states: “the major findings in repeat dose toxicity studies were attributed to lapatinib pharmacology (epithelial effect in skin and GI system.  The toxic events occurred at exposures close to the human exposure at the recommended dose.  Repeat-dose toxicity studies did not reveal important safety concerns than what would be expected from the mode of action”.

However, it should be noted that in high dose repeat studies in mice and rats, severe lethality was seen with hematologic, gastrointestinal toxicities in combination with altered blood chemistry parameters and yellowing of internal organs.

IAP Antagonists, Mechanism of Action, and Clinical Trials:

A few IAP antagonists which are in early stage development include:

  • Norvatis IAP Inhibitor LCL161: at 2012 San Antonia Breast Cancer Symposium, a phase 1 trial in triple negative breast cancer showed promising results when given in combination with paclitaxel.
  • Ascenta Therapeutics IAP inhibitor AT-406 in phase 1 in collaboration with Debiopharm S.A. showed antitumor efficacy in xenograft models of breast, pancreatic, prostate and lung cancer. The development of this compound is described in a paper by Cai et. al.

National Cancer Institute sponsored trials using antagonists of IAPs include

  • Phase II Study of Birinapant for Advanced Ovarian, Fallopian Tube, and Peritoneal Cancer (NCI-12-C-0191). Principle Investigator: Dr. Christina Annunziata. See the protocol summary. More open trials for this drug are located here.  Closed trials including safety studies can be found here.
  • A Phase 1 non-randomized dose escalation study to determine maximum tolerated dose (MTD) and characterize the safety for the TetraLogic compound TL32711 had just been completed. Results have not been published yet.
  • Closed Clinical trials with the IAP antagonist HGS1029 in advanced solid tumors determined that weekly i.v. administration of HGS1029 reported a safety issue for primary outcome measures

A great review on IAP proteins and their role as regulators of apoptosis and potential targets for cancer therapy [14] can be found as a part of a Special Issue in Experimental Oncology “Apoptosis: Four Decades Later”.  Human IAPs (inhibitors of apoptosis) consist of eight proteins involved in cell death, immunity, inflammation, cell cycle, and migration including:

In general, IAP proteins are directly involved in inhibiting apoptosis by binding and directly inhibiting the effector cysteine protease caspases (caspase 3/7) ultimately responsible for the apoptotic process [15].  IAPs were actually first identified in baculoviral genomes because of their ability to suppress host-cell death responses during viral infection [16]. IAP proteins are often overexpressed in cancers [17].

Apoptosis is separated into two pathways, defined by the initial stress or death signal and the caspases involved:

  1. Extrinsic pathway: initiated by TNFα and death ligand FasLigand;  involves caspase-8; process inhibited by IAP1/2
  2. Intrinsic pathway: initiated by DNA damage, irradiation, chemotherapeutics; mitochondrial pathway involving caspase 9 and cytochrome c release from mitochondria; mitochondria also releases SMAC/DIABLO, which binds and inhibits XIAP (XIAP inhibits the Intrinsic apoptotic pathway.

 intrinsicextrinsicapoptosiswikidot

 

Intrinsic and Extrinsic pathways of apoptosis. Figure photocredit (wikidot.com)

The Curis IAP antagonist (and others) is a SMAC small molecule mimetic. It is interesting to note [18, 19] that IAP antagonists can result in death by

  • Apoptosis: an IAP antagonist in presence of competent TNFα signaling
  • Necrosis: seen with IAP inhibitors in cells with altered TNFα signaling or with presence of caspase inhibitors

IAPs are also involved in the regulation of signaling pathways such as:

NF-ΚB signaling pathway

NF-ΚB is a “rapid-acting” transcription factor which has been found to be overexpressed in various cancers.  Under most circumstances NF-ΚB translocation to the nucleus results in transcription of genes related to cell proliferation and survival.  NF-ΚB signaling is broken down in two pathways

  1. Canonical:  Canonical pathway can be initiated (for example in inflammation) when TNF-α binds its receptors activating  death domains (TRADD)
  2. Noncanonical: since requires new protein synthesis takes longer than canonical signaling.  Can be initiated by other TNF like ligands like CD40

IAP1/2 is a negative regulator of the noncanonical NF-ΚB signaling pathway by promoting proteosomal degradation of the TRAF signaling complex. A wonderfully annotated list of NF-ΚB target genes can be found on the Thomas Gilmore lab site at Boston University at http://www.bu.edu/nf-kb/gene-resources/target-genes/ .

NF-ΚB has been considered a possible target for chemotherapeutic development however Drs. Veronique Baud and Michael Karin have pondered the utility of IAP antagonists as a good target in their review: Is NF-ΚB a good target for cancer therapy?: Hopes and pitfalls [20].  The authors discuss issues such that IAP antagonism induced both the classical and noncanonical NF-ΚB pathway thru NIK stabilization, resulting in stabilization of NF-ΚB signaling and thereby undoing any chemotherapeutic effect which would be desired.

AKT signaling

IAPs have been shown to interact with other proteins including a report that SIAP regulates AKT activity and caspase-3-dependent cleavage during cisplatin-induced apoptosis in human ovarian cancer cells and could be another mechanism involved in cisplatin resistance[21].   In addition there have been reports that IAPs can regulate JNK and MAPK signaling.

Therefore, IAPs are involved in CANONICAL and NONCANONICAL pathways.

IAPs can Regulate Pro-Inflammatory Cytokines

A recent 2013 JBC paper [22]showed that IAPs and their antagonists can regulate spontaneous and TNF-induced proinflammatory cytokine and chemokine production and release

  • IAP required for production of multiple TNF-induced proinflammatory mediators
  • IAP antagonism decreased TNF-mediated production of chemokines and cytokines
  • But increased spontaneous release of chemokines

In addition Rume Damgaard and Mads Gynd-Hansen have suggested that IAP antagonists may be useful in treating inflammatory diseases like Crohn’s disease as IAPs regulate innate and acquired immune responses[23].

