Larry H Bernstein, MD, FCAP Principal & CSO, Triplex Medical

Larry H Bernstein, MD, FCAP Principal & CSO, Triplex Medical Chief Scientific Officer Leaders in Pharmaceutical Business Intelligence, Trumbull, CT

The Future of the CLS Profession Over the Next Decade Point # 1 Pathology and CLS professions have changed every decade Point #2 Pathology and CLS professions are changing today

Outline Prime Movers of Change Human Genome Project post decade projected forward Biotechnology boom Information technology

Breakthroughs Driven by Personalized Medicine Genomic and Allied –OMICs- technology Communication Science and Open and Interactive Architectures Mathematical Innovation in Classification and Complexity Nanotechnology Integrative Scientific Discovery

What of Metabolomics and Metabolic Profiling? Metabolomics is the measurement of small molecules that interact with membrane receptors involved with regulation of genomic transcription and cellular regulation involved with upregulation or downregulation of processes provide targets for disease treatments provide further “analytes for diagnosis prediction of short-term or long-term outcomes. metabolic

Impact on CLS Metabolomics is extension of “regulatory activity of genome”, formerly deemed “DARK MATTER” Metabolomics involves the interaction with the environment (food, stress) Metabolomics takes into consideration “mutational risk” and health or disease

Expanded Role of Laboratory Improved tie in with provision of information to not only the healthcare workers, but also the patient. Achieve turnaround times for critical results through better workflow Greater control and access to a next generation of point-of-care technology integrated with the laboratory database, and a restructured electronic health record. Despite the hype about the BIG DATA revolution, this is achievable in the system here proposed because there is a published model to achieve this

George Lundberg, MD, MedPage Today The alphabet soup that describes cancer genes, mutations, and pathways includes EGFR, KRAS, EML4-ALK, AKT, BCL, MITF, CDK, C-KIT, GNAQ, BRAF, and GNA11. pathologists may become clinical molecular (& diagnostic) specialists – determining: what molecular (and other) tests, if any, should be done

Methods Used Microarrays and microfabrication Separations technology High throughput and Multiple analytes

Disease Identification and Risk Management Carbohydrate metabolism - insulin, C-peptide Lipid Metabolism – HDL, LDL, small dense LDL particles, Apo E Proteins – proteomics, immunoglobulins, coagulation, CRP (inflammatory), IL-1, 6, 8. Cellular regulation – PPARγ, p53, HER2, etc. Cytology, hemocytometry, flow cytometric analysis

Digital Microscopy 3-D visualization Receptor staining Fresh Tissue Comment: Radiographic imaging

Mathematical Analysis

Comparison of LDA vs. Logit Analysis Under LDA assumptions the discriminant function is linear in X predicted probability of Z 1 follows logistic distribution coefficient estimates more efficient than logistic regression approach Problem: distributions of covariates not gaussian

Realtime Clinical Expert Support and Validation System a software system that is the equivalent of an intelligent Electronic Health Records Dashboard provides empirical medical reference and suggests quantitative diagnostics options gathers medical information generates metrics analyzes data in realtime provides a differential diagnosis

Given medical information of a patient the system builds its unique characterization provides a list of other patients that share this unique profile utilizing the vast aggregated knowledge (diagnosis, analysis, treatment, etc.) of the medical community

patient profiling accurate patient profiling and inference methodologies anomalous subprofiles are extracted and compared to potentially relevant cases

Sample Report

Patient Course Summary

Insights into the chemical structure of DNA the basic building blocks of DNA and proteins, of nucleotide and protein-protein interactions, protein folding, allostericity, genomic structure, DNA replication, nuclear polyribosome interaction, and metabolic control.

Flow of genetic information

Genomic Methods

Novel Adipocyte Secreted Protein in Liver Glucose Regulation A particular type of protein (hormone) found in fat cells helps regulate how glucose (blood sugar) is controlled and metabolized (used for energy) in the liver. Switching off this protein leads to better control of glucose production from the liver, revealing a potential new target that may be used to treat type 2 diabetes and other metabolic diseases.

