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Posts Tagged ‘Aviva Lev-Ari’


Finding the Genetic Links in Common Disease:  Caveats of Whole Genome Sequencing Studies

Writer and Reporter: Stephen J. Williams, Ph.D.

In the November 23, 2012 issue of Science, Jocelyn Kaiser reports (Genetic Influences On Disease Remain Hidden in News and Analysis)[1] on the difficulties that many genomic studies are encountering correlating genetic variants to high risk of type 2 diabetes and heart disease.  At the recent American Society of Human Genetics annual 2012 meeting, results of several DNA sequencing studies reported difficulties in finding genetic variants and links to high risk type 2 diabetes and heart disease.  These studies were a part of an international effort to determine the multiple genetic events contributing to complex, common diseases like diabetes.  Unlike Mendelian inherited diseases (like ataxia telangiectasia) which are characterized by defects mainly in one gene, finding genetic links to more complex diseases may pose a problem as outlined in the article:

  • Variants may be so rare that massive number of patient’s genome would need to be analyzed
  • For most diseases, individual SNPs (single nucleotide polymorphisms) raise risk modestly
  • Hard to find isolated families (hemophilia) or isolated populations (Ashkenazi Jew)
  • Disease-influencing genes have not been weeded out by natural selection after human population explosion (~5000 years ago) resulted in numerous gene variants
  • What percentage variants account for disease heritability (studies have shown this is as low as 26% for diabetes with the remaining risk determined by environment)

Although many genome-wide-associations studies have found SNPs that have causality to increasing risk diseases such as cancer, diabetes, and heart disease, most individual SNPs for common diseases raise risk by about only 20-40% and would be useless for predicting an individual’s chance they will develop disease and be a candidate for a personalized therapy approach.  Therefore, for common diseases, investigators are relying on direct exome sequencing and whole-genome sequencing to detect these medium-rare risk variants, rather than relying on genome-wide association studies (which are usually fine for detecting the higher frequency variants associated with common diseases).

Three of the many projects (one for heart risk and two for diabetes risk) are highlighted in the article:

1.  National Heart, Lung and Blood Institute Exome Sequencing Project (ESP)[2]: heart, lung, blood

  • Sequenced 6,700 exomes of European or African descent
  • Majority of variants linked to disease too rare (as low as one variant)
  • Groups of variants in the same gene confirmed link between APOC3 and higher risk for early-onset heart attack
  • No other significant gene variants linked with heart disease

2.  T2D-GENES Consortium: diabetes

Sequenced 5,300 exomes of type 2 diabetes patients and controls from five ancestry groups
SNP in PAX4 gene associated with disease in East Asians
No low-frequency variant with large effect though

3.  GoT2D: diabetes

  • After sequencing 2700 patient’s exomes and whole genome no new rare variants above 1.5% frequency with a strong effect on diabetes risk

A nice article by Dr. Sowmiya Moorthie entitled Involvement of rare variants in common disease can be found at the PGH Foundation site http://www.phgfoundation.org/news/5164/ further discusses this conundrum,  and is summarized below:

“Although GWAs have identified many SNPs associated with common disease, they have as yet had little success in identifying the causative genetic variants. Those that have been identified have only a weak effect on disease risk, and therefore only explain a small proportion of the heritable, genetic component of susceptibility to that disease. This has led to the common disease-common variant hypothesis, which predicts that common disease-causing genetic variants exist in all human populations, but each individual variant will necessarily only have a small effect on disease susceptibility (i.e. a low associated relative risk).

An alternative hypothesis is the common disease, many rare variants hypothesis, which postulates that disease is caused by multiple strong-effect variants, each of which is only found in a few individuals. Dickson et al. in a paper in PLoS Biology postulate that these rare variants can be indirectly associated with common variants; they call these synthetic associations and demonstrate how further investigation could help explain findings from GWA studies [Dickson et al. (2010) PLoS Biol. 8(1):e1000294][3].  In simulation experiments, 30% of synthetic associations were caused by the presence of rare causative variants and furthermore, the strength of the association with common variants also increased if the number of rare causative variants increased. “

one_of_many rare variants

Figure from Dr. Moorthie’s article showing the problem of “finding one in many”.

(please   click to enlarge)

Indeed, other examples of such issues concerning gene variant association studies occur with other common diseases such as neurologic diseases and obesity, where it has been difficult to clearly and definitively associate any variant with prediction of risk.

For example, Nuytemans et. al.[4] used exome sequencing to find variants in the vascular protein sorting 3J (VPS35) and eukaryotic transcription initiation factor 4  gamma1 (EIF4G1) genes, tow genes causally linked to Parkinson’s Disease (PD).  Although they identified novel VPS35 variants none of these variants could be correlated to higher risk of PD.   One EIF4G1 variant seemed to be a strong Parkinson’s Disease risk factor however there was “no evidence for an overall contribution of genetic variability in VPS35 or EIF4G1 to PD development”.

These negative results may have relevance as companies such as 23andme (www.23andme.com) claim to be able to test for Parkinson’s predisposition.  To see a description of the LLRK2 mutational analysis which they use to determine risk for the disease please see the following link: https://www.23andme.com/health/Parkinsons-Disease/. This company and other like it have been subjects of posts on this site (Personalized Medicine: Clinical Aspiration of Microarrays)

However there seems to be more luck with strategies focused on analyzing intronic sequence rather than exome sequence. Jocelyn Kaiser’s Science article notes this in a brief interview with Harry Dietz of Johns Hopkins University where he suspects that “much of the missing heritability lies in gene-gene interactions”.  Oliver Harismendy and Kelly Frazer and colleagues’ recent publication in Genome Biology  http://genomebiology.com/content/11/11/R118 support this notion[5].  The authors used targeted resequencing of two endocannabinoid metabolic enzyme genes (fatty-acid-amide hydrolase (FAAH) and monoglyceride lipase (MGLL) in 147 normal weight and 142 extremely obese patients.

These patients were enrolled in the CRESCENDO trial and patients analyzed were of European descent. However, instead of just exome sequencing, the group resequenced exome AND intronic sequence, especially focusing on promoter regions.   They identified 1,448 single nucleotide variants but using a statistical filter (called RareCover which is referred to as a collapsing method) they found 4 variants in the promoters and intronic areas of the FAAH and MGLL genes which correlated to body mass index.  It should be noted that anandamide, a substrate for FAAH, is elevated in obese patients. The authors did note some issues though mentioning that “some other loci, more weakly or inconsistently associated in the original GWASs, were not replicated in our samples, which is not too surprising given the sample size of our cohort is inadequate to replicate modest associations”.

PLEASE WATCH VIDEO on the National Heart, Lung and Blood Institute Exome Sequencing Project

https://www.youtube.com/watch?v=-Qr5ahk1HEI

REFERENCES

http://www.phgfoundation.org/news/5164/  PHG Foundation

1.            Kaiser J: Human genetics. Genetic influences on disease remain hidden. Science 2012, 338(6110):1016-1017.

2.            Tennessen JA, Bigham AW, O’Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G et al: Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 2012, 337(6090):64-69.

3.            Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB: Rare variants create synthetic genome-wide associations. PLoS biology 2010, 8(1):e1000294.

4.            Nuytemans K, Bademci G, Inchausti V, Dressen A, Kinnamon DD, Mehta A, Wang L, Zuchner S, Beecham GW, Martin ER et al: Whole exome sequencing of rare variants in EIF4G1 and VPS35 in Parkinson disease. Neurology 2013, 80(11):982-989.

5.            Harismendy O, Bansal V, Bhatia G, Nakano M, Scott M, Wang X, Dib C, Turlotte E, Sipe JC, Murray SS et al: Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level. Genome biology 2010, 11(11):R118.

Other posts on this site related to Genomics include:

Cancer Biology and Genomics for Disease Diagnosis

Diagnosis of Cardiovascular Disease, Treatment and Prevention: Current & Predicted Cost of Care and the Promise of Individualized Medicine Using Clinical Decision Support Systems

Ethical Concerns in Personalized Medicine: BRCA1/2 Testing in Minors and Communication of Breast Cancer Risk

Genomics & Genetics of Cardiovascular Disease Diagnoses: A Literature Survey of AHA’s Circulation Cardiovascular Genetics, 3/2010 – 3/2013

Genomics-based cure for diabetes on-the-way

Personalized Medicine: Clinical Aspiration of Microarrays

Late Onset of Alzheimer’s Disease and One-carbon Metabolism

Genetics of Disease: More Complex is How to Creating New Drugs

Genetics of Conduction Disease: Atrioventricular (AV) Conduction Disease (block): Gene Mutations – Transcription, Excitability, and Energy Homeostasis

Centers of Excellence in Genomic Sciences (CEGS): NHGRI to Fund New CEGS on the Brain: Mental Disorders and the Nervous System

Cancer Genomic Precision Therapy: Digitized Tumor’s Genome (WGSA) Compared with Genome-native Germ Line: Flash-frozen specimen and Formalin-fixed paraffin-embedded Specimen Needed

Mitochondrial Metabolism and Cardiac Function

Pancreatic Cancer: Genetics, Genomics and Immunotherapy

Issues in Personalized Medicine in Cancer: Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

Quantum Biology And Computational Medicine

Personalized Cardiovascular Genetic Medicine at Partners HealthCare and Harvard Medical School

Centers of Excellence in Genomic Sciences (CEGS): NHGRI to Fund New CEGS on the Brain: Mental Disorders and the Nervous System

LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment: Part 2

Consumer Market for Personal DNA Sequencing: Part 4

Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research: Part 3

Whole-Genome Sequencing Data will be Stored in Coriell’s Spin off For-Profit Entity

 

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Author: Justin D. Pearlman MD ME PhD MA FACC

and

Curator: Aviva Lev-Ari, PhD, RN

Clinical Decision Support Systems (CDSS)

Clinical decision support system (CDSS) is an interactive decision support system (DSS) Computer Software, which is designed to assist physicians and other health professionals with decision making tasks, such as determining diagnosis of patient data. A working definition has been proposed by Robert Hayward of the Centre for Health Evidence; “Clinical Decision Support systems link health observations with health knowledge to influence health choices by clinicians for improved health care”. This definition has the advantage of simplifying Clinical Decision Support to a functional concept. It is a major topic of artificial intelligence in medicine.

Vinod Khosla of A Khosla Ventures investment, in a Fortune Magazine article, “Technology will replace 80% of what doctors do”, on December 4, 2012

http://tech.fortune.cnn.com/2012/12/04/technology-doctors-khosla/?source=linkedin&goback=%2Egde_4346921_member_240383059

wrote:

This is only the beginning of the many generations of improvement that are likely to happen in the next two decades, but we have already begun to see meaningful impacts on healthcare. Studies have demonstrated the ability of computerized clinical decision support systems to lower diagnostic errors of omission significantly, directly countering the ‘premature closure’ cognitive bias. Isabel is a differential diagnosis tool and, according to a Stony Book study, matched the diagnoses of experienced clinicians in 74% of complex cases. The system improved to a 95% match after a more rigorous entry of patient data. Even IBM’s fancy Watson computer, after beating all humans at the very human intelligence-based task of playing Jeopardy, is now turning its attention to medical diagnosis. It can process natural language questions and is fast at parsing high volumes of medical information, reading and understanding 200 million pages of text in 3 seconds. 

The Longer version of the FORTUNE Magazine article:

http://pharmaceuticalintelligence.com/2013/05/13/vinod-khosla-20-doctor-included-speculations-musings-of-a-technology-optimist-or-technology-will-replace-80-of-what-doctors-do/

Examples of CDSS

  1. CADUCEUS
  2. DiagnosisPro
  3. Dxplain
  4. MYCIN
  5. RODIA

Introduction

Justin D. Pearlman, MD, PhD

A Decision Support System consists of one or more tools to help achieve good decisions. For example, decisions that can benefit from DSS include whether or not to undergo surgery, whether or not to undergo a stress test first, whether or not to have an annual mammogram starting at a particular age, or a computed tomography (CT) to screen for lung cancer, whether or not to utilize intensive care support such as a ventilator, chest shocks, chest compressions, forced feeding, strong antibiotics and so on versus care directed to comfort measures only without regard to longevity.

Any DSS can be viewed like a digestive tract, chewing on input, and producing output, and like the digestive tract, the output may only be valuable to a farmer. A well designed DSS is efficient in the input, timely in its processing and useful in the output. Mathematically, a DSS is a model with input parameters and an output variable or set of variables that can be used to determine an action. The input can be categorical (alive, dead), semi-quantitative (cold-warm-hot), or quantitative (temperature, systolic blood pressure, heart rate, oxygen saturation). The output can be binary (yes-no) or it can express probabilities or confidence intervals.

The process of defining specifications for a function and then deriving a useful function is called mathematical modeling. We will derive the function for “average” as an example. By way of specifications, we want to take a list of numbers as input, and come out with a single number that represents the middle of the pack or “central tendency.”   The order of the list should not matter, and if we change scales, the output should scale the same way. For example, if we use centimeters instead of inches, and we apply 2.54 centimeters to an inch, then the output should increase by the multiplier 2.54. If the list of numbers are all the same then the output should be the consistent value. Representing these specifications symbolically:

1. order doesn’t matter: f(a,b) = f(b,a), where “a” and “b” are input values, “f” is the function.

2. multipliers pass through (linearity):  f(ka,kb)=k f(a,b), where k is a scalar e.g. 2.54 cm/inch.

3. identity:  f(a,a,a,…) = a

Properties 1 and 2 lead us to consider linear functions consisting of sums and multipliers: f(a,b,c)=Aa+Bb+Cc …, where the capital letters are multipliers by “constants” – numbers that are independent of the list values a,b,c, and since the order should not matter, we simplify to f(a,b,c)=K (a+b+c+…) because a constant multiplier K makes order not matter. Property 3 forces us to pick K = 1/N where N is the length of the list. These properties lead us to the mathematical solution: average = sum of list of numbers divided by the length of the list.

A coin flip is a simple DSS: heads I do it, tails I don’t. The challenge of a good DSS is to perform better than random choice and also perform better (more accurately, more efficiently, more reliably, more timely and/or under more adverse conditions) than an unassisted human decision making process.

Therefore, I propose the following guiding principles for DSS design: choose inputs wisely (accessible, timely, efficient, relevant), determine to what you want output to be sensitive AND to what you want output to be insensitive, and be very clear about your measures of success.

For example, consider designing a DSS to determine whether a patient should receive the full range of support capabilities of an intensive care unit (ICU), or not. Politicians have cited the large bump in the cost of the last year of life as an opportunity to reduce costs of healthcare, and now pay primary care doctors to encourage patients to establish advanced directives not to use ICU services. From the DSS standpoint, the reasoning is flawed because the decision not to use ICU services should be sensitive to benefit as well as cost, commonly called cost-benefit analysis. If we measure success of ICU services by the benefit of quality life net gain (QLNG, “quailing”), measured in quality life-years (QuaLYs) and achieve 50% success with that, then the cost per QuaLY measures the cost-benefit of ICU services. In various cost-benefit decisions, the US Congress has decided to proceed if the cost is under $20-$100,000/QuaLY. If ICU services are achieving such a cost-benefit, then it is not logical to summarily block such services in advance. Rather, the ways to reduce those costs include improving the cost efficiency of ICU care, and improving the decision-making of who will benefit.

An example of a DSS is the prediction of plane failure from a thousand measurements of strain and function of various parts of an airplane. The desired output is probability of failure to complete the next flight safely. Cost-Benefit analysis then establishes what threshold or operating point merits grounding the plane for further inspection and preventative maintenance repairs. If a DSS reports probability of failure, then the decision (to ground the plane) needs to establish a threshold at which a certain probability triggers the decision to ground the plane.

The notion of an operating point brings up another important concept in decision support. At first blush, one might think the success of a DSS is determined by its ability to correctly identify a predicted outcome, such as futility of ICU care (when will the end result be no quality life net gain). The flaw in that measure of success is that it depends on prevalence in the study group. As an extreme example, if you study a group of patients with fatal gunshot wounds to the head, none will benefit and the DSS requirement is trivial and any DSS that says no for that group has performed well. At the other extreme, if all patients become healthy, the DSS requirement is also trivial, just say yes. Therefore the proper assessment of a DSS should pay attention to the prevalence and the operating point.

The impact of prevalence and operating point on decision-making is addressed by receiver-operator curves. Consider looking at the blood concentration of Troponin-I (TnI) as the sole determinant to decide who is having a heart attack.  If one plots a graph with horizontal axis troponin level and vertical axis ultimate proof of heart attack, the percentage of hits will generally be higher for higher values of TnI. To create such a graph, we compute a “truth table” which reports whether the test was above or below a decision threshold operating point, and whether or not the disease (heart attack) was in fact present:

TRUTH TABLE

Disease  Not Disease
Test Positive

TP

FP

Test Negative

FN

TN

total

TP+FN

FP+TN

The sensitivity to the disease is the true positive rate (TPR), the percentage of all disease cases that are ranked by the decision support as positive: TPR = TP/(TP+FN). 100% sensitivity can be achieved trivially by lowering the threshold for a positive test to zero, at a cost.  While sensitivity is necessary for success it is not sufficient. In addition to wanting sensitivity to disease, we want to avoid labeling non-disease as disease. That is often measured by specificity, the true negative rate (TNR), the percentage of those without disease who are correctly identified as not having disease: TNR = TN/(FP+TN). I propose also we define the complement to specificity, the anti-sensitivity, as the false positive rate (FPR), FPR = FP/(FP+TN) = 1 – TNR. Anti-sensitivity is a penalty cost of lowering the diagnostic threshold to boost sensitivity, as the concomitant rise in anti-sensitivity means a growing number of non-disease subjects are labeled as having disease. We want high sensitivity to true disease without high anti-sensitivity to false disease, and we want to be insensitive to common distractors. In these formulas, note that false negatives (FN) are True for disease, and false positives (FP) are False for disease, so the denominators add FN to TP for total True disease, and add FP to TN for total False for disease.