Toxicity profiles of IAP antagonists

NOTE: In a paper in Toxicological Science from 2012[24], Rebecca Ida Erickson form Genentech reported on the toxicity profile of the IAP antagonist GDC-0152 from a study performed in dogs and rats. A dose-dependent toxicity profile from i.v. administration was consistent with TNFα-mediated toxicity with

  • Elevated plasma cytokines and an inflammatory leukogram
  • Increased serum transaminases
  • Inflammatory infiltrate and apoptosis/necrosis in multiple tissues

In a related note, a similar type of fatal idiosyncratic hepatotoxicity was reported in a 62 year-old man treated with the Raf kinase inhibitor sorafenib for renal cell carcinoma[25]: Fatal case of sorafenib-associated idiosyncratic hepatotoxicity in the adjuvant treatment of a patient with renal cell carcinoma; Case Report  in BMC Cancer.

At week four after initiation of sorafenib treatment, the patient noticed increasing fatigue, malaise, gastrointestinal discomfort and abdominal rash.  Although treatment was discontinued, jaundice developed and blood test revealed an acute hepatitis with

  • Elevated serum ALT
  • Elevated serum alkaline phosphatase
  • Increased prothrombin time
  • Increased LDH

…elevated levels seen in the case with the aforementioned IAP antagonist.  Autopsy revealed

  • Lobular hepatitis
  • Mononuclear cell infiltrate
  • Hepatocyte necrosis

These findings are in line with a drug-induced inflammation and IDILI. In addition to hepatotoxicity, renal insufficiency developed in this patient. The authors had suggested the death was probably due to “an idiosyncratic allergic reaction to sorafenib manifesting as hepatotoxicity with associated renal impairment”.  The authors also noted that genome wide association studies of idiosyncratic drug-induced liver injury support involvement of major histocompatibility complex (MHC) polymorphisms[26].  MHC involvement has also been associated with lapatanib and pazopanib hepatotoxicity [27, 28].

Curis has been involved in another novel oncology therapeutic, a first in class.

Last year Roche and Genentech had won approval for a Hedgehog pathway inhibitor vismodegib for treatment of advanced basal cell carcinoma (reported at FierceBiotech©). Vismodegib was initially developed in collaboration with Curis, Inc.  The hedgehog signaling pathway, which controls the function of Gli factors (involved in stem cell differentiation), is overactive in advanced basal cell carcinoma as well as other cancer types.

As an additional reference, the FDA National Center for Toxicological Research has developed THE LIVER TOXICITY KNOWLEDGE BASE (LTKB).

“The LTKB is a project designed to study drug-induced liver injury (DILI). Liver toxicity is the most common cause for the discontinuation of clinical trials on a drug, as well as the most common reason for an approved drug’s withdrawal from the marketplace. Because of this, DILI has been identified by the FDA’s Critical Path Initiatives as a key area of focus in a concerted effort to broaden the agency’s knowledge for better evaluation tools and safety biomarkers.”

A nice SlideShow of Toxicity of Targeted Therapies can be found here: http://www.slideshare.net/RashaHaggag/toxicities-of-targeted-therapies

Also please note that ALL GENES in this article are linked to their GENECARD 

UPDATED 8/12/2022

 

Zolgensma Gene Therapy Linked to 2 Deaths in SMA Patients, Novartis Reports

The 2 deaths, due to acute liver failure, occurred in patients treated in Kazakhstan and Russia.

Two children with spinal muscular atrophy (SMA) have died after being treated with onasemnogene abeparvovec (Zolgensma; Novartis) from acute liver failure, a known safety risk of the therapy.1

Novartis has updated the FDA and other regulatory agencies in countries that Zolgensma is approved in, including Russia and Kazakhstan, where the deaths occurred. The company will also update the labeling of Zolgensma to include the deaths.

“While this is important safety information, it is not a new safety signal and we firmly believe in the overall favorable risk/benefit profile of Zolgensma, which to date has been used to treat more than 2300 patients worldwide across clinical trials, managed access programs, and in the commercial setting,” Novartis said in an emailed statement to BioPharma Dive.2

Zolgensma’s labeling includes the risk of liver injury and instructs clinicians to assess liver function before treatment and to manage liver enzyme counts with steroid treatment. The 2 deaths occurred 5 to 6 weeks after the one-time infusion and 1 to 10 days after corticosteroid treatment was tapered, according to an initial report from Stat News.1

READ MORE: Zolgensma Shows Efficacy in SMA With 3 SMN2 Copies

An FDA advisory committee meeting that took place last fall identified risks of adeno associated virus (AAV) gene therapies including, specifically, Zolgensma.2 The committee recommended caution, but nothing that would hinder gene therapy development.

Zolgensma, which was approved in the US in May 2019, just recently demonstrated further positive data from SPR1NT (NCT03505099), a phase 3 multicenter, single-arm trial on its effect in presymptomatic children with SMA in 2 articles published in Nature Medicine.3,4

All children in both the type 1 and type 2 cohorts achieved the ability to independently sit and most achieved other age-appropriate milestones including standing and walking. None of the children in the study required respiratory support or nutritional support, and there were no serious treatment-related adverse events observed.

“The robust data from both the 2- and 3-copy SPR1NT cohorts are being published together for the first time, further supporting the significant and clinically meaningful benefit of Zolgensma in presymptomatic babies with SMA,” Shephard Mpofu, MD, SVP, chief medical officer, Novartis Gene Therapies, said in a previous statement.5 “When treated with Zolgensma prior to the onset of symptoms, not only did all 29 patients enrolled in SPR1NT survive, but were thriving—breathing and eating on their own, with most even sitting, standing, and walking without assistance.”

REFERENCE

1. Silverman E. Novartis reports two children died from acute liver failure after treatment with Zolgensma gene therapy. STAT. August 11, 2022. https://www.statnews.com/pharmalot/2022/08/11/novartis-zolgensma-liver-failure-gene-therapy-death/

2. Pagliarulo N. Novartis reports deaths of two patients treated with Zolgensma gene therapy. BioPharma Dive. August 12, 2022. https://www.biopharmadive.com/news/novartis-zolgensma-patient-death-liver-injury/629542/

3. Strauss KA, Farrar MA, Muntoni F, et al. Onasemnogeneabeparvovec for presymptomatic infants with two copies of SMN2 at risk for spinal muscular atrophy type 1: the Phase III SPR1NT trial. Nat Med. Published online June 17, 2022. doi:10.1038/s41591-022-01866-42

4. Strauss KA, Farrar MA, Muntoni F, et al. Onasemnogeneabeparvovec for presymptomatic infants with three copies of SMN2 at risk for spinal muscular atrophy: the Phase III SPR1NT trial. Nat Med. Published online June 17, 2022.doi: 10.1038/s41591-022-01867-3

5. Novartis announces Nature Medicine publication of Zolgensma data demonstrating age-appropriate milestones when treating children with SMA presymptomatically. News release. Novartis. June 17, 2022. https://firstwordpharma.com/story/5597735

 

REFERENCES

1.            Roth RA, Ganey PE: Intrinsic versus idiosyncratic drug-induced hepatotoxicity–two villains or one? The Journal of pharmacology and experimental therapeutics 2010, 332(3):692-697.