ProsVue PSA

NZDiA ProsVue Timeline

Mechanisms of Acute Coronary Syndromes and Their Implications for Therapy Peter Libby, M.D. N Engl J Med 2013; 368:2004-2013 The notion that heart attacks develop from coronary-artery stenosis is an oversimplification of a process involving lipid metabolism, inflammation, macrophage activation, collagen breakdown, and .plaque rupture (not always)

NO Endothelial Relaxation

Nitric Oxide cycle and vascular relaxation/vascular stiffness

Genome Wide Association studies (GWAS) Genome-wide association studies (GWAS) aim to identify causative genes for common disease such as diabetes, obesity and stroke by analysing single nucleotide polymorphisms (SNPs). SNPs are identified that show association with a disease, they are unlikely to be the actual genetic variant involved in causation of that disease most individual SNPs for common diseases raise risk by about only 20-40%

Genetic Links in Common Disease variants in the same gene confirmed link between APOC3 and early-onset heart attack APOC3, involved in fat metabolism, may delay the catabolism of triglyceride-rich particles Polymorphisms in the human APOC3 gene and promoter have been associated with lipoprotein profile cardiovascular health insulin (INS) sensitivity

novel polymorphism of the CYP2J2 gene coronary artery disease in Uygur population in China Cytochrome P450 (CYP) 2J2 is expressed in the vascular endothelium and metabolizes arachidonic acid to biologically active epoxyeicosatrienoic acids (EETs)

genomics in discovery of therapeutic targets key drivers of cellular proliferation, stepwise mutational changes coinciding with cancer progression potential therapeutic targets for reversal of the process

Melanoma Drugs approved by FDA a B-Raf inhibitor aimed to treat melanoma patients harboring V600E mutation a MEK inhibitor that was shown in phase III clinical trials to be efficient for treating melanoma patients with BRAF V600E or V600K mutations These new two drugs are now joining the first two drugs approved in 2011 to treat metastatic melanoma that are already in clinical use

Companion Diagnostics Testing The introduction of the two drugs was co-approved in concert with the THxID BRAF test from BioMérieux. This PCR-based BRAF test is designed to determine whether a melanoma patient harbors the V600E or V600K BRAF gene mutation and will assist directing the correct treatment to be given to patients. this companion diagnostic approved for BRAF mutation detection follows the approval of Roche’s cobas 4800 BRAF V600 Mutation Test in August 2011 the association of diagnostics with treatments is a step further by pharmaceutical and diagnostic companies toward establishing personalized medicine

New test gives better stratification for prognosis of CLL Innovation Department - Hospital Clinic Barcelona classify CLLs into 3 new prognostic groups: MBC-like intermediate NBC-like using only 5 epigenetic biomarkers

epigenetic signature has independent prognostic impact used bisulfite pyrosequencing primers designed to detect methylation of the 5 biomarkers. There are four possible formats to develop this test: Pyrosequencing PCR restriction enzymes Hybridization Immunoprecipitation qPCR

Rationale of Innovation current classification of M-CLL (mutated) and UCLL (unmutated) is not used in clinical protocols to decide upon patient treatment and follow-up After 10 years only Group MBC-like Intermediate NBC-like Need Treatment (%) 20 43 100

This test will allow - Improve the quality of life of CLL patients - Improve management strategies that are more adjusted to the biology of this disease - Reduce the health care costs

Epigenome The suite of epigenetic modifications, collectively forming a dynamic epigenetic code, has long been known to operate as the manager of the genomic blueprint, wielding cell-dependent control over gene expression at discrete times throughout development. Our understanding of the disease epigenome has expanded, with the inclusion of numerous gene mutations and epimutations involved in producing aberrant gene expression. these findings form inextricable causal links between our underlying genome, a dynamic epigenome, and the functional (disease) consequences stemming from both.

Non-Invasive Test for Early Detection of Colorectal Tumors Dr. Guro Elisabeth Lind and a team from Oslo University Hospital have identified altogether 12 epigenetic biomarkers for early detection of colorectal cancer a six-gene panel could outperform several previously published epi-markers, including VIM and SEPT9 which are included in commercial tests for early detection of colorectal cancer using stool and blood, respectively

a disease defined primarily by its genetic fingerprint (NY Times) By GINA KOLATA Published: May 1, 2013 Jeff Boyd, Fox Chase the similarity among breast, ovarian and endometrial tumors was the best example yet of the idea that cancers are more usefully classified by their gene mutations than by where they originate.

CD47 in cancer immunity Evasion of immune recognition is a major mechanism by which cancers establish and propagate disease. Recent data has demonstrated that the innate immune system plays a key role in modulating tumor phagocytosis through the CD47-SIRPα pathway. Careful development of reagents that can block the CD47/SIRPα interaction may indeed be useful to treat many forms of cancer

Akt in cancer Mechanisms for Akt pathway activation include loss of tumor suppressor PTEN function, amplification or mutation of PI3K, amplification or mutation of Akt, activation of growth factor receptors, inactivation of the translation repressor protein 4E-BP1, and exposure to carcinogens.