The graph in figure 1 justifies the definition of anti-sensitivity. It is an ROC or “Receiver-Operator Curve” which is a plot of sensitivity versus anti-sensitivity for different diagnostic thresholds of a test (operating points). Note, higher sensitivity comes at the cost of higher anti-sensitivity. Where to operate (what threshold to use for diagnosis) can be selected according to cost-benefit analysis of sensitivity versus anti-sensitivity (and specificity).

 untitled
FIgure 1 ROC (Receiver-Operator Curve): Graph of sensitivity (true positive rate) versus anti-sensitivity (false positive rate) computed by changing the operating point (threshold for declaring a test numeric value positive for disease). High area under the curve (AUC) is favorable because it means less anti-sensitivity for high sensitivity (upper left corner of shaded area more to the left, and higher). The dots on the curve are operating points. An inclusive operating point (high on the curve, high sensitivity) is used for screening tests, whereas an exclusive operating point (low on the curve, low anti-sensitivity) is used for definitive diagnosis.

Cost benefit analysis generally is based on a semi-lattice, or upside-down branching tree, which represents all choices and outcomes. It is important to include all branches down to final outcomes. For example, if the test is a mammogram to screen for breast cancer, the cost is not just the cost of the test, and the benefit “early diagnosis.” The cost-benefit calculation forces us to put a numerical value on the impact, such as a financial cost to an avoidable death, or we can get a numerical result in terms of quality life years expected. The cost, however, is not just the cost of the mammogram, but also of downstream events such as the cost of the needle biopsies for the suspicious “positives” and so on.

semilattice decision treeFigure 2 Semi-lattice Decision Tree: Starting from all patients, create a branch point for your test result, and add further branch points for any subsequent step-wise outcomes until you reach the “bottom line.” Assign a value to each, resulting in a numerical net cost and net benefit. If tests invoke risks (for example, needle biopsy of lung can collapse a lung and require hospitalization for a chest tube) then insert branch points for whether the complication occurs or not, as the treatment of a complication counts as part of the cost. The intermediary nodes can have probability of occurrence as their numeric factor, and the bottom line can apply the net probability of the path leading to a value as a multiplier to the dollar value (a 10% chance of costing $10,000 counts as an expectation cost of 0.1 x 10,000 = $1,000).

Evolution of DSS

Aviva Lev-Ari, PhD, RN

The examples provided above refer to sets of binary models, one family of DSS. Another type of DSS is multivariate in nature, a corollary of multivariate scenarios constitute alternative choice options. Last decade development in the DSS field involved the design of Recommendation Engines given manifested preference functions that involved simultaneous trade-off functions against cost function. Game theoretical context is embedded into Recommendation Engines. The output mentioned above, is in fact an array of options with probabilities of saving reward assigned by the Recommendation Engine.

Underlining Computation Engines

Methodological Basis of Clinical DSS

There are many different methodologies that can be used by a CDSS in order to provide support to the health care professional.[7]

The basic components of a CDSS include a dynamic (medical) knowledge base and an inference mechanism (usually a set of rules derived from the experts and evidence-based medicine) and implemented through medical logic modules based on a language such as Arden syntax. It could be based on Expert systems or artificial neural networks or both (connectionist expert systems).

Bayesian Network

The Bayesian network is a knowledge-based graphical representation that shows a set of variables and their probabilistic relationships between diseases and symptoms. They are based on conditional probabilities, the probability of an event given the occurrence of another event, such as the interpretation of diagnostic tests. Bayes’ rule helps us compute the probability of an event with the help of some more readily available information and it consistently processes options as new evidence is presented. In the context of CDSS, the Bayesian network can be used to compute the probabilities of the presence of the possible diseases given their symptoms.

Some of the advantages of Bayesian Network include the knowledge and conclusions of experts in the form of probabilities, assistance in decision making as new information is available and are based on unbiased probabilities that are applicable to many models.

Some of the disadvantages of Bayesian Network include the difficulty to get the probability knowledge for possible diagnosis and not being practical for large complex systems given multiple symptoms. The Bayesian calculations on multiple simultaneous symptoms could be overwhelming for users.

Example of a Bayesian network in the CDSS context is the Iliad system which makes use of Bayesian reasoning to calculate posterior probabilities of possible diagnoses depending on the symptoms provided. The system now covers about 1500 diagnoses based on thousands of findings.

Another example is the DXplain system that uses a modified form of the Bayesian logic. This CDSS produces a list of ranked diagnoses associated with the symptoms.

A third example is SimulConsult, which began in the area of neurogenetics. By the end of 2010 it covered ~2,600 diseases in neurology and genetics, or roughly 25% of known diagnoses. It addresses the core issue of Bayesian systems, that of a scalable way to input data and calculate probabilities, by focusing specialty by specialty and achieving completeness. Such completeness allows the system to calculate the relative probabilities, rather than the person inputting the data. Using the peer-reviewed medical literature as its source, and applying two levels of peer-review to the data entries, SimulConsult can add a disease with less than a total of four hours of clinician time. It is widely used by pediatric neurologists today in the US and in 85 countries around the world.

Neural Network

Artificial Neural Networks (ANN) is a nonknowledge-based adaptive CDSS that uses a form of artificial intelligence, also known as machine learning, that allows the systems to learn from past experiences / examples and recognizes patterns in clinical information. It consists of nodes called neuron and weighted connections that transmit signals between the neurons in a forward or looped fashion. An ANN consists of 3 main layers: Input (data receiver or findings), Output (communicates results or possible diseases) and Hidden (processes data). The system becomes more efficient with known results for large amounts of data.

The advantages of ANN include the elimination of needing to program the systems and providing input from experts. The ANN CDSS can process incomplete data by making educated guesses about missing data and improves with every use due to its adaptive system learning. Additionally, ANN systems do not require large databases to store outcome data with its associated probabilities. Some of the disadvantages are that the training process may be time consuming leading users to not make use of the systems effectively. The ANN systems derive their own formulas for weighting and combining data based on the statistical recognition patterns over time which may be difficult to interpret and doubt the system’s reliability.

Examples include the diagnosis of appendicitis, back pain, myocardial infarction, psychiatric emergencies and skin disorders. The ANN’s diagnostic predictions of pulmonary embolisms were in some cases even better than physician’s predictions. Additionally, ANN based applications have been useful in the analysis of ECG (A.K.A. EKG) waveforms.

Genetic Algorithms

Genetic Algorithm (GA) is a nonknowledge-based method developed in the 1940s at the Massachusetts Institute of Technology based on Darwin’s evolutionary theories that dealt with the survival of the fittest. These algorithms rearrange to form different re-combinations that are better than the previous solutions. Similar to neural networks, the genetic algorithms derive their information from patient data.

An advantage of genetic algorithms is these systems go through an iterative process to produce an optimal solution. The fitness function determines the good solutions and the solutions that can be eliminated. A disadvantage is the lack of transparency in the reasoning involved for the decision support systems making it undesirable for physicians. The main challenge in using genetic algorithms is in defining the fitness criteria. In order to use a genetic algorithm, there must be many components such as multiple drugs, symptoms, treatment therapy and so on available in order to solve a problem. Genetic algorithms have proved to be useful in the diagnosis of female urinary incontinence.

Rule-Based System

A rule-based expert system attempts to capture knowledge of domain experts into expressions that can be evaluated known as rules; an example rule might read, “If the patient has high blood pressure, he or she is at risk for a stroke.” Once enough of these rules have been compiled into a rule base, the current working knowledge will be evaluated against the rule base by chaining rules together until a conclusion is reached. Some of the advantages of a rule-based expert system are the fact that it makes it easy to store a large amount of information, and coming up with the rules will help to clarify the logic used in the decision-making process. However, it can be difficult for an expert to transfer their knowledge into distinct rules, and many rules can be required for a system to be effective.

Rule-based systems can aid physicians in many different areas, including diagnosis and treatment. An example of a rule-based expert system in the clinical setting is MYCIN. Developed at Stanford University by Edward Shortliffe in the 1970s, MYCIN was based on around 600 rules and was used to help identify the type of bacteria causing an infection. While useful, MYCIN can help to demonstrate the magnitude of these types of systems by comparing the size of the rule base (600) to the narrow scope of the problem space.

The Stanford AI group subsequently developed ONCOCIN, another rules-based expert system coded in Lisp in the early 1980s.[8] The system was intended to reduce the number of clinical trial protocol violations, and reduce the time required to make decisions about the timing and dosing of chemotherapy in late phase clinical trials. As with MYCIN, the domain of medical knowledge addressed by ONCOCIN was limited in scope and consisted of a series of eligibility criteria, laboratory values, and diagnostic testing and chemotherapy treatment protocols that could be translated into unambiguous rules. Oncocin was put into production in the Stanford Oncology Clinic.

Logical Condition

The methodology behind logical condition is fairly simplistic; given a variable and a bound, check to see if the variable is within or outside of the bounds and take action based on the result. An example statement might be “Is the patient’s heart rate less than 50 BPM?” It is possible to link multiple statements together to form more complex conditions. Technology such as a decision table can be used to provide an easy to analyze representation of these statements.

In the clinical setting, logical conditions are primarily used to provide alerts and reminders to individuals across the care domain. For example, an alert may warn an anesthesiologist that their patient’s heart rate is too low; a reminder could tell a nurse to isolate a patient based on their health condition; finally, another reminder could tell a doctor to make sure he discusses smoking cessation with his patient. Alerts and reminders have been shown to help increase physician compliance with many different guidelines; however, the risk exists that creating too many alerts and reminders could overwhelm doctors, nurses, and other staff and cause them to ignore the alerts altogether.

Causal Probabilistic Network

The primary basis behind the causal network methodology is cause and effect. In a clinical causal probabilistic network, nodes are used to represent items such as symptoms, patient states or disease categories. Connections between nodes indicate a cause and effect relationship. A system based on this logic will attempt to trace a path from symptom nodes all the way to disease classification nodes, using probability to determine which path is the best fit. Some of the advantages of this approach are the fact that it helps to model the progression of a disease over time and the interaction between diseases; however, it is not always the case that medical knowledge knows exactly what causes certain symptoms, and it can be difficult to choose what level of detail to build the model to.

The first clinical decision support system to use a causal probabilistic network was CASNET, used to assist in the diagnosis of glaucoma. CASNET featured a hierarchical representation of knowledge, splitting all of its nodes into one of three separate tiers: symptoms, states and diseases.

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  3. 3^ Khosla, Vinod (December 4, 2012). “Technology will replace 80% of what doctors do”. Retrieved April 25, 2013.
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  6. ^ Gluud C, Nikolova D (2007). “Likely country of origin in publications on randomised controlled trials and controlled clinical trials during the last 60 years.”Trials 8: 7. doi:10.1186/1745-6215-8-7PMC 1808475PMID 17326823.
  7. ^ Wagholikar, K. “Modeling Paradigms for Medical Diagnostic Decision Support: A Survey and Future Directions”. Journal of Medical Systems. Retrieved 2012.
  8. ^ ONCOCIN: An expert system for oncology protocol management E. H. Shortliffe, A. C. Scott, M. B. Bischoff, A. B. Campbell, W. V. Melle, C. D. Jacobs Seventh International Joint Conference on Artificial Intelligence, Vancouver, B.C.. Published in 1981

SOURCE for Computation Engines Section and REFERENCES:

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

Cardiovascular Diseases: Decision Support Systems (DSS) for Disease Management Decision Making – DSS analyzes information from hospital cardiovascular patients in real time and compares it with a database of thousands of previous cases to predict the most likely outcome.

Can aviation technology reduce heart surgery complications?

Algorithm for real-time analysis of data holds promise for forecasting
August 13, 2012 | By 

British researchers are working to adapt technology from the aviation industry to help prevent complications among heart patients after surgery. Up to 1,000 sensors aboard aircraft help airlines determine when a plane requires maintenance, reports The Engineer, serving as a model for the British risk-prediction system.

The system analyzes information from hospital cardiovascular patients in real time and compares it with a database of thousands of previous cases to predict the most likely outcome.

“There are vast amounts of clinical data currently collected which is not analyzed in any meaningful way. This tool has the potential to identify subtle early signs of complications from real-time data,” Stuart Grant, a research fellow in surgery at University Hospital of South Manchester, says in a hospital statement. Grant is part of the Academic Surgery Unit working with Lancaster University on the project, which is still its early stages.

The software predicts the patient’s condition over a 24-hour period using four metrics: systolic blood pressure, heart rate, respiration rate and peripheral oxygen saturationexplains EE Times.

As a comparison tool, the researchers obtained a database of 30,000 patient records from the Massachusetts Institute of Technology and combined it with a smaller, more specialized database from Manchester.

In six months of testing, its accuracy is about 75 percent, The Engineer reports. More data and an improved algorithm could boost that rate to 85 percent, the researchers believe. Making the software web-based would allow physicians to access the data anywhere, even on tablets or phones, and could enable remote consultation with specialists.

In their next step, the researchers are applying for more funding and for ethical clearance for a large-scale trial.

U.S. researchers are working on a similar crystal ball, but one covering an array of conditions. Researchers from the University of Washington, MIT and Columbia University are using a statistical model that can predict future ailments based on a patient’s history–and that of thousands of others.

And the U.S. Department of Health & Human Services is using mathematical modeling to analyze effects of specific healthcare interventions.

Predictive modeling also holds promise to make clinical research easier by using algorithms examine multiple scenarios based on different kinds of patient populations, specified health conditions and various treatment regimens

To learn more:
- here’s the Engineer article
- check out the hospital report
- read the EE Times article

Related Articles:
Algorithm looks to past to predict future health conditions
HHS moves to mathematical modeling for research, intervention evaluation
Decision support, predictive modeling may speed clinical research

SOURCE:

Can aviation technology reduce heart surgery complications? – FierceHealthIT http://www.fiercehealthit.com/story/can-aviation-technology-reduce-heart-surgery-complications/2012-08-13#ixzz2SITHc61J

http://www.fiercehealthit.com/story/study-decision-support-systems-must-be-flexible-adaptable-transparent/2012-08-20

Medical Decision Making Tools: Overview of DSS available to date  

http://www.openclinical.org/dss.html

Clinical Decision Support Systems – used for Cardiovascular Medical Decisions

Stud Health Technol Inform. 2010;160(Pt 2):846-50.

AALIM: a cardiac clinical decision support system powered by advanced multi-modal analytics.

Amir A, Beymer D, Grace J, Greenspan H, Gruhl D, Hobbs A, Pohl K, Syeda-Mahmood T, Terdiman J, Wang F.

Source

IBM Almaden Research Center, San Jose, CA, USA.

Abstract

Modern Electronic Medical Record (EMR) systems often integrate large amounts of data from multiple disparate sources. To do so, EMR systems must align the data to create consistency between these sources. The data should also be presented in a manner that allows a clinician to quickly understand the complete condition and history of a patient’s health. We develop the AALIM system to address these issues using advanced multimodal analytics. First, it extracts and computes multiple features and cues from the patient records and medical tests. This additional metadata facilitates more accurate alignment of the various modalities, enables consistency check and empowers a clear, concise presentation of the patient’s complete health information. The system further provides a multimodal search for similar cases within the EMR system, and derives related conditions and drugs information from them. We applied our approach to cardiac data from a major medical care organization and found that it produced results with sufficient quality to assist the clinician making appropriate clinical decisions.

PMID: 20841805 [PubMed - indexed for MEDLINE]

DSS development for Enhancement of Heart Drug Compliance by Cardiac Patients 

A good example of a thorough and effective CDSS development process is an electronic checklist developed by Riggio et al. at Thomas Jefferson University Hospital (TJUH) [12]. TJUH had a computerized physician order-entry system in place. To meet congestive heart failure and acute myocardial infarction quality measures (e.g., use of aspirin, beta blockers, and angiotensin-converting enzyme (ACE) inhibitors), a multidisciplinary team including a focus group of residents developed a checklist, embedded in the computerized discharge instructions, that required resident physicians to prescribe the recommended medications or choose from a drop-down list of contraindications. The checklist was vetted by several committees, including the medical executive committee, and presented at resident conferences for feedback and suggestions. Implementation resulted in a dramatic improvement in compliance.

http://virtualmentor.ama-assn.org/2011/03/medu1-1103.html

Early DSS Development at Stanford Medical Center in the 70s

MYCIN (1976)     MYCIN was a rule-based expert system designed to diagnose and recommend treatment for certain blood infections (antimicrobial selection for patients with bacteremia or meningitis). It was later extended to handle other infectious diseases. Clinical knowledge in MYCIN is represented as a set of IF-THEN rules with certainty factors attached to diagnoses. It was a goal-directed system, using a basic backward chaining reasoning strategy (resulting in exhaustive depth-first search of the rules base for relevant rules though with additional heuristic support to control the search for a proposed solution). MYCIN was developed in the mid-1970s by Ted Shortliffe and colleagues at Stanford University. It is probably the most famous early expert system, described by Mark Musen as being “the first convincing demonstration of the power of the rule-based approach in the development of robust clinical decision-support systems” [Musen, 1999].

The EMYCIN (Essential MYCIN) expert system shell, employing MYCIN’s control structures was developed at Stanford in 1980. This domain-independent framework was used to build diagnostic rule-based expert systems such as PUFF, a system designed to interpret pulmonary function tests for patients with lung disease.

http://www.bmj.com/content/346/bmj.f657

ECG for Detection of MI: DSS use in Cardiovascualr Disease Management

http://faculty.ksu.edu.sa/AlBarrak/Documents/Clinical%20Decision%20Support%20Systems_Ch01.pdf

also showed that neural networks did a better job than two experienced cardiologists in detecting acute myocardial infarction in electrocardiograms with concomitant left bundle branch block.

Olsson SE, Ohlsson M, Ohlin H, Edenbrandt L. Neural networks—a diagnostic tool in acute myocardial infarction with concomitant left bundle branch block. Clin Physiol Funct Imaging 2002;22:295–299.