2.            Waring JF, Liguori MJ, Luyendyk JP, Maddox JF, Ganey PE, Stachlewitz RF, North C, Blomme EA, Roth RA: Microarray analysis of lipopolysaccharide potentiation of trovafloxacin-induced liver injury in rats suggests a role for proinflammatory chemokines and neutrophils. The Journal of pharmacology and experimental therapeutics 2006, 316(3):1080-1087.

3.            Deng X, Luyendyk JP, Ganey PE, Roth RA: Inflammatory stress and idiosyncratic hepatotoxicity: hints from animal models. Pharmacological reviews 2009, 61(3):262-282.

4.            Laverty HG, Antoine DJ, Benson C, Chaponda M, Williams D, Kevin Park B: The potential of cytokines as safety biomarkers for drug-induced liver injury. European journal of clinical pharmacology 2010, 66(10):961-976.

5.            Schwabe RF, Brenner DA: Mechanisms of Liver Injury. I. TNF-alpha-induced liver injury: role of IKK, JNK, and ROS pathways. American journal of physiology Gastrointestinal and liver physiology 2006, 290(4):G583-589.

6.            Seki E, Brenner DA, Karin M: A liver full of JNK: signaling in regulation of cell function and disease pathogenesis, and clinical approaches. Gastroenterology 2012, 143(2):307-320.

7.            Kaplowitz N: Drug-induced liver injury. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2004, 38 Suppl 2:S44-48.

8.            Kindmark A, Jawaid A, Harbron CG, Barratt BJ, Bengtsson OF, Andersson TB, Carlsson S, Cederbrant KE, Gibson NJ, Armstrong M et al: Genome-wide pharmacogenetic investigation of a hepatic adverse event without clinical signs of immunopathology suggests an underlying immune pathogenesis. The pharmacogenomics journal 2008, 8(3):186-195.

9.            Aithal GP, Ramsay L, Daly AK, Sonchit N, Leathart JB, Alexander G, Kenna JG, Caldwell J, Day CP: Hepatic adducts, circulating antibodies, and cytokine polymorphisms in patients with diclofenac hepatotoxicity. Hepatology 2004, 39(5):1430-1440.

10.          Daly AK, Aithal GP, Leathart JB, Swainsbury RA, Dang TS, Day CP: Genetic susceptibility to diclofenac-induced hepatotoxicity: contribution of UGT2B7, CYP2C8, and ABCC2 genotypes. Gastroenterology 2007, 132(1):272-281.

11.          Russmann S, Kullak-Ublick GA, Grattagliano I: Current concepts of mechanisms in drug-induced hepatotoxicity. Current medicinal chemistry 2009, 16(23):3041-3053.

12.          Fontana RJ, Watkins PB, Bonkovsky HL, Chalasani N, Davern T, Serrano J, Rochon J: Drug-Induced Liver Injury Network (DILIN) prospective study: rationale, design and conduct. Drug safety : an international journal of medical toxicology and drug experience 2009, 32(1):55-68.

13.          Spraggs CF, Xu CF, Hunt CM: Genetic characterization to improve interpretation and clinical management of hepatotoxicity caused by tyrosine kinase inhibitors. Pharmacogenomics 2013, 14(5):541-554.

14.          de Almagro MC, Vucic D: The inhibitor of apoptosis (IAP) proteins are critical regulators of signaling pathways and targets for anti-cancer therapy. Experimental oncology 2012, 34(3):200-211.

15.          Deveraux QL, Takahashi R, Salvesen GS, Reed JC: X-linked IAP is a direct inhibitor of cell-death proteases. Nature 1997, 388(6639):300-304.

16.          Crook NE, Clem RJ, Miller LK: An apoptosis-inhibiting baculovirus gene with a zinc finger-like motif. Journal of virology 1993, 67(4):2168-2174.

17.          Tamm I, Kornblau SM, Segall H, Krajewski S, Welsh K, Kitada S, Scudiero DA, Tudor G, Qui YH, Monks A et al: Expression and prognostic significance of IAP-family genes in human cancers and myeloid leukemias. Clinical cancer research : an official journal of the American Association for Cancer Research 2000, 6(5):1796-1803.

18.          Laukens B, Jennewein C, Schenk B, Vanlangenakker N, Schier A, Cristofanon S, Zobel K, Deshayes K, Vucic D, Jeremias I et al: Smac mimetic bypasses apoptosis resistance in FADD- or caspase-8-deficient cells by priming for tumor necrosis factor alpha-induced necroptosis. Neoplasia 2011, 13(10):971-979.

19.          He S, Wang L, Miao L, Wang T, Du F, Zhao L, Wang X: Receptor interacting protein kinase-3 determines cellular necrotic response to TNF-alpha. Cell 2009, 137(6):1100-1111.

20.          Baud V, Karin M: Is NF-kappaB a good target for cancer therapy? Hopes and pitfalls. Nature reviews Drug discovery 2009, 8(1):33-40.

21.          Asselin E, Mills GB, Tsang BK: XIAP regulates Akt activity and caspase-3-dependent cleavage during cisplatin-induced apoptosis in human ovarian epithelial cancer cells. Cancer research 2001, 61(5):1862-1868.

22.          Kearney CJ, Sheridan C, Cullen SP, Tynan GA, Logue SE, Afonina IS, Vucic D, Lavelle EC, Martin SJ: Inhibitor of apoptosis proteins (IAPs) and their antagonists regulate spontaneous and tumor necrosis factor (TNF)-induced proinflammatory cytokine and chemokine production. The Journal of biological chemistry 2013, 288(7):4878-4890.

23.          Damgaard RB, Gyrd-Hansen M: Inhibitor of apoptosis (IAP) proteins in regulation of inflammation and innate immunity. Discovery medicine 2011, 11(58):221-231.