Akt knockout mice demonstrate that Akt is required for both cancer cell survival and oncogenic transformation. That activation of Akt is oncogenic, could be explained by preventing normal apoptosis of cells, thereby enabling accumulation of more oncogenic mutations in these cells.

Akt controls many cancer related cellular processes such as cell metabolism, growth and survival, proliferation, and motility, all of which contribute to tumor initiation and progression.

What are lncRNAs? Non-coding RNA is now known to make up the majority of transcribed RNAs and in addition to those that carry out well-known housekeeping functions (e.g. tRNA, rRNA etc), many different types of regulatory RNAs have been and continue to be discovered. Many of these non-coding RNAs are thought to have a wide range of functions in cellular and developmental processes.

This large and diverse class of transcribed RNA molecules with a length of more than 200 nucleotides do not encode proteins. Their expression is developmentally regulated and lncRNAs can be tissue- and cell-type specific. A significant proportion of lncRNAs are located exclusively in the nucleus. They are comprised of many types of transcripts that can structurally resemble mRNAs, and are sometimes transcribed as whole or partial antisense transcripts to coding genes.

Types of molecular mechanisms that may be involved in lncRNA function The Signal archetype: functions as a molecular signal or indicator of transcriptional activity. The Decoy archetype: binds to and titrates away other regulatory RNAs or proteins. The Guide archetype: directs the localization of ribonucleoprotein complexes to specific targets. The Scaffold archetype: has a structural role as platform upon which relevant molecular components (proteins and or RNA) can be assembled.

Similarities and differences between mRNA and lncRNA mRNA Tissue-specific expression Form secondary structure Undergo post-transcriptional processing, i.e. 5’cap, polyadenylation, splicing Important roles in diseases and development Protein coding transcript Well conserved between species Present in both nucleus and cytoplasm Total 20-24,000 mRNAs Expression level: low to high lncRNA Tissue-specific expression Form secondary structure Undergo post-transcriptional processing, i.e. 5’cap, polyadenylation, splicing Important roles in diseases and development Non-protein coding, regulatory functions Poorly conserved between species Predominantly in nucleus Predicted 3-100 fold of mRNA in number Expression level: very low to moderate

Structural DNA nanotechnology [1] Hybridization The self-association (self assembly) of complementary nucleic acid molecules or parts of molecules, is implicit in all aspects of structural DNA nanotechnology [2] Stably branched DNA the combination of in vitro hybridization and synthetic branched DNA that leads to the ability to use DNA as a construction material [3] Convenient synthesis of designed sequences. Biologically derived branched DNA molecules, such as Holliday junctions, are inherently unstable, because they exhibit sequence symmetry; i.e., the four strands actually consist of two pairs of strands with the same sequence.

Origami DNA origami utilizes the genome from a virus together with a large number of shorter DNA strands to enable the creation of numerous DNA-based structures (Figure 1) The shorter DNA strands forces the long viral DNA to fold into a pattern that is defined by the interaction between the long and the short DNA strands

DNA nanotechnology and Biological Application Drug delivery Biosensors capable of picking up very specific biological signals and converting them into electrical outputs that can be analyzed for identification. Computing

Reinventing as a way of life Daniel Burrus, author of “Flash Foresight” wrote: “Today you cannot just reinvent now and then: to survive and thrive in a time of vertical change, you have to be redefining and reinventing yourself continuously. --- The organizations that are winning in the new century don’t bother competing; they leapfrog the competition by redefining anything and everything about their business.”

The ultrafiltration alternative for Hormones & Therapeutic Drugs Imagine an automated workstation dedicated to rapidly prepare plasma ultrafiltrates. This workstation does not require centrifugation, and the same vessel used to prepare the ultrafiltrate, will be presented to an immunoanalyzer with a regular menu of immunoassays for measuring “Total” hormones and drugs. The ultrafiltrate will allow us to measure “Free” hormones and drugs. The workstation will be integrated in an automated line, and a standalone workstation will be available for labs that are not automated.

Drug Failures Drug failure rates, the cost to develop drugs and healthcare costs are at an all-time high. These facts are what are driving the new paradigm in drug development.

Companion Diagnostics The value companion diagnostics bring to pharma lies in their ability to mitigate risk. They can be the difference between drug approval and failure. Increasingly, pharma companies are integrating companion diagnostic programs and are developing them in conjunction with their drug development programs. Companion diagnostics can provide an extra layer of protection and a way for pharma companies to get efficacious drugs on the market without presenting safety risks to discrete patient cohorts.