Sven-Erik Olsson, Hans Öhlin, Mattias Ohlsson and Lars Edenbrandt
Neural networks – a diagnostic tool in acute myocardial infarction with concomitant left bundle branch block
Clinical Physiology and Functional Imaging 22, 295-299 (2002) 

Abstract
The prognosis of acute myocardial infarction (AMI) improves by early revascularization. However the presence of left bundle branch block (LBBB) in the electrocardiogram (ECG) increases the difficulty in recognizing an AMI and different ECG criteria for the diagnosis of AMI have proved to be of limited value. The purpose of this study was to detect AMI in ECGs with LBBB using artificial neural networks and to compare the performance of the networks to that of six sets of conventional ECG criteria and two experienced cardiologists. A total of 518 ECGs, recorded at an emergency department, with a QRS duration > 120 ms and an LBBB configuration, were selected from the clinical ECG database. Of this sample 120 ECGs were recorded on patients with AMI, the remaining 398 ECGs being used as a control group. Artificial neural networks of feed-forward type were trained to classify the ECGs as AMI or not AMI. The neural network showed higher sensitivities than both the cardiologists and the criteria when compared at the same levels of specificity. The sensitivity of the neural network was 12% (P = 0.02) and 19% (P = 0.001) higher than that of the cardiologists. Artificial neural networks can be trained to detect AMI in ECGs with concomitant LBBB more effectively than conventional ECG criteria or experienced cardiologists.

http://home.thep.lu.se/~mattias/publications/papers/lu_tp_00_38_abs.html

Additional SOURCES:

http://www.implementationscience.com/content/6/1/92

http://www.fiercehealthit.com/story/study-decision-support-systems-must-be-flexible-adaptable-transparent/2012-08-20

 Comment of Note

During 1979-1983 Dr. Aviva Lev-Ari was part of Prof. Ronald A. Howard, Stanford University, Study Team, the consulting group to Stanford Medical Center during MYCIN feature enhancement development.

Professor Howard is one of the founders of the decision analysis discipline. His books on probabilistic modeling, decision analysis, dynamic programming, and Markov processes serve as major references for courses and research in these fields.

https://engineering.stanford.edu/profile/rhoward

It was Prof. Howard from EES, Prof. Amos Tversky of Behavior Science  (Advisor of Dr. Lev-Ari’s Masters Thesis at HUJ), and Prof. Kenneth Arrow, Economics, with 15 doctoral students in the early 80s, that formed the Interdisciplinary Decision Analysis Core Group at Stanford. Students of Prof. Howard, chiefly, James E. Matheson, started the Decision Analysis Practice at Stanford Research Institute (SRI, Int’l) in Menlo Park, CA.

http://www.sri.com/

Dr. Lev-Ari  was hired on 3/1985 to head SRI’s effort in algorithm-based DSS development. The models she developed were applied in problem solving for  SRI Clients, among them Pharmaceutical Manufacturers: Ciba Geigy, now NOVARTIS, DuPont, FMC, Rhone-Poulenc, now Sanofi-Aventis.

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Curator: Aviva Lev-Ari, PhD, RN

As an Introduction to the Genetics of Conduction Disease, we selected the following article which represents the MOST comprehensive review of the Human Cardiac Conduction System presented to date:

Circulation.2011; 123: 904-915 doi: 10.1161/​CIRCULATIONAHA.110.942284

The Cardiac Conduction System

  1. David S. Park, MD, PhD;
  2. Glenn I. Fishman, MD

+Author Affiliations


  1. From the Leon H. Charney Division of Cardiology, New York University School of Medicine, New York, NY.
  1. Correspondence to Glenn I. Fishman, MD, Leon H. Charney Division of Cardiology, New York University School of Medicine, 522 First Ave, Smilow 801, New York, NY 10016. E-mail glenn.fishman@med.nyu.edu

Key Words:

The human heart beats 2.5 billion times during a normal lifespan, a feat accomplished by cells of the cardiac conduction system (CCS). The functional components of the CCS can be broadly divided into the impulse-generating nodes and the impulse-propagating His-Purkinje system. Human diseases of the conduction system have been identified that alter impulse generation, impulse propagation, or both. CCS dysfunction is primarily due to acquired conditions such as myocardial ischemia/infarct, age-related degeneration, procedural complications, and drug toxicity. Inherited forms of CCS disease are rare, but each new mutation provides invaluable insight into the molecular mechanisms governing CCS development and function. Applying a multidisciplinary approach, which includes human genetic screening, biophysical analysis, and transgenic mouse technology, has yielded a broad array of gene families involved in maintaining normal CCS physiology (Figure 1). In this review, we discuss gene families that have been implicated in human CCS diseases of rhythm, conduction block, accessory conduction, and development (Table). We also investigate evolving therapeutic strategies that may serve as adjuvant or replacement therapy to current implantable pacemakers.

Figure 1.

View larger version:
Figure 1.

Cardiac conduction system cell. Genes identified in human cardiac conduction system disease are highlighted.

Table.

Genetic Basis of Conduction System Disease

Diseases of Automaticity

The human sinoatrial node (SAN) is a crescent-shaped, intramural structure with its head located subepicardially at the junction of the right atrium and the superior vena cava and its tail extending 10 to 20 mm along the crista terminalis.26 The SAN has complex 3-dimensional tissue architecture with central and peripheral components made up of distinct ion channel and gap junction expression profiles.27 Central and peripheral cells have different action potential characteristics and conduction properties (Figure 2).27Experimental and computational models have demonstrated that SAN heterogeneity is necessary to maintain normal automaticity and impulse conduction.28,,30

Figure 2.

Figure 2.

Electrophysiological heterogeneity of the sinoatrial node (SAN). The central SAN, the site of dominant pacemaking, is electronically insulated from the hyperpolarizing atrial myocardium through the differential expression of connexins and ion channels. Peripheral SAN cells are electrophysiologically intermediate between central cells and atrial cardiomyocytes. SR indicates sarcoplasmic reticulum.

Pacemaker automaticity is due to spontaneous diastolic depolarization of phase 4, which depolarizes the membrane to threshold potential generating rhythmic action potentials. The current paradigm of SAN automaticity has been modeled as 2 clocks that function in concert, the “membrane voltage clock” and the “calcium clock.” The membrane voltage clock is produced by the net disequilibrium between the decay of outward potassium currents (IK) and the activation of inward currents that include, but are not limited to, background sodium-sensitive current (Ib Na), L- and T-type calcium currents (ICa,L,ICa,T), sustained inward (Ist) current, and hyperpolarization-activated current (If) (Figure 2).27,31,,33

The subsarcolemmal calcium clock contributes to SAN diastolic depolarization through the spontaneous, rhythmic release of Ca2+ from the sarcoplasmic reticulum (SR) via the ryanodine type 2 receptor (RYR2).34 The local intracellular calcium (Cai) elevations drive the sodium-calcium exchange current (INCX) to substitute 1 intracellular Ca2+ for 3 extracellular Na+. The net gain in positive charge results in membrane depolarization.35The elevation of intracellular Ca2+ occurs in the latter third of diastolic depolarization and is sensitive to β-adrenergic stimulation.36

Human mutations affecting the voltage clock

  • (SCN5A and HCN4),

  • calcium clock (RYR2 and CASQ2), or both mechanisms

  • (ANKB) have been identified that negatively affect sinus node function.37,38

Diseases of Conduction BlockConduction block can occur at any level of the CCS and can manifest as sinoatrial exit block, atrioventricular block, infra-Hisian block, or bundle branch block. Impaired conduction can be caused by ion channel defects that alter action potential shape or by defective coupling between cardiomyocytes. Inherited defects in cardiac conduction have been linked to mutations in SCN5A and SCN1B (both affect phase 0) and KCNJ2 (affects phase 3 and 4). 

The cardiac sodium channel consists of the pore-forming α-subunit (encoded by SCN5A) and a modulatory β-subunit (encoded by SCN1B). The α-subunit contains a voltage sensor that allows for rapid activation in response to membrane depolarization. After depolarization, the sodium channel undergoes a period of inactivation, in which it is refractory to further impulses. SCN5A requires membrane repolarization to relieve the inactivated state. The inward rectifier potassium channel, Kir2.1, encoded by KCNJ2, maintains the resting membrane potential. Therefore, proper functioning of Nav1.5 and Kir2.1 is necessary for normal cardiac excitability.

SCN5A

Progressive cardiac conduction defect, or Lev-Lenègre disease, is characterized by age-related, fibrosclerotic degeneration of the His-Purkinje system.6 Impulse propagation through the proximal ventricular conduction system progressively declines, resulting in bundle branch blocks and eventually complete atrioventricular block. An inherited form of Lev-Lenègre disease is associated with loss of function mutations in SCN5A and can exist alone or as overlap syndromes with Brugada or long QT syndrome 3.6 Inherited progressive cardiac conduction defect is associated with a high risk of complete atrioventricular block and Stoke-Adams syncope without ventricular dysrhythmia.7 Schott et al8 identified a mutation in SCN5A that cosegregates with Lenègre disease in a large French family. Affected individuals had variable degrees of conduction block requiring pacemaker implantation in 4 family members because of syncope or complete heart block. Linkage analysis and candidate gene sequencing identified a T>C substitution at position +2 of the donor splice site of intron 22 (IVS22+2 T>C), which results in a mutant lacking the voltage-sensitive segment.8 Functional analysis demonstrated no transient inward sodium current in response to depolarization, consistent with a loss-of-function mutation.6

SCN1B

The majority of patients with Brugada and conduction disease do not have SCN5Amutations. Therefore, modifiers of Nav1.5 expression or function have become the target of candidate gene sequencing approaches. Watanabe et al9 identified SCN1B mutations in 3 families with conduction disease with or without Brugada syndrome. Coexpression of mutant β-subunits with Nav1.5 resulted in diminished sodium current.

KCNJ2

Mutations in KCNJ2 have been found in a rare autosomal dominant condition called Andersen-Tawil syndrome, characterized by periodic paralysis, dysmorphic features, polymorphic ventricular tachycardia, and cardiac conduction disease.10,11 ECG evaluation of 96 patients with Andersen-Tawil syndrome from 33 unrelated kindreds revealed conduction defects at multiple levels from the atrioventricular node to the distal conduction system.55 Cardiomyocytes expressing a dominant-negative subunit of Kir2.1 exhibited a 95% reduction in IK1, resulting in significant action potential prolongation. Mouse models of Andersen-Tawil syndrome exhibited a slower heart rate and significant slowing of conduction.56,57

Diseases of Accessory Conduction

Wolff-Parkinson-White (WPW) syndrome is characterized by preexcitation of ventricular myocardium via an accessory pathway (bundle of Kent) that bypasses the normal slow conduction through the atrioventricular node. Ventricular preexcitation is common, with a disease prevalence of 1.5 to 3 per 1000 people.22,58 Histological evaluation of Kent bundles resected from human subjects displayed features of typical ventricular myocytes with expression of connexin 43 (Cx43).59 The expression of high-conductance gap junctions in bypass tracts enables them to preexcite ventricular myocardium, manifesting as a short PR and a slurred QRS complex, or “delta wave,” on the ECG. The vast majority of WPW cases are sporadic, and the underlying mechanism remains unknown; however, rare inherited forms have been reported. Vidaillet et al60 determined that 3.4% of probands with WPW had 1 or more first-degree relatives with accessory conduction.

PRKAG2

A familial form of WPW with an autosomal dominant mode of transmission was identified in 2 families. Thirty-one affected individuals had evidence of preexcitation and cardiac hypertrophy. A missense mutation in PRKAG2 was identified that results in a constitutively active form of the γ2 regulatory subunit of AMP-activated protein kinase.22,23 Under normal conditions, AMP-activated protein kinase responds to energy-depleted states by increasing glucose uptake and promoting glycolysis. Transgenic mice expressing a heart-restricted, constitutively active mutant, PRKAG2N488I, recapitulated the human WPW phenotype of cardiac hypertrophy, preexcitation, and conduction defects. The predominant histological finding was ventricular myocyte engorgement with glycogen-laden vacuoles. The disruption of the annulus fibrosus by vacuolated ventricular myocytes resulted in the preexcitation phenotype.61 Using a mouse model of reversible glycogen-storage defect, Wolf et al62 demonstrated that the cardiomyopathy and CCS degeneration seen in PRKAG2N488I mice were reversible processes.

BMP2

Lalani et al24 reported a novel WPW syndrome associated with microdeletion of the bone morphogenetic protein-2 (Bmp2) region within 20p12.3 that is characterized by variable cognitive deficits and dysmorphic features. The BMPs are members of the transforming growth factor-β superfamily and play a critical role in cardiac development. Mice with cardiac deletion of BMP receptor type Ia (Bmpr1a) were embryonic lethal before E18.5 because of abnormal development of trabecular and compact myocardium, interventricular septum, and endocardial cushion.63 More restricted deletion of Bmpr1a in the atrioventricular canal resulted in defective atrioventricular valve formation and maturation defects in the annulus fibrosus, resulting in preexcitation.64,65

 

Diseases of CCS Development

Congenital heart disease is the most common form of birth defect, affecting 1% to 2% of live births.66 Arrhythmias may result from defective CCS specification/patterning, malformation or displacement of the conduction system, altered hemodynamics, prolonged hypoxic states, or postoperative sequelae.67,68 Developmentally, the conduction system derives from myocardial precursor cells within the fetal heart.69,,71The process by which conduction cells are specified or recruited into a “conduction” versus “working myocyte” lineage is determined by the regional expression of transcription factors.69,,74 The main transcription factors identified in human CCS development are the T-box and homeobox factors.

TBX5

Holt-Oram syndrome is an autosomal dominant condition characterized by preaxial radial ray limb deformities (defects of the radius, carpal bones, and/or thumbs) and cardiac septation defects. The septal defects are typically ostium secundum atrial septal defects, muscular ventricular septal defects, and atrioventricular canal defects. Patients with Holt-Oram syndrome manifest variable degrees of CCS dysfunction, such as sinus bradycardia and atrioventricular block, even in the absence of overt structural heart disease. In 1997, Basson et al18 screened 2 families with Holt-Oram syndrome and identified mutations in the T-box transcription factor, TBX5. The T-box transcription factors can function as transcriptional activators or repressors and are known to be critical regulators of cardiac specification and differentiation. Seven TBX family members are expressed in the developing heart, 3 of which (TBX1, TBX5, TBX20) have been linked to human congenital heart disease.75

Mice deficient in Tbx5 were embryonic lethal at E10.5 because of arrested development of the atria and left ventricle. Tbx5+/− mice recapitulated the upper limb and cardiac manifestations of human Holt-Oram syndrome, including the conduction abnormalities.72,76 Significant maturation defects in the atrioventricular canal and ventricular conduction system were present.76 Moskowitz et al76 demonstrated thatTbx5+/− mice have maturation failure of the atrioventricular canal manifesting as persistent atrioventricular rings around the tricuspid and mitral valves. Patterning defects were noted in the His bundle and bundle branches, including complete absence of right bundle branch formation in some cases. Expression of CCS-enriched markers, such as atrial natriuretic factor and Cx40, were found to be significantly downregulated, implicating TBX5 as a transcriptional activator of these genes. TBX5 and the homeobox transcription factor NKX2-5 were found to act synergistically in upregulating atrial natriuretic factor and Cx40 expression.76

Conduction Disease Associated With Neuromuscular Disorders

Neuromuscular disorders represent a diverse collection of diseases that commonly present with cardiac involvement. Mutations have been identified in genes involved in the cytoskeleton, nuclear envelope, and mitochondrial function. Cardiac involvement typically manifests as dilated or hypertrophic cardiomyopathy, atrioventricular conduction defects, and atrial and ventricular dysrhythmias.82

EMD and LMNA

Mutations affecting the nuclear envelope have been associated with significant CCS dysfunction. The inner membrane of the nuclear envelope is a highly organized structure, composed of integral membrane proteins and nuclear cytoskeletal proteins that function together in higher-order chromatin structure and transcriptional regulation. The lamins (A, B, and C) are an integral part of an intermediate filament network that imparts structural rigidity to the inner nuclear membrane. Emerin, a member of the nuclear lamina-associated protein family, putatively mediates anchoring of chromatin to the cytoskeleton. Mutations in emerin (EMD) or lamin A/C (LMNA) result in X-linked Emery-Dreifuss muscular dystrophy and autosomal dominant Emery-Dreifuss muscular dystrophy,20respectively. Individuals with Emery-Dreifuss muscular dystrophy develop progressive skeletal muscle weakness in the first decade of life and cardiac involvement (dilated cardiomyopathy and atrioventricular block) in the second decade.82,83

Arimura et al84 engineered a mouse model of autosomal dominant Emery-Dreifuss muscular dystrophy by knocking-in an Lmna missense mutation (H222P) previously identified from a family with typical autosomal dominant Emery-Dreifuss muscular dystrophy. The mouse model faithfully recapitulated the human disease with LmnaH222P/H222P mice exhibiting locomotive defects, dilated cardiomyopathy, and CCS dysfunction. Telemetric evaluation of the mutant mice revealed PR prolongation and QRS complex widening. A similar CCS defect was seen in mice haploinsufficient in the Lmna gene. Lmna+/− mice exhibited sinus bradycardia with variable degrees of atrioventricular block. Histological evaluation of these mice revealed nuclear deformation and apoptosis in atrioventricular node cells.85 Another engineered mouse line expressing LmnaN195K, known to cause autosomal dominant dilated cardiomyopathy with conduction disease in humans,86 exhibited high-grade atrioventricular block and complete heart block. Biochemical evaluation revealed reduced expression and mislocalization of Cx40 and Cx43 in mutant atrial tissue.87 Desmin staining also revealed structural defects of the sarcomere and intercalated discs.87

Genome-wide expression profiling of Lmna H222P mouse hearts revealed significant increases in mitogen-activated protein kinase (MAPK) signaling pathways.88Hyperactivation of MAPK pathways is associated with cardiomyopathy and CCS dysfunction. A significant increase of the activated forms of 2 MAPKs, JNK and ERK1/2, was noted in mutant hearts that predated the onset of overt or molecularly defined cardiomyopathy.88 Treatment of Lmna H222P mice with an inhibitor of ERK phosphorylation abrogated the increase in biomarkers of cardiomyopathy and restored ejection fraction to normal levels. These findings directly link MAPK hyperactivation to the cardiomyopathic phenotype in Lmna H222P mice.89

On the basis of the phenotypes of these mouse models, lamin A/C appears to maintain the functional integrity of the CCS in 2 ways: (1) protection of the nucleus against mechanical stress and (2) maintenance of proper chromatin organization to ensure accurate gene expression, such as in connexin expression and MAPK signaling pathways.83

Future Directions

Linkage analysis with positional cloning has been a highly effective means of identifying gene mutations within kindreds of monogenic disease. More than 1000 genes have been identified with this approach, including those in this review. With the sequencing of the human genome, the promise of identifying genetic causes of complex, multifactorial diseases is becoming more of a reality. One major step in this direction was the development of genome-wide association studies.94

The genome-wide association study is a test of association between a disease and genetic markers that span the entire genome. The technique relies on the fact that variance at one locus predicts with high probability variance of an adjacent locus because of linkage disequilibrium. In other words, there is nonrandom cosegregation of a series of genetic markers that are close together in the genome. This cluster of linked markers is known as a haplotype. The first study of haplotype structure within 4 populations (Yoruban, Northern/Western Europeans, Chinese, and Japanese) was published in Naturein 2005 by the International HapMap Consortium. Their work reported that individual genetic markers (single nucleotide polymorphisms) predict adjacent markers typically with a resolution of ≈30 000 bp. Considering that the human genome is ≈3×109 bp, they projected that <500 000 single nucleotide polymorphisms would be needed to survey the entire genome for all common genetic variants.94,95

Genome-wide association studies have now been used to identify genetic variants that influence ECG parameters in different populations. Intermediate parameters, such as heart rate or PR interval, were used as surrogate markers of disease for 2 reasons: (1) They have an association with cardiovascular morbidity and atrial fibrillation, and (2) they have tighter associations with gene variants than the actual disease. Holm et al96reported several genome-wide associations using a cutoff P value <1.6×10−9. One locus harboring MYH6 was associated with heart rate, 4 loci (TBX5SCN10ACAV1, andARHGAP24) were associated with PR interval, and 4 loci (TBX5SCN10A6p21, and10q21) were associated with QRS duration. They went on to test these associations with individuals manifesting different arrhythmias in an Icelandic and Norwegian population. Correlations were found between atrial fibrillation and TBX5 and CAV1 (P=4.0×10−5 andP=0.00032, respectively), between advanced atrioventricular block and TBX5 (P=0.0067), and between pacemaker implantation and SCN10A (P=0.0029).