24.          Erickson RI, Tarrant J, Cain G, Lewin-Koh SC, Dybdal N, Wong H, Blackwood E, West K, Steigerwalt R, Mamounas M et al: Toxicity profile of small-molecule IAP antagonist GDC-0152 is linked to TNF-alpha pharmacology. Toxicological sciences : an official journal of the Society of Toxicology 2013, 131(1):247-258.

25.          Fairfax BP, Pratap S, Roberts IS, Collier J, Kaplan R, Meade AM, Ritchie AW, Eisen T, Macaulay VM, Protheroe A: Fatal case of sorafenib-associated idiosyncratic hepatotoxicity in the adjuvant treatment of a patient with renal cell carcinoma. BMC cancer 2012, 12:590.

26.          Daly AK: Drug-induced liver injury: past, present and future. Pharmacogenomics 2010, 11(5):607-611.

27.          Spraggs CF, Budde LR, Briley LP, Bing N, Cox CJ, King KS, Whittaker JC, Mooser VE, Preston AJ, Stein SH et al: HLA-DQA1*02:01 is a major risk factor for lapatinib-induced hepatotoxicity in women with advanced breast cancer. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2011, 29(6):667-673.

28.          Xu CF, Reck BH, Goodman VL, Xue Z, Huang L, Barnes MR, Koshy B, Spraggs CF, Mooser VE, Cardon LR et al: Association of the hemochromatosis gene with pazopanib-induced transaminase elevation in renal cell carcinoma. Journal of hepatology 2011, 54(6):1237-1243.

Other articles on the site about Toxicology and Pharmacology of New Classes of Cancer Chemotherapy include:

FDA Guidelines For Developmental and Reproductive Toxicology (DART) Studies for Small Molecules

Gamma Linolenic Acid (GLA) as a Therapeutic tool in the Management of Glioblastoma

DNA Methultransferases – Implications to Epigenetic Regulation and Cancer Therapy Targeting: James Shen, PhD

Molecular Profiling in Cancer Immunotherapy: Debraj GuhaThakurta, PhD

AT13148 – A Novel Oral Multi-AGC Kinase Inhibitor Has Potent Antitumor Activity

Targeting Mitochondrial-bound Hexokinase for Cancer Therapy

Breast Cancer, drug resistance, and biopharmaceutical targets

Ubiquitin-Proteosome pathway, Autophagy, the Mitochondrion, Proteolysis and Cell Apoptosis: Part III

Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Read Full Post »

Cocoa and Heart Health

Reporter: Larry H. Bernstein, MD, FCAP

Nutrients 2013, 5(10), 3854-3870;   http://dx.doi.org/10.3390/nu5103854

Cocoa and Heart Health: A Historical Review of the Science

Deanna L. Pucciarelli

Department of Family and Consumer Sciences, Ball State University, Muncie, IN

Accepted: 11 September 2013 / Published: 26 September 2013

(This article belongs to the Special Issue Chocolate and Cocoa in Human Health)

Download PDF Full-Text[263 KB, uploaded 26 September 2013

Abstract: The medicinal use of cocoa has a long history dating back almost five hundred years when Hernán Cortés’s first experienced the drink
in Mesoamerica.  Doctors in Europe recommended the beverage to patients in the 1700s, and later American physicians followed suit  and prescribed the drink in early America—ca. 1800s.  This article delineates the historic trajectory of cocoa consumption, the linkage between cocoa’s bioactive-
mechanistic properties, paying special attention to

  • nitric oxides role in vasodilation of the arteries,
  • to the current indicators purporting the benefits of cocoa and cardiovascular health.

Keywords: cocoa; heart-health; nitric oxide; cardiovascular disease; medical history

Pucciarelli, D.L. Cocoa and Heart Health: A Historical Review of the Science. Nutrients 2013; 5(10): 3854-3870.

Comment

Aldujaili Emad

Senior Lecturer at Queen Margaret University

This review highlights the beneficial effect of dark chocolate intake on CVD risk factors. We have been doing trials
on dark chocolate
since 2007 studying its effects on several risk factors influencing the heart function such as

  • blood pressure, 
  • BMI, 
  • insulin resistancce
  • and body fat. 

It is important here to emphasize the issue of what type of dark chocolate is the most beneficial? Not every dark
chocolate in the market is useful. It depends on the processing. some methods destroy the polyphenols and therefore
reduce the benefits. Below some
of our publications using the Barry Callebaut chocolate produced by the Acticoa process:

S. Almoosawi, C. Tsang, L. M. Ostertag, L. Fyfe and E. A. S. Al-Dujaili (2012) Differential effect of polyphenol-rich
dark chocolate on
biomarkers of glucose metabolism and cardiovascular risk factors in healthy, overweight and obese subjects: a randomized clinical trial.Food and Function.
Cite this: http://dx.doi.org/10.1039/c2fo30060e. This journal is of The Royal Society of Chemistry 2012


Almoosawi, Suzana and Fyfe, Lorna and Ho, Clement and Al-Dujaili, Emad A S (2010) The effect of polyphenol-rich dark
chocolate on fasting
capillary whole blood glucose, total cholesterol, blood pressure and glucocorticoids in healthy overweight and obese subjects.
British Journal of Nutrition 2010;103(6):842-850. ISSN 0007-1145

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Author: Tilda Barliya PhD

Metastasis is a complex series of steps in which cancer cells leave the original tumor site and migrate to a distant organ. Certain cancers tend to spread to specific organ sites; however, the underlying mechanism is not completely understood. After lymph nodes, the liver is the most common site for colorectal cancer metastasis, and liver metastasis is a common cause of cancer-related mortality. Understanding the mechanisms and genetic alterations that predispose to the metastatic phenotype in colorectal cancer is imperative for early detection, prevention and treatment (1). Studies reveal that genomic instability in cancer cells leads to cellular heterogeneity, which may guide tumor cell aggression and specific organ colonization during the metastatic process.

Nat Clin Pract Oncol. 2008;5(4):206-219.

In 2008, Patricia S Steeg, Dan Theodorescu have published a great overview on the cancer metastases (1a).  Figure 1 represents Molecular distinctions between primary colorectal carcinomas and their liver metastases.