Similar loci were identified by 2 additional independent genome-wide association studies in a European population and an Indian Asian population. Pfeufer et al97 reported 9 loci that were highly associated with PR interval (P<5×10−8) from a meta-analysis of the CHARGE Consortium with >28 000 European subjects. One locus had associations with 2 sodium channels (SCN10A and SCN5A), and 6 loci were near genes involved in cardiac development (CAV1-CAV2NKX2-5SOX5WNT11MEIS1and TBX5-TBX3). Of these,SCN10ASCN5ACAV1-CAV2NKX2-5, and SOX5 were found to be associated with atrial fibrillation. Chambers et al98 also reported the association between SCN10A and PR interval in 6543 Indian Asians. Physiological testing of Scn10a-deficient mice revealed shortened PR intervals in knockout mice with no significant difference in all other ECG and echocardiographic parameters.

The discovery of novel gene families associated with human conduction and arrhythmic diseases with the use of genome-wide association studies is well under way. Identification of SCN10A by 3 independent groups studying different populations confirms the fidelity of this approach. Further experiments confirming the significance of these associations will need to be performed. In addition to identifying novel gene targets, this technique will also aid in the discovery of new associations with noncoding regions in which new epigenetic modifiers and transcriptional/translational regulators, such as microRNAs, will be identified.

Therapeutic Strategies

The current standard of care for symptomatic bradycardia due to conduction system disease is the implantation of an electronic pacemaker. Despite their success, electronic pacemakers have limitations, which include lead complications, finite battery life, potential for infection, lack of autonomic responsiveness, and size restriction in younger patients. These limitations have spurred on the development of biological pacemakers, the premise of which is to restore pacemaking activity with the use of viral-based or stem cell–based gene delivery systems.99 The identification and characterization of genes involved in generating pacemaker currents have allowed biological pacemaker technology to become a reality.

The restoration of sinus pacing rates can be achieved by modulating inward and outward currents to establish or increase the slope of diastolic depolarization in cardiac tissue. Increasing inward currents and/or decreasing outward currents increase the slope of diastolic depolarization and therefore the pacing rate. Genes that have been investigated or are under current investigation include the following: (1) β2-adrenergic receptor,100,101(2) dominant-negative Kir2.1 mutants,102 (3) adenylate cyclase type VI (ACVI),103,104and (4) HCN channels.105 The β2-adrenergic receptor and adenylate cyclase type VI both increase cAMP levels, leading to activation of endogenous HCN channels and calcium clock mechanisms. Although initial animal models using the β2-adrenergic receptor showed promise with transient increases in heart rate, the potential for proarrhythmia and the inability of this approach to establish de novo pacemaker activity limited its efficacy.101

Another approach focused on modifying ionic currents that convert working myocardial cells, which have relatively stable diastolic potentials, into cells with phase 4 diastolic depolarization. It was postulated that atrial and ventricular myocytes have the potential for automaticity, but that hyperpolarizing currents, such as IK1, prevent diastolic depolarization by stabilizing the resting membrane potential. Miake et al102 confirmed this hypothesis when they demonstrated that adenoviral delivery of a dominant-negative Kir2.1 construct into the left ventricle of guinea pigs resulted in conversion of quiescent myocytes into pacemaker cells. Unfortunately, significant action potential prolongation limited the clinical utility of this treatment strategy.102

Rosen and colleagues105,106 demonstrated that automaticity could be induced in quiescent myocardium with the use of heterologous expression of HCN channels that produce the pacemaker current If. Qu and Plotnikov et al demonstrated that stable autonomous rhythms could be generated when adenovirus encoding HCN2 was injected into the left atrium105 or left bundle branch106 of a canine heart. To bypass the limitations of viral-based systems, such as host immune response, several groups reported the successful use of cell-based delivery systems. Plotnikov et al107 reported the successful implantation of human mesenchymal stem cells expressing HCN2 in the left ventricle of a canine model of atrioventricular block. Dogs maintained stable ectopic pacemaker activity for >6 weeks without the use of immunosuppression.107 Human mesenchymal stem cells electronically couple to host myocardium through gap junctions; therefore, conditions with significant gap junction remodeling may affect the efficacy of this method.

Although standalone biological pacemakers may be far into the future, adjuvant biological pacemakers may find real-world utility for current deficiencies of electronic pacemakers, such as limited battery life and device infections. For example, biological preparations used in conjunction with device therapy may be used to extend battery life, decreasing the frequency of generator changes. Transient injectable pacemakers may also function as bridge therapy after lead extraction of an infected device. The need for adjuvant biological pacemakers is clear, but continued refinement of gene- and cell-based delivery systems will be necessary to make this technology a reality.99

Conclusion

Although rare, inherited arrhythmias have become an invaluable tool in identifying the genetic determinants of CCS function. Each new mutation enhances our understanding and appreciation of the biochemical and structural complexity needed for cardiac impulse generation and propagation. This methodology is hampered, however, by the relative scarcity of inherited conditions affecting the CCS. The addition of genome-wide association studies has broadened this search for novel genes beyond rare familial afflictions to include common, multifactorial conditions. It is hoped that this exciting new frontier will bring to light the complex interplay of genes and genetic/epigenetic modifiers that influence the prevalence of common diseases. These genetic screens will ultimately yield a bevy of new gene targets for pharmaceutical or gene-based therapeutics of the future.

Sources of Funding

Studies in the Fishman laboratory are supported by National Institutes of Health grants HL64757, HL081336, and HL82727 and a New York State STEM award (to Dr Fishman) and a Heart Rhythm Foundation Fellowship (to Dr Park).

Genetics of Atrioventricular Conduction Disease in Humans.

Benson DW.

Source

Division of Cardiology, ML7042, Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA. woody.benson@cchmc.org

Abstract

Atrioventricular (AV) conduction disease (block) describes impairment of the electrical continuity between the atria and ventricles. Classification of AV block has utilized biophysical characteristics, usually the extent (first, second, or third degree) and site of block (above or below His bundle recording site). The genetic significance of this classification is unknown. In young patients, AV block may result from injury or be the major cardiac manifestation of neuromuscular disease. However, in some cases, AV block has unknown or idiopathic cause. In such cases, familial clustering has been noted and published pedigrees show autosomal dominant inheritance; associated heart disease is common (e.g., congenital heart malformation, cardiomyopathy). The latter finding is not surprising given the common origin of working myocytes and specialized conduction system elements. Using genetic models incorporating reduced penetrance (disease absence in some individuals with disease gene), variable expressivity (individuals with disease gene have different phenotypes), and genetic heterogeneity (similar phenotypes, different genetic cause), molecular genetic causes of AV block are being identified. Mutations identified in genes with diverse functions (transcription, excitability, and energy homeostasis) for the first time provide the means to assess risk and offer insight into the molecular basis of this important clinical condition previously defined only by biophysical characteristics.

http://www.ncbi.nlm.nih.gov/pubmed/15372490

Additional Studies on Genetic Congenital AV Block

1) 12738236
Na+ channel mutation leading to loss of function and non-progressive cardiac conduction defects.
BACKGROUND: We previously described a Dutch family in which congenital cardiac conduction disorder has clinically been identified. The ECG of the index patient showed a first-degree AV block associated with extensive ventricular conduction delay. Sequencing of the SCN5A locus coding for the human cardiac Na+ channel revealed a single nucleotide deletion at position 5280, resulting in a frame-shift in the sequence coding for the pore region of domain IV and a premature stop codon at the C-terminus. METHODS AND RESULTS: Wild type and mutant Na+ channel proteins were expressed in Xenopus laevis oocytes and in mammalian cells. Voltage clamp experiments demonstrated the presence of fast activating and inactivating inward currents in cells expressing the wild type channel alone or in combination with the beta1 subinut (SCN1B). In contrast, cells expressing the mutant channels did not show any activation of inward current with or without the beta1 subunit. Culturing transfected cells at 25 degrees C did not restore the Na+ channel activity of the mutant protein. Transient expression of WT and mutant Na+ channels in the form of GFP fusion proteins in COS-7 cells indicated protein expression in the cytosol. But in contrast to WT channels were not associated with the plasma membrane. CONCLUSIONS: The SCN5A/5280delG mutation results in the translation into non-function channel proteins that do not reach the plasma membrane. This could explain the cardiac conduction defects in patients carrying the mutation.

2) 12956334
The genetic origin of atrioventricular conduction disturbance in humans.
Atrioventricular (AV) conduction disturbance (block) describes impairment of the electrical continuity between the atria and ventricles. Clinical classification of AV block has utilized biophysical characteristics, usually the extent (1st, 2nd, 3rd degree) and site of block (above or below His bundle recording site). The genetic significance of this classification is not known. In some casesAV block occurrence is associated with intrauterine exposure to maternal antibody (anti-Ro, anti-La), and other cases are associated with injury (e.g. surgery). Based on familial clustering of idiopathic AV block, a genetic cause has also been suspected. Published pedigrees show autosomal dominant inheritance, and associated heart disease is common (e.g. congenital heart malformation, cardiomyopathy, etc.). The latter finding is not unexpected given the common origin of working myocytes and elements of the specialized conduction system. Using genetic models incorporating reduced penetrance (presence of disease genotype in absence of phenotype), variable expressivity (presence of a disease genotype with variable phenotypes) and genetic heterogeneity (similar phenotypes, different disease genotypes), molecular genetic causes of AV block are being identified. These findings are significant as they provide insight into the molecular basis of a clinical condition previously defined only by biophysical characteristics.

3) 15372490
Genetics of atrioventricular conduction disease in humans.
Atrioventricular (AV) conduction disease (block) describes impairment of the electrical continuity between the atria and ventricles. Classification of AV block has utilized biophysical characteristics, usually the extent (first, second, or third degree) and site of block (above or below His bundle recording site). The genetic significance of this classification is unknown. In young patients, AV block may result from injury or be the major cardiac manifestation of neuromuscular disease. However, in some cases, AV blockhas unknown or idiopathic cause. In such cases, familial clustering has been noted and published pedigrees show autosomal dominant inheritance; associated heart disease is common (e.g., congenital heart malformation, cardiomyopathy). The latter finding is not surprising given the common origin of working myocytes and specialized conduction system elements. Using genetic models incorporating reduced penetrance (disease absence in some individuals with disease gene), variable expressivity (individuals with disease gene have different phenotypes), and genetic heterogeneity (similar phenotypes, different genetic cause), molecular genetic causes of AV block are being identified. Mutations identified in genes with diverse functions (transcription, excitability, and energy homeostasis) for the first time provide the means to assess risk and offer insight into the molecular basis of this important clinical condition previously defined only by biophysical characteristics.

SOURCE:

New Research on the Genetics of Conduction Disease

2010  
Heart failure clinics

  

conduction diseases (CD) include defects in impulse generation and conduction. Patients with CD may manifest a wide range of clinical presentations, from asymptomatic to potentially life-threatening arrhythmias. The pathophysiologic mechanisms underlying CD are diverse and may have implications for diagnosis, treatment, and prognosis. Known causes of functional CD include cardiac ion channelopathies or defects in modifying proteins, such as cytoskeletal proteins. Progress in molecular biology and genetics along with development of animal models has increased the understanding of the molecular mechanisms of these disorders. This article discusses the genetic basis for CD and its clinical implications.
(Beinart et al. 2010)
Beinart R, Ruskin J, et al. (2010). The genetics of conduction disease. Heart Fail Clin 6 (2): 201-14.
PMID: 20347788  DOI: 10.1016/j.hfc.2009.11.006  PII: S1551-7136(09)00108-1
2012  
PLoS genetics

  

(Curran and Mohler 2012)
Curran J and Mohler PJ (2012). Defining the Pathways Underlying the Prolonged PR Interval in Atrioventricular Conduction Disease. PLoS Genet. 8 (12): e1003154.
PMID: 23236297  DOI: 10.1371/journal.pgen.1003154  PII: PGENETICS-D-12-02668
2003  
BMC medical genetics

  

BACKGROUND: Mutations in the gene encoding the nuclear membrane protein lamin A/C have been associated with at least 7 distinct diseases including autosomal dominant dilated cardiomyopathy withconduction system disease, autosomal dominant and recessive Emery Dreifuss Muscular Dystrophy, limb girdle muscular dystrophy type 1B, autosomal recessive type 2 Charcot Marie Tooth, mandibuloacral dysplasia, familial partial lipodystrophy and Hutchinson-Gilford progeria.METHODS: We used mutation detection to evaluate the lamin A/C gene in a 45 year-old woman with familial dilated cardiomyopathy and conduction system disease whose family has been well characterized for this phenotype 1.RESULTS: DNA from the proband was analyzed, and a novel 2 base-pair deletion c.908_909delCT in LMNA was identified.CONCLUSIONS: Mutations in the gene encoding lamin A/C can lead to significant cardiac conductionsystem disease that can be successfully treated with pacemakers and/or defibrillators. Genetic screening can help assess risk for arrhythmia and need for device implantation.
(MacLeod et al. 2003)
MacLeod HM, Culley MR, et al. (2003). Lamin A/C truncation in dilated cardiomyopathy with conduction disease. BMC Med. Genet. 4: 4.
PMID: 12854972  DOI: 10.1186/1471-2350-4-4
2012  
Heart (British Cardiac Society)

  

(MacRae 2012)
MacRae CA (2012). Pattern recognition: combining informatics and genetics to re-evaluate conduction disease. Heart 98 (17): 1263-4.
PMID: 22875820  DOI: 10.1136/heartjnl-2012-302408  PII: heartjnl-2012-302408
2004  
The anatomical record. Part A, Discoveries in molecular, cellular, and evolutionary biology

  

Atrioventricular (AV) conduction disease (block) describes impairment of the electrical continuity between the atria and ventricles. Classification of AV block has utilized biophysical characteristics, usually the extent (first, second, or third degree) and site of block (above or below His bundle recording site). The genetic significance of this classification is unknown. In young patients, AV block may result from injury or be the major cardiac manifestation of neuromuscular disease. However, in some cases, AV block has unknown or idiopathic cause. In such cases, familial clustering has been noted and published pedigrees show autosomal dominant inheritance; associated heart disease is common (e.g., congenital heart malformation, cardiomyopathy). The latter finding is not surprising given the common origin of working myocytes and specialized conduction system elements. Using genetic models incorporating reduced penetrance (disease absence in some individuals with diseasegene), variable expressivity (individuals with disease gene have different phenotypes), and genetic heterogeneity (similar phenotypes, different genetic cause), molecular genetic causes of AV block are being identified. Mutations identified in genes with diverse functions (transcription, excitability, and energy homeostasis) for the first time provide the means to assess risk and offer insight into the molecular basis of this important clinical condition previously defined only by biophysical characteristics.
(Benson 2004) – ORIGINAL FIRST PAPER on the Subject
Benson DW (2004). Genetics of atrioventricular conduction disease in humans. Anat Rec A Discov Mol Cell Evol Biol 280 (2): 934-9.
PMID: 15372490  DOI: 10.1002/ar.a.20099
SOURCE:
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Other related articles published on this Open Access Online Scientific Journal, include the following:

Aviva Lev-Ari, PhD, RN and Larry H. Bernstein, MD, FCAP

Read Full Post »


Reporter: Aviva Lev-Ari, PhD, RN

UPDATED on 5/9/2013 – based on Sondra’s e-mail to me on 5/9/2013

Sondra’s Voice on 5/9

I was SHOCKED and ecstatic to discover that the book hit #1 Amazon best seller among cell biology books.  It was also in the top 100 of “new thought” books.

Thank you so much for helping it get there.  If you already purchased a book, please take the time to write a review at Amazon,  GoodReads, Sounds True, wherever you enjoy reading about books.

If you haven’t yet received a copy, here’s an opportunity to win a free copy.

As mentioned last time, Tami Simon, founder and publisher of Sounds True, interviewed me recently for her Insights at the Edge series -Part 1:  YOUR CELLS ARE LISTENING.  If you’d like a candid look at my current and controversial interpretation of our cells’ intelligence, please listen.  You can also read the transcript of the interview. You may even discover for yourself, what your cells know to help you thrive.

Part two of the interview is now out.  It was fun to do.  You can download a file, read the transcript, enjoy!

I’m keeping this short and to the point.  You’ve helped make the book reach one goal – it can now be called an Amazon best-seller.  However an even bigger goal is to share the helpful information inside the book to folks who can use it – healers, people challenged by illness, stress, spiritual seekers, thinkers and tinkerers.

To that end, I am once again ‘out in the world’ doing book signings (July, August), workshops (August), and talks (September-November). I’d like to offer experential programs also to children so if you have any ideas or leads for that possibility, please let me know.

We’re also working on radio interviews and other media outreach.  What I am discovering – it’s as much work, if not more, promoting the book as it was to write it.  It is not so much just about the book, it’s what’s  inside.  Just like you and me, it’s what’s inside that is the most important to other people.

Stretch Your Self

One of the core themes in Secrets of Your Cells is the fact that tensions and stresses on our cells’ inner matrix  influence their actions and health.  When we extrapolate what has been learned by science about this structure of our cells, we find that it is a place where yoga, walking, stretching, dancing, singing, qigong, can have their beneficial effects.

A profound scientific discovery, first by Harvard scientist Dr. Donald Ingber, showed that stretching  and releasing tensions by the cell affects genetic expression. In other words, the simple practice of contracting and releasing physical tensions reverberates to our tiniest cells and even to our invisible consciousness.

Take your cells for a walk.  They will show their thanks in many ways.

Most promising forthcoming book by my friend, another University of California, Berkeley Alumna, Sondra Barett, PhD

Her acclaimed gift in Photography adorns the Cover Page of our forthcoming e-Book on Genomics, scroll down for the second image by Sondra Barett, PhD

http://pharmaceuticalintelligence.com/biomed-e-books/genomics-orientations-for-personalized-medicine/volume-one-genomics-orientations-for-personalized-medicine/

Sondra’s Voice:

I’m writing to tell you about a forthcoming book, Secrets of Your Cells: Discovering

Your Body’s Inner Intelligence (Sounds True, on sale May 1, 2013) by Sondra Barrett,

PhD, biochemist, mind-body medicine teacher, and author.

About the book:

Secrets of Your Cells: Discovering Your Body’s Inner Intelligence puts cutting-edge

biology into practice for healing body, mind, and spirit. Bringing together a powerful

synthesis of easy-to understand science and ancient wisdom

traditions, “Secrets” offers a compelling and controversial new

look at our cells as our hidden teachers.

Researching children’s cancers brought medical scientist Sondra

Barrett, PhD into real life issues of families suffering, life, and

death. It also catapulted her into a spiritual quest to discover

more about healing.

In Secrets of Your Cells, Dr. Barrett takes an expansive

approach to our cellular universe. As she moves from our

molecular creation, she frames our cells’ roles in human health

and culture in a completely new and fresh way. By exploring the

development, design, and intelligence of human cells and working with people with lifethreatening

illnesses, Dr. Barrett became intrigued that perhaps the inner life of our cells

could add value to our own personal lives.

Beyond their biochemical abilities and knowledge for living, listening and thriving, our

cells carry powerful intelligence to assist us in letting go, diminishing stress and finding

deeper meaning in life.

• What can cells teach us about letting go that may influence genetic expression?

• What 5 things do our cells reveal about thriving physically and spiritually?

• What and where is cellular intelligence?

Willingly embracing the deep-rooted conflict between science and spirituality, Dr. Barrett

offers new controversial ideas that ancient sacred traditions may, in fact, have roots in

our cells and molecules. By searching for the sacred within our cells we might well find

the divine within ourselves.

One tip from your cells: Remembering gratitude with your heart, senses and mind of

your cells brings peacefulness to all of you.

For fans of Dr. Bruce Lipton (Biology of Belief) or Dr. Candace Pert (Molecules of

Emotion), Dr. Barrett’s provocative ideas and practical strategies will further inspire and

educate them.

Author’s BIO

Sondra Barrett, PhD, is a medical scientist and teacher with a degree in biochemistry

from the University of Illinois Medical School followed by a post-doctoral fellowship in

immunology and hematology at the University of California Medical School (UCSF). She

was on the faculty at UCSF for a decade engaged in basic cancer research, which led

her to bridge medical science and healing strategies for children and adults with lifethreatening

illnesses.

She has delivered programs throughout the United States as well as for University of

California, California Pacific Medical Center, Sonoma State, Apple Computer, Esalen,

California Institute of Integral Studies and numerous institutions throughout the Bay

Area. An award-winning photographer and long-time student of qigong and shamanism,

Sondra also explores the inner world of wine and our senses and is the author of book

Wine’s Hidden Beauty.

Book Title: SECRETS OF YOUR CELLS: Discovering Your Body’s Inner Intelligence

Author: Sondra Barrett, PhD

ISBN: 978-1-60407-626-4

ebook ISBN: 978-1-60407-819-0

Publication date: May 1, 2013

Publisher: Sounds True

Books are available online at Sounds True, Amazon, Barnes and Noble, Indie Books

and bookstores.

Additional Links

Online Interviews - “Insights at the Edge” – Sounds True publisher Tami Simon

Part 1 Your Cells are listening.

PART 2: Your Cells are listening. (Imagery, genetic expression, sacred symbols in our

cells

Press Room

Author’s website:

PRESS CONTACT: Wendy Gardner, WendyG@soundstrue.com,

303.665.3151 x114

CONTACT:

Sondra Barrett 707-799-0833

sondra@sondrabarrett.com

3171 Ross Rd. #305, Graton, CA 95444

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Heroes in Medical Research: Dr. Robert Ting, Ph.D. and Retrovirus in AIDS and Cancer

Curator and Reporter: Stephen J. Williams, PhD

This is the second posting in this series in which I highlight the basic research which led to seminal breakthroughs in the medical field, brought on by the result of basic inquiry, thorough and detailed investigation, meticulously following the scientific method, and eventually leading to development of important medical therapies.

In his autobiography, Virus Hunting: AIDS, Cancer & the Human Retrovirus: A Story of Scientific Discovery, Dr. Robert Gallo, M.D. describes a wonderful story of the history behind, scientific biographies, and chronology of the discoveries which led he and his colleagues (including co-discoverer Dr. Luke Montagnier) to recognize retroviruses (in particular HIV) as the leading culprit for the cause of AIDS and in the etiology of Kaposi’s sarcoma.   For anyone who appreciates the history behind scientific discoveries and appreciates learning about the multitude of individual efforts which are the crux of seminal research, this book is a must read.

Recommendations from the back cover include:

Virus Hunting will be read and reread, for years to come.” —New York Newsday

“Provides a human, revealing look into the arcane, usually secret confines of laboratory science.”

Martin Delany, Project Inform

..as well as others.

While a fascinating aspect of this book is the description, like fitting pieces of a puzzle, of the important discoveries throughout history which are the necessary foundations for further investigations and discoveries, more important is a telling, personal narrative of the people involved in those initial and subsequent discoveries.  In fact, the book has over 396 colleagues, mentors, technicians, students, and even critiques who are given credit, in one form or another, for the ultimate discovery of HIV as a causative agent for the development of AIDS. The book is a literal Who’s Who in Science and shows how important personal collaboration and friendships are in the process of scientific discovery.

In 1972, Dr. Seymour Perry had appointed the young Dr. Robert Gallo as head of a new department, the Human Tumor Cell Biology Branch, renamed the Laboratory of Tumor Cell Biology.  The lab was carrying on the work on tRNA that Dr. Gallo had performed in Dr. Sid Perska’s group at NIH.  However, with the help of new lab members Dr. David Gillespie, Dr. Flossie Wong-Staal, and Dr. Marjorie Robert-Guroff the lab focused on the search for disease-causing retroviruses, especially in human leukemias.  This was, in part, due to conversations with Dr. Robert Huebner and Todaro, who insisted that

“within the genetic makeup of this endogenous retroviral material was, they suggested, a special gene, the oncogene, that was the parent of the cancer-causing protein”

which may explain some of the early work by Rous concerning the Rous sarcoma virus.

Enter in Gallo’s good friend Dr. Bob Ting.  Dr. Gallo had known Dr. Ting socially since 1966, shortly after Gallo had arrived at NIH.  Dr. Bob Ting was a well-established NCI investigator, who was doing work on DNA and RNA oncogenic viruses of animals.  Originally from a large and wealthy family in Hong Kong, Dr. Ting had worked with Nobel Prize winners Salvatore Luria (who worked on phages) and Renato Dulbecco, who, along with his well-known cell culture media, had made the seminal discoveries that led to our knowledge how some DNA viruses can transform normal animal cells into neoplastic-like cells in culture.

Bob Ting gave a talk on these oncogenic viruses and Gallo was very interested in his observations that oncogenic viruses like Rous and Maloney, could transform cells in vitro in a matter of days.

A friendship developed between the two over tennis matches and Chinese food.  During this time, Dr. Ting made the important suggestion that they both collaborate and use the viral systems developed by Dulbecco.  Ting also introduced him to RNA viruses, Dr. Robert Huebner, and Dr. Howard Temin.  It was, in part, due to these associations that Gallo started looking, in earnest, at the possibility of RNA retroviruses in leukemias. Thus, just like the internet today, connections and networking provided new insights into current research, and helped lead the advent of new discoveries, therapies, and scientific disciplines.

Therefore, “after some late-night discussion with Bob Ting, I decided to enter the fray. My own laboratory, … would immediately be set up to compare the properties of reverse transcriptase enzymes from many different animal retroviruses”.

Although the rest is more history, this early friendship, collaboration, and mentoring by Bob Ting had “transformed” Gallo’s research efforts to set him up to make some of the important discoveries eventually leading to the discovery of the role of HIV in AIDS.

A video interviewing Dr. Gallo can be found here:

VIEW VIDEO

https://www.youtube.com/watch?v=ELRlXLGWu4I

A very nice writeup/obituary for Dr. Ting was written by Patricia Sullivan of the Washington Post and is included below.

Robert Ting, 77; Biotech Pioneer

ME/Ting-ob

Dr. Robert Ting’s biotech company in Rockville developed the first FDA-approved diagnostic test kits to test for HIV antibodies. (By Gerald Martineau — The Washington Post)

 

By Patricia Sullivan

Washington Post Staff Writer
Friday, September 22, 2006

Robert C.Y. Ting, 77, a research scientist who started one of the early biotechnology companies in the Washington area, died Sept. 11 of complications after cardiac surgery at the Cleveland Clinic in Cleveland.

Dr. Ting founded Biotech Research Laboratories Inc. in Rockville in 1973, producing cells for government scientists to use in research. Eleven years later, his firm obtained a federal license to develop and produce the first FDA-approved diagnostic test kits for HIV antibody confirmation.

Robert C. Gallo, who co-discovered the HIV virus as the cause of AIDS, called Dr. Ting a pioneer in the field who popularized the term “biotechnology” when he moved from research to entrepreneurship.

“He introduced me to virology, and he did it twice,” said Gallo, director of the Institute of Human Virology in Baltimore. The men had known each other since the 1960s, and while playing tennis one day, Dr. Ting advised the cancer researcher to look at new research in viruses. Later, when Gallo was studying leukemia, Dr. Ting directed him to animal research in leukemia. “First he showed me how viruses change cells. Then he introduced me to retrovirology. . . . I went into retrovirology solely because of those discussions with Bob Ting on tennis courts,” Gallo said.

Dr. Ting, whom Gallo described as a quiet, modest man, was born in Shanghai, the son of a physician to Gen. Chiang Kai-Shek. His family fled the country during the Japanese invasion of China during World War II and moved to Hong Kong. Soon after, he moved to the United States, where he received a bachelor’s degree and in 1956 a master’s degree in genetics from Amherst College.

He received a doctoral degree in microbiology and biochemistry from the University of Illinois in 1960 under Salvador E. Luria, who later won the 1969 Nobel Prize in Medicine and Physiology. Dr. Ting spent the next two years on a postdoctoral fellowship at the California Institute of Technology, working with Renato Dulbecco, who later won the 1975 Nobel Prize in Medicine and Physiology. Their work focused on how viruses cause tumors.

“A lot of molecular biology developed from this,” Dr. Ting told The Washington Post in 1984 from his Rockville office, cluttered with scientific journals, awards and a large blackboard. “There was so much evidence in animal systems [that viruses cause tumors], that the next question was obvious — can you find the equivalent in humans.”

Dr. Ting joined the National Institutes of Health in 1962 as a visiting fellow and then a senior research scientist at the National Cancer Institute. From 1966 to 1968, he was an associate editor for the Journal of the National Cancer Institute.

In 1969, he joined Litton Bionetics Inc. in Rockville as director of experimental oncology, leading a project funded by the institute to search for viruses in human leukemia patients. He became scientific director of the cancer research branch the next year.

With academic, government and private business experience under his belt, Dr. Ting decided to go into business on his own and in 1973 started Biotech Research Laboratories in Rockville. It was a profitable supplier of research services and supplies until 1981, when it went public and produced the HIV diagnostic test kits. It became one of the most successful public biotech companies in the area in the mid-1980s.

The Economic Development Board of Singapore invited him to return to Asia to start a biotech company, which he did in 1985, forming Diagnostic Biotechnology Ltd. He also joined the Institute of Molecular and Cell Biology at the National University of Singapore, which Gallo called “the most prominent Asian academic biotechnology center.”

He returned to the United States in 1998 to join the board of Cell Works Inc. in Baltimore, and became chair and chief executive of a joint venture, Cell Works Asia Limited, in 2000.

Most recently, Dr. Ting was the founding president and chief executive of Profectus Biosciences Inc. of Baltimore, previously known as Maryland BioTherapeutics Inc.

Dr. Ting was past chairman of the F.F. Fraternity, one of the oldest Chinese fraternities in the United States. He was also a member of the Organization of Chinese Americans in the D.C. area since its inception in the early 1970s. He enjoyed tennis, golf, ballroom dancing and international travel. He also was a wine connoisseur.

Survivors include his wife of 44 years, Sylvia Han Ting of Potomac; three children, Anthony Ting of Shaker Heights, Ohio, Andrew Ting of Beverly, Mass., and Jennifer Chow of Potomac; seven sisters; and seven grandchildren.

An obituary written from his son Anthony can be found here:

https://www.amherst.edu/aboutamherst/magazine/in_memory/1953/robertting

Sources:

http://www.amazon.com/Virus-Hunting-Retrovirus-Scientific-Discovery/dp/0465098150

http://www.washingtonpost.com/wp-dyn/content/article/2006/09/21/AR2006092101936.html

Other articles/postings related to this topic and HIV on this site includes:

Heroes in Medical Research: Barnett Rosenberg and the Discovery of Cisplatin

History of medicine, science, and society: 200 Years of the New England Journal of Medicine

Why did Pauling Lose the “Race” to James Watson and Francis Crick? How Crick Describes his Discovery in a Letter to his Son

John Randall’s MRC Research Unit and Rosalind Franklin’s role at Kings College

Interview with the co-discoverer of the structure of DNA: Watson on The Double Helix and his changing view of Rosalind Franklin

Otto Warburg, A Giant of Modern Cellular Biology

Inspiration From Dr. Maureen Cronin’s Achievements in Applying Genomic Sequencing to Cancer Diagnostics

Nanotechnology and HIV/AIDS treatment

HIV vaccine: Caltech puts us One step further

Getting Better: Documentary Videos on Medical Progress — in Surgery, Leukemia, and HIV/AIDS.

Read Full Post »


Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing[1]

Curator and Reporter: Stephen J. Williams, Ph.D.

Genomic instability is considered a hallmark and necessary for generating the mutations which drive tumorigenesis. Multiple studies had suggested that there may be multiple driver mutations and a plethora of passenger mutations driving a single tumor.  This diversity of mutational spectrum is even noticed in cultured tumor cells (refer to earlier post Genome-Wide Detection of Single-Nucleotide and Copy-Number Variation of a Single Human Cell).  Certainly, intratumor heterogeneity has been a concern to clinicians in determining the proper personalized therapy for a given cancer patient, and has been debated if multiple biopsies of a tumor is required to acquire a more complete picture of a tumor’s mutations.  In the New England Journal of Medicine, lead author Dr. Marco Gerlinger in the laboratory of Dr. Charles Swanton of the Cancer Research UK London Research Institute, and colleagues reported the results of a study to determine if intratumoral differences exist in the mutational spectrum of primary and metastatic renal carcinomas, pre- and post-treatment with the mTOR (mammalian target of rapamycin) inhibitor, everolimus (Afinitor®)[1].

The authors compared exome sequencing of multiregion biopsies from four patients with metastatic renal-cell carcinoma who had been enrolled in the Personalized RNA Interference to Enhance the Delivery of Individualized Cytotoxic and Targeted Therapeutics clinical trial of everolimus (E-PREDICT) before and after cytoreductive surgery.

Biopsies taken:

  • Multiregion spatial biopsy of primary tumor (representing 9 regions of the tumor)
  • Chest-wall metastases
  • Perinephric metastases
  • Germline DNA as control

Multiple platforms were used to determine aberrations as follows:

  1. Illumina Genome Analyzer IIx and Hiseq: for sequencing and mutational analysis
  2. Illumina Omni 2.5: for SNP (single nucleotide polymorphism)-array-based allelic imbalance detection for chromosomal imbalance and ploidy analysis
  3. Affymetrix Gene 1.0 Array: for mRNA analysis

A phylogenetic reconstruction of all somatic mutations occurring in primary disease and associated metastases was  performed to determine the clonal evolution of the metastatic disease given the underlying heterogeneity of the tumor.  Basically the authors wanted to know if the mutational spectra of one metastasis could be found in biopsies taken from the underlying primary tumor or if the mutational landscape of metastases had drastically changed.

Results

Multiregion exon-capture sequencing of DNA from pretreatment biopsy samples of the primary tumor, chest wall metastases, and perinephrous metastasis revealed 128 mutations classified as follows:

  • 40 ubiquitous mutations
  • 59 mutations shared by several but not all regions
  • 29 mutations unique to specific regions
  • 31 mutations shared by most primary tumor regions
  • 28 mutations shared by most metastatic regions

The authors mapped these mutations out with respect to their location, in order to determine how the metastatic lesions evolved from the primary tumor, given the massive heterogeneity in the primary tumor.  Construction of this “phylogenetic tree” (see Merlo et. al[2]) showed that the disease evolves in a branched not linear pattern, with one branch of clones evolving into a metastatic disease while another branch of clones and mutations evolve into the primary disease.

One of the major themes of the study is shown by results that an average of 70 somatic mutations were found in a single biopsy (a little more than just half of all tumor mutations) yet only 34% of the mutations in multiregion biopsies were detected in all tumor regions.