Studies have identified distinct expression trends at the RNA or protein levels in primary tumors and metastases, including genes that control metastasis (MTA1, N-Wasp, NCAML1), extracellular matrix function (fibronectin, collagens), microtubule dynamics (stathmin), transcription (Snail), drug-processing enzymes (DPD, TS) and kinases (Yes1).

It is worth mentioning that not every overexpressed or mutated gene is directly and primarily correlated with tumor metastases.

In order to answer this question, Ding Q and colleagues (1b) have done a great job identifying the gene expression signature for colorectal cancer liver metastases. Using an orthotopic colorectal cancer mouse model and transcriptomic microarray analysis, they found that 4 major genes are essential in mediating CRC-liver metastasesAPOBEC3GCD133LIPC, and S100P.

APOBEC3G– Is an apolipoprotein B mRNA-editing enzyme that has been suggested to play a role in the innate anti-viral immune system. Notably, this is the first time it has been shown that APOBEC3G, a gene involved in RNA editing, is able to promote tumor metastasis. APOBEC3G may downregulate miR-29 expression and hamper miR-29 activity in repressing MMP2.

CD133 – is a glycoprotein that is expressed in hematopoetic stem cells, endothelial progenitor cells, intestinal stem cells as well as saeveral types of tumor stem cells. It was related to a high incidence of metastasis in cholangiocarcinoma and melanoma has been indicated, However, questions regarding how CD133 is involved in metastasis and in which cancer stages, how CD133 expression is regulated, and what controls the transition of CD133+ to CD133– cells remain to be addressed.

LIPC –  is Hepatic Triacylglycerol Lipase. It is expressed in the liver and adrenal gland. One of the principal functions of hepatic lipase is to convert intermediate-low density lipoprotein (IDL) to low-density lipoprotein (LDL). A recent study also implicates a role for monoacylglycerol lipase in promoting tumor growth, migration, and invasion, as this lipase translates lipogenic phenotype to oncogenic signals in tumor cells.

S100P –  S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation.  This protein may paly a role in the etiology of prostate cancer.

The authors (1b) found that overexpressing of these 4 genes increases the invasion and migration abilities of the SW620-control cells (= lymph node metastatic cell line) in vitro and also significantly enhances the frequency of hepatic metastasis in vivo (1b).

To determine the clinical correlation of our identified gene signatures with colorectal cancer hepatic metastasis, the authors examined the protein levels of APOBEC3GCD133LIPC, and S100P in 7 freshly isolated human colorectal cancer hepatic metastatic tumors and 7 nonmetastatic primary colorectal carcinomas. We showed that expression levels of these 4 genes are significantly increased in the metastatic tumors compared with the nonmetastatic primary tumors (1b).

Knocking down either one of these genes was not sufficient to decrease the liver metastasis rate in the orthotopic animal model, if compared with knocking down all 4 genes, indicating that the process of liver metastasis may require the cooperation/synergism of the 4 genes.

EGFR  was also identified to be a potential key player for liver metastases. There is somewhat conflicting data regarding the importance or use of EGF as an indicator for liver metasteses.  While some clinical protocols suggest patients with KRAS wild-type should be considered for combination therapy with EGFR inhibitors, because this strategy has led to promising results with improved R0 resection (2), others have shown that EGFR expression in the primary tumor site was not predictive of its level in the metastasis. EGFR expression levels in the primaries and in the metastases do not appear to be useful prognostic markers (3).

Additionally, recent studies also revealed that certain genes and signaling pathways might play a role in colon cancer liver metastasis. Metastasis-associated in colon cancer-1 (Macc1) was identified as a key regulator of HGF-MET signaling and is able to enhance colon cancer cell migration in vitro and liver metastasis in mouse model. TGF-β/Smad4 signaling was found to suppresses colon cancer metastasis in mice and the balance between Smad4/Smad7 and the TGF-β pathway in colorectal cancer may be critical for the metastatic process (1b).

Wulfkuhle and colleagues recently published an innovative study comparing the proteomic profiles of hepatic metastases generated by tumors from different primary organ sites. They strongly suggest that the microenviornment of the host organ plays a pivotal role in the activation of specific survival pathways (4).

The role of microenvironment and heterogeneity is reviewed by Bert Vogelstein  and colleagues in their outstanding paper on the Cancer Genome Landscape (5). They outline the multiplex orchestra of genes and their mutations that play role in cancer initiation, progressions and invasion into new metastatic niches,

In summary:

Many of the molecular pathways that promote tumorigenesis also promote metastasis and are important in the treatment of both aspects of cancer progression. This is a multiplex process that involves alternations/mutations in many genes and metastases, much like primary tumors, varies within a single patient and between patient.  The biology of liver metastases has been intensively investigated and several  genes where identified yet, one must remember that these set of gene may be true to one source of primary tumor origin and not not to another.  From a technical standpoint, the development of new and improved methods for early detection and prevention will not be easy, but there is no reason to assume that it will be more difficult than the development of new therapies aimed at treating widely metastatic disease. For further review on concurrent treatments for colorectal liver metastases, please go to liver metastases_treatments (I)

References:

1a. Patricia S Steeg, Dan Theodorescu. Metastasis: A Therapeutic Target for Cancer. Nat Clin Pract Oncol. 2008;5(4):206-219. http://www.medscape.com/viewarticle/571455_2.

1b. Qingqing Ding, Chun-Ju Chang, Xiaoming Xie, Weiya Xia, Jer-Yen Yang ,Shao-Chun Wang, Yan Wang, Jiahong Xia, Libo Chen, Changchun Cai, Huabin Li, Chia-Jui Yen, Hsu-Ping Kuo, Dung-Fang Lee, Jingyu Lang, Longfei Huo,Xiaoyun Cheng, Yun-Ju Chen, Chia-Wei Li, Long-Bin Jeng, Jennifer L. Hsu, Long-Yuan Li , Alai Tan, Steven A. Curley, Lee M. Ellis, Raymond N. DuBois and Mien-Chie Hung. APOBEC3G promotes liver metastasis in an orthotopic mouse model of colorectal cancer and predicts human hepatic metastasis. J Clin Invest. 2011;121(11):4526–4536. doi:10.1172/JCI45008. http://www.jci.org/articles/view/45008

2. Macelo R.S Cruz and Gilberto de Lima Lopes. Colon Cancer Liver Metastasis: Addition of Antiangiogenesis or EGFR Inhibitors to Chemotherapy. Current Colorectal Cancer Reports March 2013, 9(1); pp 68-73. http://link.springer.com/article/10.1007%2Fs11888-012-0148-z

3. Nirit Yarom N, Celia Marginean, Terence Moyana, Ivan Gorn-Hondermann , H. Chaim Birnboim, Horia Marginean, Rebecca C. Auer, Micheal Vickers, Timothy R. Asmis, Jean Maroun, Derek Jonker EGFR expression variance in paired colorectal cancer primary and metastatic tumors. Cancer Biol Ther 2010 Sep 1;10(5):416-421. https://www.landesbioscience.com/journals/cbt/article/12610/

4. Wulfkuhle J, Espina V, Liotta L, Petricoin E. Genomic and proteomic technologies for individualisation and improvement of cancer treatment. Eur J Cancer. 2004 Nov;40(17):2623-2632. http://www.ncbi.nlm.nih.gov/pubmed/15541963.