This indicated to the authors that “a single biopsy was not representative of the mutational landscape of the entire bulk tumor”. In addition, microarray studies concluded that gene-expression signatures from a single biopsy would not be able to predict outcome.

Everolimus therapy did not change the mutational landscape.  Interestingly, allelic composition and ploidy analyses revealed an extensive intratumor heterogeneity, with ploidy heterogeneity in two of four tumors and 26 of 30 tumor samples containing divergent allelic-imbalances.  This strengthens the notion that multiple clones with diverse genomic instability exist in various regions of the tumor.

 The intratumor heterogeneity reveals a convergent tumor evolution with associated heterogeneity in target function

Genes commonly mutated in clear cell carcinoma[3, 4] (and therefore considered the prevalent driver mutations for renal cancer) include:

Only VHL mutations were found in all regions of a given tumor, however there were three distinct SETD2 mutations (frameshift, splice site, missense) which were located in different regions of the tumor.

SETD2 trimethylates histones at various lysine residues, such as lysine residue 36 (H3K36).  The trimethylation of H3K36 is found on many actively transcribed genes.  Immunohistochemistry showed trimethylated H3K36 was reduced in cancer cells but positive in most stromal cells and in SETD2 wild-type clear-cell carcinomas.

Interestingly most regions of the primary tumor, except one, contained a kinase-domain activating mutation in mTOR.  Immunohistochemistry analysis of downstream target genes of mTOR revealed that mTOR activity was enhanced in regions containing this mutation.  Therefore the intratumoral heterogeneity corresponded to therapeutic activity, leading to the impression that a single biopsy may result in inappropriate targeted therapy.   Additional downstream biomarkers of activity confirmed both the intratumoral heterogeneity of mutational spectrum as well as an intratumoral heterogeneity of therapeutic-target function.

The authors conclude that “intratumor heterogeneity can lead to underestimation of the tumor genomics landscape from single tumor biopsies and may present major challenges to personalized-medicine and biomarker development”.

In an informal interview with Dr. Swanton, he had stressed the importance of performing these multi-region biopsies and the complications that intratumoral heterogeneity would present for personalized medicine, biomarker development, and chemotherapy resistance.

Q: Your data clearly demonstrates that multiple biopsies must be done to get a more complete picture of the tumor’s mutational landscape.  In your study, what percentage of the tumor would be represented by the biopsies you had performed?

Dr. Swanton: Realistically this is a very difficult question to answer, the more biopsies we sequence, the more we find, in the near term it may be very difficult to ever formally address this in large metastatic tumours

Q:  You have very nice data which suggest that genetic intratumor heterogeneity complicates the tumor biomarker field? do you feel then that quests for prognostic biomarkers may be impossible to attain?

Dr. Swanton: Not necessarily although heterogeneity is likely to complicate matters

Identifying clonally dominant lesions may provide better drug targets

Predicting resistance events may be difficult given the potential impact of tumour sampling bias and the concern that in some tumours a single biopsy may miss a relevant subclonal mutation that may result in resistance

Q:  Were you able to establish the degree of genomic instability among the various biopsies?

Dr. Swanton:  Yes, we did this by allelic imbalance analysis and found that the metastases were more genomically unstable than the primary region from which the metastasis derived

Q: I was actually amazed that there was a heterogeneity of mTOR mutations and SETD2 after everolimus therapy?   Is it possible these clones obtained a growth advantage?

Dr. Swanton: We think so yes, otherwise we wouldn’t identify recurrent mutations in these “driver genes”

Dr. Swanton will present his results at the 2013 AACR meeting in Washington D.C. (http://www.aacr.org/home/scientists/meetings–workshops/aacr-annual-meeting-2013.aspx)

The overall points of the article are as follows:

  • Multiple biopsies of primary tumor and metastases are required to determine the full mutational landscape of a patients tumor
  • The intratumor heterogeneity will have an impact on the personalized therapy strategy for the clinician

 

  • Metastases arising from primary tumor clones will have a greater genomic instability and mutational spectrum than the tumor from which it originates

 

  • Tumors and their metastases do NOT evolve in a linear path but have a branched evolution and would complicate biomarker development and the prognostic and resistance outlook for the patient

A great video of Dr. Swanton discussing his research can be viewed here

VIEW VIDEO

Everolimus: an inhibitor of mTOR

The following information was taken from the New Medicine Oncology Database (http://www.nmok.net)

Developer

Designation

Description

Approved/Filed Indications

Novartis PharmaCurrent as of: August 30, 2012 Generic Name: Everolimus
Brand Name: Afinitor
Other Designation: RAD001, RAD001C
RAD001, an ester of the macrocytic immunosuppressive agent sirolimus (rapamycin), is an inhibitor of mammalian target of rapamycin (mTOR) kinase.Administration Route: intravenous (IV) • PO • solid organ transplant
• renal cell carcinoma (RCC), metastatic after failure of treatment with sunitinib, sorafenib, or sunitinib plus sorafenib
• renal cell carcinoma, advanced, refractory to treatment with vascular endothelial growth factor (VEGF)-targeted therapy
• treatment of progressive neuroendocrine tumors (NET) of pancreatic origin (PNET) in patients with inoperable, locally advanced or metastatic disease

Marker Designation
Alias
Gene Location

Marker Description

Indications

5’-AMP-activated Protein Kinase (AMPK)AMPK beta 1 (beta1 non-catalytic subunit) • HAMPKb (beta1 non-catalytic subunit) • MGC17785 (beta1 non-catalytic subunit) • AMPK2 (alpha1 catalytic subunit) • PRKAA (alpha1 catalytic subunit) • AMPK alpha 1 (alpha1 catalytic subunit) • AMPKa1 ( AMPK is a member of a metabolite-sensing protein kinase family found in all eukaryotes. It functions as a cellular fuel sensor and its activation strongly suppresses cell proliferation in non-malignant cells and cancer cells. AMPK regulates the cell cycle by upregulating the p53-p21 axis and modulating the TSC2-mTOR (mammalian target of rapamycin) pathway. The AMPK signaling network contains a number of tumor suppressor genes including LKB1, p53, TSC1 and TSC2, and modulates growth factor signaling involving proto-oncogenes including PI3K, Akt and ERK. AMPK activation is therefore therapeutic target for cancer (Motoshima H, etal, J Physiol, 1 Jul 2006; 574(Pt 1): 63–71).AMPK is a protein serine/threonine kinase consisting of a heterotrimeric complex of a catalytic alpha subunit and regulatory ß and gamma subunits. AMPK is activated by increased AMP/ATP ratio, under conditions such as glucose deprivation, hypoxia, ischemia and heat shock. It is also activated by several hormones and cytokines. AMPK inhibits ATP-consuming cellular events, protein synthesis, de novo fatty acid synthesis, and generation of mevalonate and the downstream products in the cholesterol synthesis pathway (Motoshima H, etal, J Physiol, 1 Jul 2006; 574(Pt 1): 63–71). - ovarian cancer
- brain cancer
- liver cancer
- leukemia
- colon cancer
CREB regulated transcription coactivator 2 (CRTC2)TOR complex 2 (TORC2, mTORC2) • RP11-422P24.6 • transducer of regulated cAMP response element-binding protein (CREB)2 • transducer of CREB protein 2 • TOR1Location: 1q21.3 The mammalian target of rapamycin (mTOR) exists in two complexes, TORC1 and TORC2, which are differentially sensitive to rapamycin. cAMP response element-binding protein (CREB) regulated transcription coactivator 2 (CRTC2) or TORC2 is a multimeric kinase composed of mTOR, mLST8, mSin1, and rictor. The complex is insensitive to acute rapamycin exposure and functions in controlling cell growth and actin cytoskeletal assembly.TORC2 controls gene silencing, telomere length maintenance, and survival under DNA-damaging conditions. It is primaily located in the cytoplasm but also shuttles into the nucleus (Schonbrun M, etal, Mol Cell Biol, Aug 2009;29(16):4584-94). - brain cancer
Hypoxia inducible factor 1 alpha (HIF1A)HIF1-alpha (HIF-1 alpha) • HIF-1A • PASD8 • MOP1 • bHLHe78Location: 14q21-q24 The alpha subunit of the hypoxia inducible factor 1 (HIF-1alpha) is a 826 amino acid antigen consisting of a basic helix-loop-helix (bHLH)-PAS domain at its N-terminus. HIF-1alpha is rapidly degraded by the proteasome under normal conditions, but is stabilized by hypoxia resulting in the transactivation of several proangiogenic genes. HIF-1alpha is responsible for inducing production of new blood vessels as needed when tumors outgrow existing blood supplies. HIF-1alpha serves as a transcriptional factor that regulates gene expression involved in response to hypoxia and promotes angiogenesis.HIF-1alpha is a proangiogenic transcription factor induced primarily by tumor hypoxia that is critically involved in tumor progression, metastasis and overall tumor survival. HIF-1alpha functions as a survival factor that is required for tumorigenesis in many types of malignancies, and is expressed in a majority of metastases and late-stage tumors. HIF-1alpha is overexpressed in brain, breast, colon, endometrial, head and neck, lung, ovarian, and pancreatic cancer, and is associated with increased microvessel density and/or VEGF expression - prostate cancer
- bladder cancer
- nasopharyngeal cancer
- head and neck cancer
- kidney cancer
- pancreatic cancer
- endometrial cancer
- breast cancer
Mammalian target of rapamycin (mTOR)FK506 binding protein 12-rapamycin associated protein 1 • RAFT1 • FK506 binding protein 12-rapamycin associated protein 2 • FRAP • FRAP1 • FRAP2 • RAPT1 • FKBP-rapamycin associated protein • FKBP12-rapamycin complex-associated protein 1 • rapamycin target protein • TOR • FLJ44809 • MTORC1 • MTORC2 • RPTOR • RAPTOR • KIAA1303 • mammalian target of rapamycin complex 1Location: 1p36.22 The mammalian target of rapamycin (mTOR) is a large serine/threonine protein (Mr 300,000) having heat repeats, and protein-protein interaction domains at its amino terminus, and a protein kinase domain at its carboxy terminus. mTOR is a member of the phosphoinositide 3-kinase (PI3K)-related kinase (PIKK) family and a central modulator of cell growth. It regulates cell growth, proliferation and survival by impacting on protein synthesis and transcription. mTOR is present in two multi-protein complexes, a rapamycin-sensitive complex, TOR complex 1 (TORC1), defined by the presence of Raptor and a rapamycin insensitive complex, TOR complex 2 (TORC2), with Rictor, Protor and Sin1. Rapamycin selectively inhibits mTORC1 by binding indirectly to the mTOR/Raptor complex via FKBP12, resulting in inhibition of p70S6kinase but not the mTORC2 substrate AKTSer473. Selective inhibition of p70S6K attenuates negative feedback loops to IRS1 and TORC2 resulting in an increase in pAKT which may limit the activity of rapamycin.In a hypoxic environment the increase in mass of solid tumors is dependent on the recruitment of mitogens and nutrients. As a function of nutrient levels, particularly essential amino acids, mTOR acts as a checkpoint for ribosome biogenesis and cell growth. Ribosome biogenesis has long been recognized in the clinics as a predictor of cancer progression; increase in size and number of nucleoli is known to be associated with the most aggressive tumors and a poor prognosis. In bacteria, ribosome biogenesis is independently regulated by amino acids and energy charge. The mTOR pathway is controlled by intracellular ATP levels, independent of amino acids, and mTOR itself is an ATP sensor (Kozma SC, etal, AACR02, Abs. 5628). - breast cancer
- pancreatic cancer
- multiple myeloma
- liver cancer
- brain cancer
- prostate cancer
- kidney cancer
- lymphoma
Signal transducer and activator of transcription 3 (STAT3)Stat-3 • acute-phase response factor (APRF) • FLJ20882 • HIESLocation: 17q21 Signal transducer and activator of transcription 3 (STAT3) is a member of the STAT protein family. STAT3, plays a critical role in hematopoiesis. STAT3 is located in the cytoplasm and translocated to the nucleus after tyrosine phosphorylation. In response to cytokines and growth and other activation factors, STAT family members are phosphorylated by the receptor associated kinases and then form homo- or heterodimers, which translocate to the cell nucleus where they act as transcription activators. - multiple myeloma
- hematologic malignancy
- lymphoma
Sonic hedgehog homolog (SHH)Shh • HHG1 • HHG-1 • holoprosencephaly 3 (HPE3) • HLP3 • SMMCILocation: 7q36 Sonic hedgehog, a secreted hedgehog ligand, is a human homolog of the Drosophila segment polarity gene hedgehog, cloned by investigators at Harvard University (Marigo V, etal, Genomics, 1 Jul 1995;28 (1):44-51).The mammalian sonic hedgehog (Shh) pathway controls proliferation of granule cell precursors in the cerebellum and is essential for normal embryonic development. Shh signaling is disrupted in a variety of malignancies. - pancreatic cancer
- CNS cancer

References:

1.         Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P et al: Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. The New England journal of medicine 2012, 366(10):883-892.

2.         Merlo LM, Pepper JW, Reid BJ, Maley CC: Cancer as an evolutionary and ecological process. Nature reviews Cancer 2006, 6(12):924-935.

3.         Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, Davies H, Jones D, Lin ML, Teague J et al: Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 2011, 469(7331):539-542.

4.         Dalgliesh GL, Furge K, Greenman C, Chen L, Bignell G, Butler A, Davies H, Edkins S, Hardy C, Latimer C et al: Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature 2010, 463(7279):360-363.

Other Articles related to this topic appeared on this Open Access Online Scientific Journal, including the following:

AMPK Is a Negative Regulator of the Warburg Effect and Suppresses Tumor Growth In Vivo

Genomics of bronchial epithelial dysplasia

Genomics in Medicine- Tomorrow’s Promise

Prostate Cancer: Androgen-driven “Pathomechanism” in Early-onset Forms of the Disease

CRACKING THE CODE OF HUMAN LIFE: Recent Advances in Genomic Analysis and Disease – Part IIC

CRACKING THE CODE OF HUMAN LIFE: The Birth of BioInformatics and Computational Genomics – Part IIB

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variation of a Single Human Cell

Directions for Genomics in Personalized Medicine

LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment: Part 2

Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine – Part 1

Harnessing Personalized Medicine for Cancer Management, Prospects of Prevention and Cure: Opinions of Cancer Scientific Leaders @ http://pharmaceuticalintelligence.com

In Focus: Targeting of Cancer Stem Cells

Modulating Stem Cells with Unread Genome: microRNAs

What can we expect of tumor therapeutic response?

 

Read Full Post »


ethicspersonalizedmedicine-page1

Ethical Concerns in Personalized Medicine: BRCA1/2 Testing in Minors and Communication of Breast Cancer Risk

Reporter/Curator: Stephen J. Williams, Ph.D.

Dealing with the unexpected: consumer responses to direct-access BRCA mutation testing[1]

Direct-to-consumer (DTC) genetic testing and genetic health information in 2007 with the advent of personalized testing services by companies who offered microarray-based genotyping of single-nucleotide-polymorphisms (SNP) which had strong correlations to disease risk.  Three companies started to offer such services directly to the consumer:

A common test which is offered analyzes the consumers BRCA1/2 mutation status.  Three mutations in the BRCA gene are known to predispose women to hereditary breast and ovarian cancer: BRCA1 185delAG, BRCA1 538insC, and BRCA2 617delT.  These BRCA1 mutation confer a 60% breast cancer risk and a 40% risk of ovarian cancer while the BRCA2 mutation confers a breast cancer risk of 50% and 20% risk of ovarian cancer.

However, the commercial availability of this genetic disease-risk associated testing has led to certain ethical issues concerning communication and responses of risk information by:

  1. Consumers who request BRCA1/2 testing (focus of the Francke article
  2. BRCA1/1 testing and communication of results to minors and relatives (Bradbury: see below)

There has been much opinion, either as commentary in literature, meeting proceedings, or communiques from professional societies warning that this type of “high-impact” genetic information should not be given directly to the consumer as consumers will not fully understand the information presented to them, be unable to make proper risk-based decisions, results could cause panic and inappropriate action such as prophylactic oophorectomy or unwarranted risk-reduction mastectomy, or false reassurance in case of negative result and reduced future cancer screening measures taken by the consumer.  However, there have been few studies to investigate these concerns.

A report by Dr. Uta Francke in the open access journal PeerJ, assesses and quantifies the emotional and behavioral reactions of consumers to their 23andMe Personal Genome Service® report of the three BRCA mutations known to be associated with high risk for breast/ovarian cancer.  One hundred thirty six (136) individuals, who tested positive for BRCA1 and/or BRCA2 mutations as well as 160 users of the service, who tested mutation-free were invited to participate in phone interviews addressing personal and family history of cancer, decision and timing of viewing the BRCA report, recollection of results, emotional responses, perception of personal cancer risk, information sharing, and actions taken.  Thirty two (32) mutation carriers (16 female and 16 male) and 31 non-carriers responded to the phone questionnaire.

Questions were based on the following themes:

  1. When you purchased the 23andME Personal Genome Service® were you aware that it included testing for mutations that predispose to breast and ovarian cancer?
  2. Were you aware that having Ashkenazi Jewish ancestry influences your risk of carrying one of the three mutations?
  3. Have you or a first or second degree relative been diagnosed with breast, ovarian or any other cancer?
  4. What did you learn from your results?
  5. Were you surprised by the result?
  6. How did you feel about this information (extremely, moderately, somewhat upset or extremely relieved)?

Results:  Eleven women and 14 men had received an unexpected result that they are carriers of one of the three mutations however none of them reported extreme anxiety and only four reported moderate anxiety which did not last long.  Participants were at least 8 years of age. Five women and six men described their reaction as neutral.  Most carrier women sought medical advice and four underwent risk-reducing procedures. Some to the male carriers felt burdened to share their test results with their female relatives, which led to additional screenings of relatives.  Almost all of the mutation-positive customers appreciated learning their BRCA mutational status.

Other highlights of the results include:

  • More women got tested if they had a first or second degree relative previously diagnosed with breast/ovarian cancer
  • Ten mutation-positive individuals who were surprised at the test results cited the lack of family history of breast/ovarian cancer as the reason for their surprise.  The rest who were surprised at their positive test results believed that the frequency of these mutations were low in the general population so they shouldn’t have been affected.
  • For the mutation-positive group, none of the 32 reported as being “extremely upset”.
  • Interestingly, on male who learned, for the first time, he was a positive carrier for BRCA mutation, reported feeling “relieved” because his daughter who was also tested by 23andMe had not acquired his mutation.