5. Bert Vogelstein, Nickolas Papadopoulos, Victor E. Velculescu, Shibin Zhou, Luis A. Diaz Jr., Kenneth W. Kinzler. Cancer Genome Landscapes. Science 29 March 2013:  Vol. 339 no. 6127 pp. 1546-1558  http://www.sciencemag.org/content/339/6127/1546.full

Other articles from our open access journal:

I. By Tilda Barliya PhD. Liver metastases_treatments. http://pharmaceuticalintelligence.com/2013/08/10/liver-metastasis/

II. By Tilda Barliya PhD. Cancer metastasis. http://pharmaceuticalintelligence.com/2013/07/06/cancer-metastasis/

III. By. Tilda Barliya PhD. Colon Cancer. http://pharmaceuticalintelligence.com/2013/04/30/colon-cancer/

IV. By. Stephen J. Williams. Issues in Personalized Medicine in Cancer: Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing. http://pharmaceuticalintelligence.com/2013/04/10/issues-in-personalized-medicine-in-cancer-intratumor-heterogeneity-and-branched-evolution-revealed-by-multiregion-sequencing/

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Author Tilda Barliya PhD

Hepatic metastatic disease from colorectal cancer (CRC) is a significant clinical problem. The liver is the dominant metastatic site for patients with CRC, and although two-thirds of affected patients have extrahepatic spread, some have disease that is isolated to the liver. For patients with isolated liver metastases, regional treatment approaches may be considered as an alternative to systemic chemotherapy (1).

Metastases from CRC most commonly develop within 2 years of resection of the primary tumor and are usually asymptomatic; rarely, patients may complain of vague upper abdominal pain. Hepatic metastases associated with CRC may occur regardless of the initial stage of the primary tumor although nodepositive primary lesions are more likely to precede hepatic metastasis (2).

The available regional treatments for hepatic metastases from CRC include (1):

  • Surgical resection
  • Local tumor ablation (ie, instillation of alcohol or acetic acid directly into the metastatic lesions
  • Radiofrequency ablation [RFA])
  • Regional hepatic intraarterial chemotherapy or chemoembolization
  • Radiation therapy (RT)

**Among these treatments, only surgery is associated with a survival plateau.

Screening for Hepatic metastasis (3):

  • A biopsy may be indicated to confirm the diagnosis, depending upon the clinical picture. However, fine needle aspiration cytology has not been advocated as a screening test, because of its high risk of complications. It has been shown that the incidence of needle tract metastases is 0.4%-5.1% after fine needle aspiration and use of the procedure in abdominal tumors is fatal in 0.006%-0.031% of cases.  Most deaths are due to hemorrhage of liver tumors (3).
  • Laparoscopy has not been advocated as a screening test for colorectal liver metastases due to its invasiveness.
  • Imaging modalities, such as contrast enhanced computed tomography (CT), magnetic resonance imaging (MRI) and positron emission tomography CT (PET-CT), may establish the diagnosis of liver metastasis of colorectal cancer. However, it is more difficult to make the clinical diagnosis of early liver metastases of colorectal cancer due to the absence of typical symptoms or signs.
  • Serological examination including tumor and biochemical markers for liver function evaluation is routinely performed, though its accuracy is not high.  In that aspect, carcinoembryonic antigen (CEA) levels is elevated in 63% of patients, while the activity of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) is increased in about 30% of patients with liver metastases of colorectal cancer.

Surgical Resection (1)

Resection offers the greatest likelihood of cure for patients with liver-isolated CRC. In surgical case series, five-year survival rates after resection range from 24 to 58 percent, averaging 40 percent and surgical mortality rates are generally <5 percent (1). It’s worth noted that subgroups with advanced age, comorbid disease, and synchronous hepatic and colon resection may have higher procedure-related mortality and worse long-term outcomes.

The five-year survival rate was only 25 percent, Even so, five-year survival rates with the most active systemic chemotherapy regimens are only 10 to 11 percent, only about one-fifth of whom have a sustained disease remission. More so, approximately one-third of five-year survivors suffer a cancer-related death, while those who survive 10 years appear to be cured (4).

Because of its clear survival impact, surgical resection is the treatment of choice when feasible. Unfortunately, no more than 20 percent of patients with isolated hepatic metastases are amenable to potentially curative resection. Most are not surgical candidates because of tumor size, location, multifocality, or inadequate hepatic reserve.

Patient candidates for resection – The criteria for resectability differ among individual liver surgeons regarding borderline cases, from center to center and from country to country. One consensus statement defined absolute unresectability as nontreatable extrahepatic disease, unfitness for surgery, or involvement of more than 70 percent of the liver or six segments (1,2).  Patients are evaluaed using preoperative liver MRI and intraoperative ultrasound which offer the optimal assessment of the number, size, and proximity of tumors to key vascular and biliary structures.

Modern multidisciplinary consensus for resectable CRC liver metastases:

  • Tumors that can be resected completely (leaving an adequate liver remnant)
  • No  involvement of the hepatic artery, major bile ducts, main portal vein, orceliac/paraaortic lymph nodes
  • Adequate predicted functional hepatic reserve postresection

Criteria for unresectable liver metastases (5):

  • Pateitns with more than three lesions, those
  • Patients with bilobar distribution (ie, tumor involving any segments of the left and right hemi-liver),
  • Patients in whom it was not possible to achieve 1 cm margins,
  • Patients with portal lymph node or other extrahepatic metastases, and
  • Patients with liver metastases from cancers other than colorectal tumors

Some of these exclusion criteria have been challenged.