A brief interview with Dr. Francke follows:

Q:     In your results you had noted that none of the mutation carriers showed extreme anxiety about their reports however there were many of Ashkenazi descent who was well aware of the increased risk to breast cancer.  In another study by Dr. Angela Bradbury, anxieties and communication to their children depended on mutation status and education status.  Do you feel that most women in your study were initially aware they could be in a high risk category for cancer, whether breast, ovarian, or other?

Dr. Francke:   As we show in Table 1, 6 of 16 women and 6 of 16 men who found out that they were BRCA mutation carriers had not been aware that being of Ashkenazi descent confers an increased risk of breast/ovarian cancer.  In Table S1, we show that 6 of these 32 people did not self-identify as Ashkenazi.
Q:     The reporting and communication of test results to offspring and genetic testing of offspring as a result of positive tests has been under much debate.  I had noticed that there was a high proportion of relatives who went for screening after learning of a family members BRCA testing, whether it showed a mutation or not.  Some studies have shown that offspring of carriers may misinterpret genetic testing results and take inappropriate action, such as considering having early testing  before age 25.  It appears some anxiety may be due to misinformation and lack of genetic counseling.  Should these test results be considered in guidelines for oncologist such as NCCN guidelines with respect to informing family members using genetic counselors as an intermediary?

Dr. Francke:    The “high proportion of relatives who went for screening after learning of a family member’s BRCA testing”, were only those related to a BRCA-positive person. Most of the BRCA testing of relatives was done through health care providers at Myriad as these people were eligible for insurance coverage of the test. In our interviews we found no evidence for inappropriate action of carriers or non-carriers. With one exception, we found no evidence for misinterpretation or “anxiety due to lack of genetic counseling”.  In our online reports we recommend genetic counseling for all customers who have questions about their results.

Q:     I was also particularly interested the male carrier felt a heightened burden to tell their offspring.  This has been suggested in other studies.  I would assume the mothers and not the fathers would feet more pressure to tell their children.  Is there a reason for this?
Dr. Francke:     The heightened burden reported by the male carriers was mostly about the realization of the risk for their daughters, not so much about to telling their offspring.  Female carriers were primarily concerned about their own health risk and management, and decision-making about preventive measures – therefore, the risk for offspring appeared to be of secondary concern for them.

However, the availability of this type of predictive genetic testing for hereditary cancer has raised some ethical issues regarding the communication of risk and genetic results to family members and especially offspring, specifically whether informing minors would incur unnecessary testing, anxiety among minors of parents who tested positive for genetic risk-factors, or even premature risk-reduction surgeries or medical interventions.

The aforementioned ethical issues concerning communicating results of BRCA mutational testing to offspring was addressed by two large studies conducted by Dr. Angela Bradbury M.D. and colleagues at Fox Chase Cancer Center Family Risk Assessment Program (now she is at University of Pennsylvania) and University of Chicago Cancer Risk Clinic.  These studies evaluated the parental opinions regarding BRCA1/2 testing of minors, and how parents communicate BRCA1/2 genetic testing with their children.

In the JCO article (Parent Opinions Regarding the Genetic Testing of Minors for BRCA1/2)[2], Bradbury and colleagues used semistructured interviews (yes/no questions and open-ended questions) of 246 parents at Fox Chase and University of Chicago, who underwent BRCA1/2 whether they supported testing of minors in general and testing of their own offspring.  Parents were asked, “If you were deciding, do you think children under 18 years old should be given the opportunity to be tested” and followed by the open-ended question: “Why do (don’t) you support the genetic testing of minors for BRCA1/2?”.

Results:  In response to the first question (Would you support testing in minors) 37% of parents supported testing of minors in the general population.  The follow-up open-ended question revealed that 4% support testing minors in some or all circumstances.  This decision was independent of parent sex or race.  44% of parents would test their own offspring.  Parents who opposed testing in minors thought testing would cause fear and anxiety for their children but those who supported unconditional testing (regardless of whether they were positive for the BRCA mutation or not) mentioned that the medical information would foster better health behaviors in their offspring.  21% of parents who opposed testing minors, in general, actually supported testing of their own children.  Interestingly parents who tested positive for the BRCA1 overwhelmingly (64%) opposed testing of minors, in general.  In addition, statistical analysis of the open-ended questions revealed that parents who did not have a college degree, had a negative test result, and were non white favored testing of their own children.  The authors had suggested larger studies before any guidelines were given as to whether testing in minors of BRCA mutation carriers should be standard.

In a recent publication by Dr. Bradbury and colleagues (Knowledge and perceptions of familial and genetic risks for breast cancer risk in adolescent girls)[3],  studied how adolescent girls understood and responded to breast cancer risk by interviewing 11-19 year-old girls at high-risk and population-risk for breast cancer. Although most girls said they were aware of increased risk because either a family member had or was predisposed to breast cancer (66 %) only 17 % of girls were aware of BRCA1/2 genes. Mother was the most frequently reported source of information for breast cancer among both high-risk (97 %) and population-risk (89 %) girls.  The study also showed that most girls who believe they are at high-risk could alter their lifestyles or change dietary habits to lower their risk.

In an adjacent study in the journal Cancer[4], Bradbury and colleagues at Fox Chase Cancer Center had gauged the frequency with which parents had told their children of their BRCA1/2 teat results and how their children felt about the results.

When parents disclose BRCA1/2 test results: Their communication and perceptions of offspring response[4]

Semi-structured interviews were conducted with parents who had BRCA1/2 testing and at least 1 child <25 YO.  A total of 253 parents completed interviews (61% response rate), reporting on 505 offspring. Twenty-nine percent of parents were BRCA1/2 mutation carriers. Three hundred thirty-four (66%) offspring learned of their parent’s test result. Older offspring age (P ≤ .01), offspring gender (female, P = .05), parents’ negative test result (P = .03), and parents’ education (high school only, P = .02) were associated with communication to offspring. The most frequently reported initial offspring responses were neutral (41%) or relief (28%). Thirteen percent of offspring were reported to experience concern or distress (11%) in response to parental communication of their test results. Distress was more frequently perceived among offspring learning of their parent’s BRCA1/2 positive or variant of uncertain significance result.

CONCLUSIONS:

Many parents communicate their BRCA1/2 test results to young offspring. Parents’ perceptions of offspring responses appear to vary by offspring age and parent test result. A better understanding of how young offspring respond to information about hereditary risk for adult cancer could provide opportunities to optimize adaptive psychosocial responses to risk information and performance of health behaviors, in adolescence and throughout an at-risk life span.

Below is an excellent article by Steven Reinberg from HealthDay interviewing Dr. Angela Bradbury concerning their JCO study: (reported for ABC News at http://abcnews.go.com/Health/Healthday/story?id=4508346&page=1#.UVNJUVef2RM)

Many Parents Share Genetic Test Findings With Kids

By Steven Reinberg
HealthDay Reporter

Mar. 23

FRIDAY, Aug. 17 (HealthDay News) — As genetic testing for diseases becomes more commonplace, the impact of those findings on family members may be underestimated, researchers say.

For instance, some women who discover they have the BRCA gene mutation, which puts them at higher risk for breast cancer, choose to tell their children about it before the children are old enough to understand the significance or deal with it, a new study found.

“Parents with the BRCA mutation are discussing their genetic test results with their offspring often many years before the offspring would need to do anything,” said study author Dr. Angela Bradbury, director of the Fox Chase Cancer Center’s Family Risk Assessment Program, in Philadelphia.

According to Bradbury, more than half of parents she surveyed told their children about genetic test results. Some parents reported that their children didn’t seem to understand the significance of the information, and some had initial negative reactions to the news.

“A lot of genetic information is being shared within families and there hasn’t been a lot of guidance from health-care professionals,” Bradbury said. “While this genetic risk may be shared accurately, there is risk of inaccurate sharing.”

In the study, Bradbury’s team interviewed 42 women who had the BRCA mutation. The researchers found that 55 percent of parents discussed the finding and the risk of breast cancer with at least one of their children who was under 25.

Also, most of the women didn’t avail themselves of the services of a doctor or genetic counselor in helping to tell their children, Bradbury’s group found.

Bradbury is concerned that sharing genetic information with young children can create anxiety. “The children could be overly concerned about their own risk at a time when there is nothing that they need to do,” she said.

But, she added, “it may be possible that sharing may be good for children in adapting to this information.”

The findings are published in the Aug. 20 issue of the Journal of Clinical Oncology.

The lack of definitive data on when — or if — to discuss genetic test results with children is a real problem, Bradbury said.

“As we move genetic testing forward for cancer or other illnesses, we have to consider the context of the whole family and focus our counseling to the whole family, and not just the person who comes in for testing,” Bradbury said. “We should learn more about how and when we should talk to children about this, so that we can promote healthy behaviors without causing too much anxiety for the offspring.”

Barbara Brenner, executive director of Breast Cancer Action, agreed that the psychological component of genetic testing needs more attention.

“This is the tip of a very scary iceberg,” Brenner said. “We don’t know the psychological consequences [of BRCA testing], not only to the person who has the test, but to her family members.”

Brenner thinks guidelines to help parents deal with this information are needed. So is help from doctors and genetic counselors in counseling family members, especially children, she added.

LEGACY (Lessons in Epidemiology and Genetics of Adult Cancer from Youth), supported by the National Institutes of Health. This study will follow the girls prospectively in order to evaluate epidemiologic and epigenetic pathways of childhood exposures in relation to pubertal development, age at menarche, breast tissue characteristics, biomarkers of exposure, genomic DNA methylation, and the psychosocial impact of increased breast cancer susceptibility in 6-13 YO girls. http://legacygirlsstudy.org/

1.         Francke U, Difamco C, Kiefer AK, Eriksson N, Moiseff B, Tung JY, Mountain JL: Dealing with the unexpected: consumer responses to direct-access BRCA mutation testing. PeerJ 2013:1-21.

2.         Bradbury AR, Patrick-Miller L, Egleston B, Sands CB, Li T, Schmidheiser H, Feigon M, Ibe CN, Hlubocky FJ, Hope K et al: Parent opinions regarding the genetic testing of minors for BRCA1/2. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2010, 28(21):3498-3505.

3.         Bradbury AR, Patrick-Miller L, Egleston BL, Schwartz LA, Sands CB, Shorter R, Moore CW, Tuchman L, Rauch P, Malhotra S et al: Knowledge and perceptions of familial and genetic risks for breast cancer risk in adolescent girls. Breast cancer research and treatment 2012, 136(3):749-757.

4.         Bradbury AR, Patrick-Miller L, Egleston BL, Olopade OI, Daly MB, Moore CW, Sands CB, Schmidheiser H, Kondamudi PK, Feigon M et al: When parents disclose BRCA1/2 test results: their communication and perceptions of offspring response. Cancer 2012, 118(13):3417-3425.

Sources:

http://abcnews.go.com/Health/Healthday/story?id=4508346&page=1#.UVNJUVef2RM

Other article on Ethics and Personalized Medicine on the site include:

Genomics in Medicine- Tomorrow’s Promise

Attitudes of Patients about Personalized Medicine

Genomics & Ethics: DNA Fragments are Products of Nature or Patentable Genes?

Volume One: Genomics Orientations for Individualized Medicine

Directions for Genomics in Personalized Medicine

The Way With Personalized Medicine: Reporters’ Voice at the 8th Annual Personalized Medicine Conference,11/28-29, 2012, Harvard Medical School, Boston, MA

Highlights from 8th Annual Personalized Medicine Conference, November 28-29, 2012, Harvard Medical School, Boston, MA

Clinical Genetics, Personalized Medicine, Molecular Diagnostics, Consumer-targeted DNA – Consumer Genetics Conference (CGC) – October 3-5, 2012, Seaport Hotel, Boston, MA

Genetic basis of Complex Human Diseases: Dan Koboldt’s Advice to Next-Generation Sequencing Neophytes

2013 Genomics: The Era Beyond the Sequencing of the Human Genome: Francis Collins, Craig Venter, Eric Lander, et al.

Improving Mammography-based imaging for better treatment planning

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Personalized Medicine: Clinical Aspiration of Microarrays

Reporter, Writer: Stephen J. Williams, Ph.D.

 In this month’s Science, Mike May (at http://www.sciencemag.org/site/products/lst_20130215.xhtml) describes some of the challenges and successes in introducing microarray analysis to the clinical setting.  Traditionally used for investigational research, microarray is now being developed, customized and used for biomarker analysis, prognostic and predictive value, in a disease-specific manner.

Challenges in data interpretation

      In an interview with Seth Crosby, director of the Genome Technology Access Center at Washington University School of Medicine in St. Louis, “the biggest challenge” in moving microarray to the clinical setting is data interpretation.  The current technology makes it possible to evaluate expression of thousands of genes from a patient’s sample however as Crosby describes is assigning clinical relevance to the data.  For example Crosby explains that Washington University had validated a panel of 45 oncology genes by next generation sequencing and are using these genes to develop diagnostic tests to screen patient tumors for the purpose of determining a personalized therapeutic strategy. Seth Crosby noted it took “hundreds of Ph.D. and M.D. hours” to sift through the hundreds of papers to determine which genes were relevant to a specific cancer type. However, he notes, that once we better understand which changes in the patient’s genome are related to a specific disease we will be able to narrow down the list and be able to produce both economical and more disease-relevant microarrays.

Is this aberration pathogenic or not?

     Microarrays are becoming an invaluable tool in cytogenetics, as eluded by Andy Last, executive vice president of the genetic analysis business unit at Affymetrix.  Certain diseases like Down syndrome have well characterized chromosomal alterations like additions or deletions of parts or entire chromosomes.  According to Affymetrix, the most common use of microarrays is for determining copy number variation.  However according to James Clough, vice president of clinical and genomic services at Oxford Gene Technology, given the hundreds of syndromes associated with chromosomal rearrangements, the challenge will be to determine if a small chromosomal aberration has pathologic significance, given that microarray affords much higher diagnostic yield and speed of analysis than traditional microscopic techniques.  To address this challenge, Oxford Gene Technologies, PerkinElmer, Affymetrix, and Agilent all have custom designed microarrays to evaluate disease specific copy number and SNP (single nucleotide polymorphism) microarrays.  For example PerkinElmer designed OncoChip™ to evaluate copy number variation in more than 1.800 cancer genes.  Agilent makes microarrays that evaluates both copy number variation such as its CGH (comparative genomic hybridization) plus SNP microarrays.  Patricia Barco, product manager for cytogenetics at Agilent, notes these arrays can be used in prenatal and postnatal research and cancer, and “can be customized from more than 28 million probes in our library”.

Custom Tools and Software to Handle the Onslaught of Big Data

     There is a need for FDA approved diagnostic tools based on microarrays. Pathwork Diagnostic’s has one such tool (the Pathwork Tissue of Origin test), which uses 2,000 transcript markers and a proprietary computational algorithm to determine from expression analysis, the tissue of origin of a patient’s tumor.  Pathwork also provides a fast, custom turn-around analytical service for pathologists who encounter difficult to interpret samples.  Illumina provides the Infinium HumanCore BeadChip family of microarrays, which can determine genetic variations for purposes of biological tissue banking.  This system uses a set of over 300,000 SNP probes plus 240,000 exome-based markers.

     Tools have also been developed to validate microarray results.  A common validation strategy is the use of quantitative real-time PCR to verify the expression changes seen on the microarray.  Life Technologies developed the TaqMan OpenArray Real Time PCR plates, which have 3,072 wells and can be custom-formatted using their library of eight million validated TaqMan assays.

Making Sense of the Big Data: Bridging the Knowledge Gap using Bioinformatics

          The use of microarray has spurned industries devoted to developing the bioinformatics software to analyze the massive amounts of data and provide clinical significance.  For example companies such as Expression Analysis use their bioinformatics software to provide pathway analysis for microarray data in order to translate the data into the biology.  Using such strategies can also validate the design of microarrays for various diseases.

Foundation Medicine, Inc., a molecular information company, provides cancer genomics test solutions. It offers FoundationOne, an informative genomic profile to identify a patient’s individual molecular alterations and match them with relevant targeted therapies and clinical trials. The company’s product enables physicians to recommend treatment options for patients based on the molecular subtype of their cancer.

The Canadian Bioinformatics Workshops series recently offered a course on using bioinformatic approaches to analyze clinical data generated from microarray approaches (http://bioinformatics.ca/workshops/2012/bioinformatics-cancer-genomics-bicg).   The course objectives are described below:

Course Objectives

Cancer research has rapidly embraced high throughput technologies into its research, using various microarray, tissue array, and next generation sequencing platforms. The result has been a rapid increase in cancer data output and data types. Now more than ever, having the bioinformatic skills and knowledge of available bioinformatic resources specific to cancer is critical. The CBW will host a 5-day workshop covering the key bioinformatics concepts and tools required to analyze cancer genomic data sets. Participants will gain experience in genomic data visualization tools which will be applied throughout the development of the skills required to analyze cancer -omic data for gene expression, genome rearrangement, somatic mutations and copy number variation. The workshop will conclude with analyzing and conducting pathway analysis on the resultant cancer gene list and integration of clinical data.

Successful Examples of Clinical Ventures Integrating Bioinformatics in Cancer Treatment Decision –Making

The University of Pavia, Italy developed a fully integrated oncology bioinformatics workflow as described on their website and at the ESMO 2012 Congress meeting:

http://abstracts.webges.com/viewing/view.php?congress=esmo2012&congress_id=370&publication_id=2530

ESMO

ONCO-I2B2 PROJECT: A BIOINFORMATICS TOOL INTEGRATING –OMICS AND CLINICAL DATA TO SUPPORT TRANSLATIONAL RESEARCH

Abstract:

2530

Congress:

ESMO 2012

Type:

Abstract

Topic:

Translational research

Authors:

A. Zambelli, D. Segagni, V. Tibollo, A. Dagliati, A. Malovini, V. Fotia, S. Manera, R. Bellazzi; Pavia/IT

  • Body

The ONCO-i2b2 project, supported by the University of Pavia and the Fondazione Salvatore Maugeri (FSM), aims at supporting translational research in oncology and exploits the software solutions implemented by the Informatics for Integrating Biology and the Bedside (i2b2) research centre, an initiative funded by the NIH Roadmap National Centres for Biomedical Computing. The ONCO-i2b2 software is designed to integrate the i2b2 infrastructure with the FSM hospital information system and the Bruno Boerci Biobank, in order to provide well-characterized cancer specimens along with an accurate patients clinical data-base. The i2b2 infrastructure provides a web-based access to all the electronic medical records of cancer patients, and allow researchers analyzing the vast amount of biological and clinical information, relying on a user-friendly interface. Data coming from multiple sources are integrated and jointly queried.