  • Better and safer surgical techniques are now more suitable for patients with multiple, even bilobar tumors.
  • A two-stage approach to hepatic resection may be needed in the presence of multiple bilobar metastases
  • Achieving wide margins doesn’t increase the 5-year survival. **** Only patients with a positive margin had worse survival and a higher intrahepatic recurrence rate.
  • Presence of portal lymph node metastases – still been challenged and results are controversy.
  • A major problem is the prediction of metastatic lymph nodes in the hepatic pedicle in patients with CRC liver metastases.  The presence of portal node metastases is not inevitably associated with distant metastases.  Outcome was more favorable if nodal involvement was limited to the porta as compared to along the common hepatic artery.
  • The presence of other sites of limited extrahepatic metastases (particularly lung) should not be considered a contraindication to resection as long as the disease is amenable to complete extirpation. However, outcomes in this group are not as favorable, particularly when there are >6 liver metastases.

Diagnostic Laparoscopy

In modern treatment paradigms, laparoscopy is infrequently performed, particularly since many patients have undergone surgical exploration of the peritoneum at the time of resection of a synchronous primary tumor. Laparoscopy is usually reserved for those thought to be at the highest risk for occult metastatic disease.

A growing number of authors report that staging laparoscopy (including laparoscopic US) performed under general anesthesia just prior to planned resection will identify 16 to 64 percent of patients with unresectable disease.

This approach is particularly useful in identifying small peritoneal metastases, additional hepatic metastases, and unsuspected cirrhosis. Laparoscopy in this setting is less likely to identify lymph node metastases, vascular compromise, and extensive biliary involvement that might render a patient unresectable (2,6).

Neoadjuvant chemotherapy

The availability of increasingly effective systemic chemotherapy has prompted interest in preoperative or neoadjuvant systemic chemotherapy prior to liver resection.  It may  be considered as a means of “downsizing” liver metastases prior to resection to lessen the complexity of hepatic metastasectomy or for initially unresectable metastatic disease (1). Chemotherapy, has many side effects including liver toxicity such as:  steatosis (chemotherapy-associated steatohepatitis, CASH), vascular injury, and nodular regenerative hyperplasia in the livers.

Due to high number of patients with liver toxicity and morbidity, these instructions have been suggested:

  • For low-risk (medically fit, four or fewer lesions), potentially resectable patients, initial surgery rather than neoadjuvant chemotherapy should be chosen, followed by postoperative chemotherapy.
  • For patients who have higher risk, borderline resectable or unresectable disease, neoadjuvant chemotherapy is the preferred approach.

Neoadjuvant Chemotherapy Guidelines from the National Comprehensive Cancer Network (NCCN) suggest any of the following:

  • FOLFOX or CAPOX or FOLFIRI with or without bevacizumab or
  • FOLFOX or CAPOX or FOLFIRI plus cetuximab (wild-type K-ras only) or
  • FOLFOXIRI alone

Bevacizumab – Its addition to traditional chemotherapy results in a modestly higher frequency of tumor regression compared to regimens that do not include bevacizumab. However, these benefits have come at the cost of significant treatment-related toxicity. Such as: such as stroke and arterial thromboembolic events, bowel perforation and bleeding.  Data regarding the need and timing of use of bevacizumab is somewhat conflicting.

Cetuximab (if K-ras wild type) and panitumumab (if K-ras wild type) are also suggested as part of the  chemotherapy regimen in certain clinics are regional dependent.

Intraarterial (HIA) chemotherapy – The administration of chemotherapy into the hepatic artery. The benefit of this approach is remains unclear. A combined approach of HIA floxuridine plus systemic chemotherapy (oxaliplatin plus irinotecan) was explored in a single institution study of 49 patients with initially unresectable CRC liver metastases. Overall, 92 percent had either a complete or partial response rate to chemotherapy, and 23 (43 percent) were able to undergo a later resection, 19 with negative margins. The median overall survival from pump placement for the entire cohort was 40 months (1, 7).  Another approach is HIA oxaliplatin combined with systemic 5-FU and leucovorin for patients with initially unresectable but isolated hepatic CRC metastasis.

It should be noted that this approach is not used by many clinicians outside of New York City. The only way to assess the contribution of HIA chemotherapy to neoadjuvant systemic chemotherapy is with a randomized controlled trial.

Portal vein infusion — Because HIA FUDR carries a risk for biliary sclerosis, administration into the portal vein has been explored as an alternative. hepatic micrometastases (as well as the biliary tree) are primarily dependent on the portal vein for their blood supply. Like HIA infusion, portal vein infusion (PVI) carries with it a significant regional exposure advantage.

The potential benefit of adjuvant PVI with FUDR after resection or ablation of isolated hepatic metastases was evaluated in two trials conducted at the City of Hope Medical Center (1, 8).  The benefit of this approach was somewhat lower than has been reported with HIA FUDR and systemic 5-FU. Therefore, the use of this approach is limited.

Hepatic radiotherapy — The use of external beam radiotherapy and internal application of radiation therapy through the use of yttrium-labeled microspheres.  Radiation therapy (RT) has traditionally had a limited role in the treatment of liver tumors, primarily because of the low whole-organ tolerance of the liver to radiation (9).   When radiation is applied to the entire liver, RT doses of 30 to 33 Gy carry about a 5% risk of radiation-induced liver disease (RILD). The risk rises rapidly, such that by 40 Gy, the risk is approximately 50%.  Considering that most solid tumors require RT doses higher than 60 Gy to provide a reasonable chance for local control, it is not surprising that wholeorgan liver RT provides only a modest palliative benefit rather than durable tumor control. Hepatic dysfunction after RT is a very frequent event.

Summary:

Liver metastasis are a very tough disease to battle and the outcome is not encouraging. Currently, surgical resection is the only potentially curative option for patients with liver-isolated metastatic colorectal cancer. For appropriately selected patients with four or fewer metastases, five-year relapse-free survival rates average 30 percent.  Diagnostic laparoscopy is suggested only in patients with a suspicion of low-volume carcinomatosis based on preoperative radiographic imaging and for selected other cases at high risk for intraperitoneal metastatic disease. The optimal chemotherapy regimen is still not fully established but some suggestions have been made and the benefits of using HIA is still not clear.