In 2011 at AIOM Meeting we reported the preliminary experience of the ONCO-i2b2 project, now we’re able to present the up and running platform and the extended data set. Currently, more than 4400 specimens are stored and more than 600 of breast cancer patients give the consent for the use of specimens in the context of clinical research, in addition, more than 5000 histological reports are stored in order to integrate clinical data.

Within the ONCO-i2b2 project is possible to query and merge data regarding:

• Anonymous patient personal data;

• Diagnosis and therapy ICD9-CM subset from the hospital information system;

• Histological data (tumour SNOMED and TNM codes) and receptor profile testing (Her2, Ki67) from anatomic pathology database;

• Specimen molecular characteristics (DNA, RNA, blood, plasma and cancer tissues) from the Bruno Boerci Biobank management system.

The research infrastructure will be completed by the development of new set of components designed to enhance the ability of an i2b2 hive to utilize data generated by NGS technology, providing a mechanism to apply custom genomic annotations. The translational tool created at FSM is a concrete example regarding how the integration of different information from heterogeneous sources could bring scientific research closer to understand the nature of disease itself and to create novel diagnostics through handy interfaces.

Disclosure

All authors have declared no conflicts of interest.

NCI has under-taken a similar effort under the Recovery Act (the full text of the latest report is taken from their website http://www.cancer.gov/aboutnci/recovery/recoveryfunding/investmentreports/bioinformatics:

Cancer Bioinformatics: Recovery Act Investment Report

November 2009

Public Health Burden of Cancer

Cancer is the second leading cause of death in the United States after heart disease. In 2009, it is estimated that nearly 1.5 million new cases of invasive cancer will be diagnosed in this country and more than 560,000 people will die of the disease.

To learn more, visit:

Cancer Bioinformatics Program Overview

Over the past five years, NCI’s Center for Biomedical Informatics and Information Technology (CBIIT) has led the effort to develop and deploy the cancer Biomedical Informatics Grid® (caBIG) in partnership with the broader cancer community.  The caBIG network is designed to enable the integration and exchange of data among researchers in the laboratory and the clinic, simplify collaboration, and realize the potential of information-based (personalized) medicine in improving patient outcomes. caBIG has connected major components of the cancer community, including NCI-designated Cancer Centers, participating institutions of the NCI Community Cancer Centers Program (NCCCP), and numerous large-scale scientific endeavors, as well as basic, translational, and clinical researchers at public and private institutions across the United States and around the world.  Beyond cancer research, caBIG capabilities—infrastructure, standards, and tools—provide a prototype for linking other disease communities and catalyzing a new 21st-century biomedical ecosystem that unifies research and care. ARRA funding will allow NCI to accelerate the ongoing development of the Cancer Knowledge Cloud and Oncology Electronic Health Records (EHRs) initiatives, thereby providing for continued job creation in the areas of biomedical informatics development and application as well as healthcare delivery.

The caBIG Cancer Knowledge Cloud: Extending the Research Infrastructure

The Cancer Knowledge Cloud is a virtual biomedical capability that utilizes caBIG tools, infrastructure, and security frameworks to integrate distributed individual and organizational data, software applications, and computational capacity throughout the broad cancer research and treatment community. The Cancer Knowledge Cloud connects, integrates, and facilitates sharing of the diverse primary data generated through basic and clinical research and care delivery to enable personalized medicine. The cloud includes information generated through large-scale research projects such as The Cancer Genome Atlas (TCGA), the cancer Human Biobank (caHUB) tissue acquisition network, the NCI Functional Biology Consortium, the NCI Patient Characterization Center, and the NCI Preclinical Development Pipeline, academic and industry counterparts to these projects, and clinical observations (from entities such as the NCCCP) captured in oncology-extended Electronic Health Records.  Through the use of the caBIG Data Sharing and Security Framework, the Cloud will support appropriate sharing of information, supporting in silico hypothesis generation and testing, and enabling a learning healthcare system.

A caBIG-Based Rapid-Learning Healthcare System: Incorporating Oncology-Extended Electronic Healthcare Records (EHRs)

The 21st-century Cancer Knowledge Cloud will connect individuals, organizations, institutions, and their associated information within an information technology-enabled cycle of discovery, development, and clinical care—the paradigm of a rapid-learning healthcare system. This will transform these disconnected sectors into a system that is personalized, preventive, pre-emptive, and patient-participatory.  To be realized, this model requires the adoption of standards-based EHRs. Presently, however, no certified oncology-based EHR exists, and fewer than 3 percent of oncologists with outpatient-based practices utilize EHRs. caBIG has recently established a collaboration with the American Society of Clinical Oncology (ASCO) to develop an oncology-specific EHR (caEHR) specification based on open standards already in use in the oncology community that will utilize caBIG standards for interoperability. NCI will implement an open-source version of this specification to validate the specification and to provide a free alternative to sites that choose not to purchase a commercial system. The launch customer for the caEHR will be NCCCP participating sites. NCI will work with appropriate entities to provide a mechanism for certifying that caEHR implementations are consistent with the NCI/ASCO specification.

Bards Cancer Institute has another clinical bioinformatics program to support their clinical efforts:

Clinical Bioinformatics Program in Oncology at Barts Cancer Institute at Barts and the London School of Medicine

http://www.bci.qmul.ac.uk/cancer-bioinformatics

BCI HomeCancer Bioinformatics

Bards

Why we focus on Cancer Bioinformatics

Bioinformatics is a new interdisciplinary area involving biological, statistical and computational sciences. Bioinformatics will enable cancer researchers not only to manage, analyze, mine and understand the currently accumulated, valuable, high-throughput data, but also to integrate these in their current research programs. The need for bioinformatics will become ever more important as new technologies increase the already exponential rate at which cancer data are generated.

What we do

  • We work alongside clinical and basic scientists to support the cancer projects within BCI.  This is an ideal partnership between scientific experts, who know the research questions that will be relevant from a cancer biologist or clinician’s perspective, and bioinformatics experts, who know how to develop the proposed methods to provide answers.
  • We also conduct independent bioinformatics research, focusing on the development of computational and integrative methods, algorithms, databases and tools to tackle the analysis of the high volumes of cancer data.
  • We also are actively involved in the development of bioinformatics educational courses at BCI. Our courses offer a unique opportunity for biologists to gain a basic understanding in the use of bioinformatics methods to access and harness large complicated high-throughput data and uncover meaningful information that could be used to understand molecular mechanisms and develop novel targeted therapeutics/diagnostic tools.

Developing Criteria for Genomic Profiling in Lung Cancer:

A Report from U.S. Cancer Centers

In a report by Pao et. al., a group of clinicians organized a meeting to standardize some protocols for the integration of microarray and genomic data from lung cancer patients into the clinical setting.[1]  There has been ample evidence that adenocarcinomas could be classified into “clinically relevant molecular subsets” based on distinct genomic changes.  For example EGFR (epidermal growth factor receptor) exon 19 deletions and exon 21 point mutations predict sensitivity to tyrosine kinase inhibitors (TKIs) like gefitinib, whereas exon 20 insertions predict primary resistance[2].

However, as the authors note, “mutational profiling has not been widely accepted or adopted into practice in thoracic oncology”.  

     Therefore, a multi-institutional workshop was held in 2009 among participants from Massachusetts General Hospital (MGH) Cancer Center, Memorial Sloan-Kettering Cancer Center (MSKCC), the Dana-Farber/Bingham & Women’s Cancer Center (DF/BWCC), the M.D. Anderson Cancer Center (VICC), and the Vanderbilt-Ingram Cancer Center (VICC) to discuss their institutes molecular profiling programs with emphasis on:

·         Organization/workflow

·         Mutation detection technologies

·         Clinical protocols and reporting

·         Patient consent

In addition to the aforementioned challenges, the panel discussed further issues for developing improved science-driven criteria for determining targeted therapies including:

1)      Including pathologists into criteria development as pathology departments are usually the main repositories for specimens

2)      Developing integrated informatics systems

3)      Standardizing new target validation methodology across cancer centers

 References

1.            Pao W, Kris MG, Iafrate AJ, Ladanyi M, Janne PA, Wistuba, II, Miake-Lye R, Herbst RS, Carbone DP, Johnson BE et al: Integration of molecular profiling into the lung cancer clinic. Clinical cancer research : an official journal of the American Association for Cancer Research 2009, 15(17):5317-5322.

2.            Wu JY, Wu SG, Yang CH, Gow CH, Chang YL, Yu CJ, Shih JY, Yang PC: Lung cancer with epidermal growth factor receptor exon 20 mutations is associated with poor gefitinib treatment response. Clinical cancer research : an official journal of the American Association for Cancer Research 2008, 14(15):4877-4882.

Other posts on this website on Cancer and Genomics include:

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AMPK Is a Negative Regulator of the Warburg Effect and Suppresses Tumor Growth In Vivo

Reporter-Curator: Stephen J. Williams, Ph.D.

There has been a causal link between alterations in cellular metabolism and the cancer phenotype.  Reorganization of cellular metabolism, marked by a shift from oxidative phosphorylation to aerobic glycolysis for cellular energy requirements (Warburg effect), is considered a hallmark of the transformed cell.  In addition, if tumors are to survive and grow, cancer cells need to adapt to environments high in metabolic stress and to avoid programmed cell death (apoptosis). Recently, a link between cancer growth and metabolism has been supported by the discovery that the LKB1/AMPK signaling pathway as a tumor suppressor axis[1].

LKB1/AMPK/mTOR Signaling Pathway

The Liver Kinase B1 (LKB1)/AMPK  AMP-activated protein kinase/mammalian Target of Rapamycin Complex 1 (mTORC1) signaling pathway links cellular metabolism and energy status to pathways involved in cell growth, proliferation, adaption to energy stress, and autophagy.  LKB1 is a master control for 14 other kinases including AMPK, a serine-threonine kinase which senses cellular AMP/ATP ratios.  In response to cellular starvation, AMPK is allosterically activated by AMP, leading to activation of ATP-generating pathways like fatty acid oxidation and blocking anabolic pathways, like lipid and cholesterol synthesis (which consume ATP).  In addition, AMPK regulates cell growth, proliferation, and autophagy by regulating the mTOR pathway.  AMPK activates the tuberous sclerosis complex 1/2, which ultimately inhibits mTORC1 activity and inhibits protein translation.  This mTOR activity is dis-regulated in many cancers.

LKB1AMPK pathway

LKB1/AMPK in Cancer

  • Somatic mutations of the STK11 gene encoding LKB1 are detected in lung and cervical cancers
  • Therefore LKB1 may be a strong tumor suppressor
  • Pharmacologic activation of LKB1/AMPK with metformin can suppress cancer cell growth

In a recent Cell Metabolism paper[2], Brandon Faubert and colleagues describe how AMPK activity reduces aerobic glycolysis and tumor proliferation while loss of AMPK activity promotes tumor proliferation by shifting cells to aerobic glycolysis and increasing anabolic pathways in a HIF1-dependent manner.

The paper’s major findings were as follows:

  • Loss of AMPKα1 cooperates with the Myc oncogene to accelerate lymphomagenesis
  • AMPKα dysfunction enhances aerobic glycolysis (Warburg effect)
  • Inhibiting HIF-1α reverses the metabolic effects of AMPKα loss
  • HIF-1α mediates the growth advantage of tumors with reduced AMPK signaling

Summary

AMPK is a metabolic sensor that helps maintain cellular energy homeostasis. Despite evidence linking AMPK with tumor suppressor functions, the role of AMPK in tumorigenesis and tumor metabolism is unknown. Here we show that AMPK negatively regulates aerobic glycolysis (the Warburg effect) in cancer cells and suppresses tumor growth in vivo. Genetic ablation of the α1 catalytic subunit of AMPK accelerates Myc-induced lymphomagenesis. Inactivation of AMPKα in both transformed and nontransformed cells promotes a metabolic shift to aerobic glycolysis, increased allocation of glucose carbon into lipids, and biomass accumulation. These metabolic effects require normoxic stabilization of the hypoxia-inducible factor-1α (HIF-1α), as silencing HIF-1α reverses the shift to aerobic glycolysis and the biosynthetic and proliferative advantages conferred by reduced AMPKα signaling. Together our findings suggest that AMPK activity opposes tumor development and that its loss fosters tumor progression in part by regulating cellular metabolic pathways that support cell growth and proliferation.

Below is the graphical abstract of this paper.

Graphical Abstract FINAL.pptx

(Photo credit reference(2; Faubert et. al) permission from Elsevier)

However, this regulation of tumor promotion by AMPK may be more complicated and dependent on the cellular environment.

Nissam Hay from the University of Illinois College of Medicine, Chicago, Illinois, USA and his co-workers Sang-Min Jeon and Navdeep Chandel were investigating the mechanism through which LKB1/AMPK regulate the balance between cancer cell growth and apoptosis under energy stress[3]. In their system, the loss of function of either of these proteins makes cells more sensitive to apoptosis in low glucose environments, and cells deficient in either AMPK or LKB1 were shown to be resistant to oncogenic transformation.  Whereas previous studies showed (as above) AMPK opposes tumor proliferation in a HIF1-dependent manner, their results showed AMPK could promote tumor cell survival during periods of low glucose or altered redox status.

The researchers incubated LKB1-deficient cancer cells in the presence of either glucose or one of the non-metabolizable glucose analogues 2-deoxyglucose (2DG) and 5-thioglucose (5TG), and found that 2DG, but not 5TG, induced the activation of AMPK and protected the cells from apoptosis, even in cells that were deficient in LKB1.

The authors demonstrated that glucose deprivation depleted NADPH levels, increased H2O2 levels and increased cell death, and that this was accelerated in cells deficient in the enzyme glucose-6-phosphate dehydrogenase. Anti-oxidants were also found to inhibit cell death in cells deficient in either AMPK or LKB1.

Knockdown or knockout of either LKB1 or AMPK in cancer cells significantly increased levels of H2O2 but not of peroxide (O2-) during glucose depletion. The glucose analogue 2DG was able to activate AMPK and maintain high levels of NADPH and low levels of H2O2 in these cells.

The nucleotide coenzyme NADPH is generated in the pentose phosphate pathway and mitochondrial metabolism, and consumed in H2O2 elimination and fatty acid synthesis. If glucose is limited mitochondrial metabolism becomes the major source of NADPH, supported by fatty acid oxidation. AMPK is known to be a regulator of fatty acid metabolism through inhibition of two acetyl-CoA carboxylases, ACC1 and ACC2.

Short interfering RNAs (siRNAs) to knock down levels of both ACC1 and ACC2 in A549 cancer cells and found that only ACC2 knockdown significantly increased peroxide accumulation and apoptosis, while over-expression of mutant ACC1 and ACC2 in LKB1-proficient cells increased H2O2 and apoptosis.

Therefore, it was concluded AMPK acts to promote early tumor growth and prevent apoptosis in conditions of energy stress through inhibiting acetyl-CoA carboxylase activity, thus maintaining NADPH levels and preventing the build-up of peroxide in glucose-deficient conditions.

This may appear to be conflicting with the previous report in this post however, it is possible that these reports reflect differences in the way cells respond to various cellular stresses, be it hypoxia, glucose deprivation, or changes in redox status.  Therefore a complex situation may arise:

  • AMPK promotes tumor progression under glucose starvation
  • AMPK can oppose tumor proliferation under a normoxic, HIF1-dependent manner
  • Could AMPK regulation be different in cancer stem cells vs. non-stem cell?

References:

1.            Green AS, Chapuis N, Lacombe C, Mayeux P, Bouscary D, Tamburini J: LKB1/AMPK/mTOR signaling pathway in hematological malignancies: from metabolism to cancer cell biology. Cell Cycle 2011, 10(13):2115-2120.

2.            Faubert B, Boily G, Izreig S, Griss T, Samborska B, Dong Z, Dupuy F, Chambers C, Fuerth BJ, Viollet B et al: AMPK is a negative regulator of the Warburg effect and suppresses tumor growth in vivo. Cell metabolism 2013, 17(1):113-124.

3.            Jeon SM, Chandel NS, Hay N: AMPK regulates NADPH homeostasis to promote tumour cell survival during energy stress. Nature 2012, 485(7400):661-665.

 Other posts on this site related to Warburg Effect and Cancer include:

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Larry H. Bernstein, MD, Reporter
Leaders in Pharmaceutical Intelligence

http://PharmaceuticalIntelligence.com/Unraveling retrograde signaling pathways

Unraveling retrograde signaling pathways: finding candidate signaling molecules via metabolomics and systems biology driven approaches
C Caldana, AR Fernie, L Willmitzer and D Steinhauser
Front. Plant Sci. 2012; 3:267.                    http://dx.doi.org/10.3389/fpls.2012.00267

http://fpls.com/Unraveling retrograde signaling pathways: finding candidate signaling molecules via
metabolomics and systems biology driven approaches

signals can be generated within organelles, such as chloroplasts and mitochondria,

  • modulating the nuclear gene expression in a process called
    • retrograde signaling.

Recently, integrative genomics approaches, in which correlation analysis has been applied on transcript and metabolite profiling data
of Arabidopsis thaliana, revealed the identification of metabolites which are

  • putatively acting as mediators of nuclear gene expression.

http://fpls.com/unraveling_retrograde_signaling_pathways:_finding_candidate_signaling_molecules_
via_metabolomics_and_systems_biology_driven_approaches

 

English: Plant Pathology in Arabidopsis thaliana

English: Plant Pathology in Arabidopsis thaliana (Photo credit: Wikipedia)

B0004313 Gene expression in normal and cancer ...

B0004313 Gene expression in normal and cancer cells (Photo credit: wellcome images)

 

 

 

 

 

 

 

 

 

 

 

 

 

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