Standardization of scoring, timing, surgical techniques , results from clinical trials and advanced research will offer better hope for these patients, who now, have a very bad prognosis and survival rates.

Reference:

1.  Venook AP and Curley SA. Management of potentially resectable colorectal cancer liver metastases. UpToDate Jun 2013. http://www.uptodate.com/contents/management-of-potentially-resectable-colorectal-cancer-liver-metastases

2. Smith AJ., DeMatteo RP., Fong Y and Blumgart LH.  Metastatic Liver Cancer.  HEPATOBILIARY CANCER. http://web.squ.edu.om/med-Lib/MED_CD/E_CDs/Hepatobiliary%20Cancer/DOCS/Ch4.pdf

3. Wu XZ., Ma F., and Wang XL. Serological diagnostic factors for liver metastasis in patients with colorectal cancer. World J Gastroenterol. 2010 August 28; 16(32): 4084–4088. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928464/

4. Tomlinson JS, Jarnagin WR, DeMatteo RP, Fong Y, Kornprat P, Gonen M, Kemeny N, Brennan MF, Blumgart LH, D’Angelica M. Actual 10-year survival after resection of colorectal liver metastases defines cure. J Clin Oncol. 2007;25(29):4575. http://www.ncbi.nlm.nih.gov/pubmed?term=17925551

5. Tanabe KK. Palliative liver resections. J Surg Oncol. 2002;80(2):69. http://onlinelibrary.wiley.com/doi/10.1002/jso.10108/abstract;jsessionid=F19964733A4A1A2708A0BA0E274CF586.d01t03

6.  Ravikumar TS. Laparoscopic staging and intraoperative ultrasonography for liver tumor management. Surg Oncol Clin N Am 1996;5:271–282. http://www.ncbi.nlm.nih.gov/pubmed/9019351

7, Kemeny NE, Melendez FD, Capanu M, Paty PB, Fong Y, Schwartz LH, Jarnagin WR, Patel D, D’Angelica M.  Conversion to resectability using hepatic artery infusion plus systemic chemotherapy for the treatment of unresectable liver metastases from colorectal carcinoma. J Clin Oncol. 2009;27(21):3465. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646304/

8.  Faynsod M, Wagman LD, Longmate J, Carroll M, Leong LA. Improved hepatic toxicity profile of portal vein adjuvant hepatic infusional chemotherapy.J Clin Oncol. 2005;23(22):4876. http://www.ncbi.nlm.nih.gov/pubmed?term=16009960

9. I. Frank Ciernik and Theodore S. Lawrence. Radiation Therapy for Liver Tumors. Book: Systemic and Regional Therapies. Chapter 7.  http://www.jblearning.com/samples/0763718572/Chapter_07.pdf

Other articles from our open journal access

I.  By: Dr. Sudipta Saha PhD . Treatment for Endocrine Tumors and Side Effects. http://pharmaceuticalintelligence.com/2013/06/24/treatment-for-endocrine-tumors-and-side-effects/

II. By: Dr. Stephen J. Williams PhD. Differentiation Therapy – Epigenetics Tackles Solid Tumors. http://pharmaceuticalintelligence.com/2013/01/03/differentiation-therapy-epigenetics-tackles-solid-tumors/

III. By: Dr.  Ritu Saxena, PhD. In focus: Circulating Tumor Cells. http://pharmaceuticalintelligence.com/2013/06/24/in-focus-circulating-tumor-cells/

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Reporter and Curator: Dr. Sudipta Saha, Ph.D.

Hepatocellular carcinoma is one of the most common malignancies worldwide, and it has a poor prognosis due to its rapid development and early metastasis. An understanding of tumor metabolism would be helpful for the clinical diagnosis and therapy of hepatocellular carcinoma. Chronic hepatitis B virus infection is the primary risk factor for hepatocellular carcinoma, and the majority of hepatocellular carcinoma cases develop from hepatitis infections and subsequent cirrhosis. Rapid development and early metastasis are the typical characteristics of hepatocellular carcinoma, which always results in a poor prognosis. Therefore, investigating the hepatocarcinogenesis mechanism is very important for decreasing the incidence and mortality of hepatocellular carcinoma. The abnormal metabolism of cancer has been considered an important characteristic of tumors, which could clarify the pathogenesis and provide potential therapeutic targets for clinical treatments. According to the Warburg effect, the deregulated energy metabolism of cancer cells may also modify many related metabolic pathways that influence various biological processes, such as cell proliferation and apoptosis. As a common characteristic of cancer cells, modified metabolism has been the focus of cancer research.

Because of its asymptomatic nature, hepatocellular carcinoma is usually diagnosed at late and advanced stages, for which there are no effective therapies. Thus, biomarkers for early detection and molecular targets for treating hepatocellular carcinoma are urgently needed. Emerging high-throughput metabolomics technologies have been widely applied, aiming at the discovery of candidate biomarkers for cancer staging, prediction of recurrence and prognosis, and treatment selection. Tissue metabolomics is a useful tool for studying the abnormal metabolisms of diseases, and it can provide information about the metabolic modifications and the upstream regulative mechanism in diseases. More importantly, the systemic metabolic characteristics of tissues could provide opportunities for exploring novel diagnostic markers or therapeutic targets for clinical applications. Tissue metabolomics is conducted using a pairwise comparison of different parts of tissue from each patient, which can remove individual differences, such as age, sex, region, etc. The differences between the tumor cells and their surrounding host cells may reflect the interactions of the tumor and the host, which are important clues for studying the invasion and metastasis of tumors. Metabolic profiles, which are affected by many physiological and pathological processes, may provide further insight into the metabolic consequences of this severe liver disease. Small-molecule metabolites have an important role in biological systems and represent attractive candidates to understand hepatocellular carcinoma phenotypes. The power of metabolomics allows an unparalleled opportunity to query the molecular mechanisms of hepatocellular carcinoma.

Source References:

http://www.ncbi.nlm.nih.gov/pubmed/23824744

http://www.ncbi.nlm.nih.gov/pubmed/23150189

http://onlinelibrary.wiley.com/doi/10.1002/hep.26350/abstract

http://www.ncbi.nlm.nih.gov/pubmed/21114800

http://www.ncbi.nlm.nih.gov/pubmed/19305372

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