Genetics/Genomics in Hepatitis

Transcription

1 Title slide Genetics/Genomics in Hepatitis and Liver Disease Scott L. Friedman MD

2 Overview Definitions / basics of genetics, genomics & epigenetics Why learn about genetics and genomics? Applications of genomics in liver disease - HCV response to Alpha IF IL28B SNP - SNPs that predict fibrosis progression in HCV - Pharmacogenomics and hepatic drug toxicity Summary / Predictions

3 Genetics and Genomics - Definitions Genetics focus on single genes and their effects Genomics refers to the action of all genes in an organism - concerned with the structure, function, evolution and mapping of genomes

4 The Basics DNA to RNA to Protein 3' 5' 3' DNA to RNA 5' RNA to protein NH 2 Translation trna 5' mrna Transcription Unwound DNA Peptide C O O H A A A A

5 Typical Gene Organization Regulatory unit Core promoter Transcriptional unit 5' Ex1 Ex2 Ex3 3' Enhancer CCAAT box TATA box Transcription Silencer RNA: CAP AAAA mrna: AAAA Protein: NH 2 - Met - aa-aa-aa-aa... aa - COOH 6

6 5 Alternative Gene Splicing RNA 5 Exon 1 Gene transcription Exon 2 Splice A Exon 3 Exon 4 Splice B 3 3 AAAA Exon 1 Exon 2 Exon 3 Exon 4 Exon 1 Exon 3 Exon 4 mrna Protein A mrna Protein B

7 Genetic Code Genetic Code Universal Redundant Wobble - 3rd base Start = AUG = Met Stop = UAA, UAG, UGA

8 Assessment of Disease Risk using Single Nucleotide Polymorphisms (SNPs) Single Base Variants found in > 1% of population ~ 300,000 Common SNPS per Genome Useful for Gene Discovery for Complex Diseases Pt. A:...CTGATACAATGCATC Pt. B:...CGGATACCATGTATC Pt. C:...CTGATGCCATGCATC

9 Insights from the Human Genome Project Project began in 1990, completed in 13 years Transfer information to public for discovery Consider ethical, legal, & social implications (ESLI) FINDINGS: Only 2% of genome is genes 98% is junk DNA Sequence is >98.5% identical in all humans - Including across races/ethnic groups

10 Humans Have Many Fewer Genes than Expected Why? Organism No. Genes Drosophila (fruit fly) 13,600 Arabidopsis (flowering plant) 25,500 Mouse 23,000 Humans? 22,000! Humans have large regions that don t code for genes: - highly conserved regions (e.g., long non-coding (linc) RNA) - alternative splicing, which generates multiple transcripts from single genes - epigenetic regulation may be far more important in humans

11 Definition: Changes in gene expression or cellular phenotype without affecting the DNA sequence Epigenetics

12 ENCODE The Next Step after the Human Genome Project ENCODE Encyclopedia of human DNA elements Goal: to identify all regions of transcription, transcription factor association, chromatin structure and histone modification in the human genome sequence A large consortium of scientists to explore all components that influence gene expression and phenotype Results published in > 30 papers in 2012

13 ENCODE Highlights 80% of genome contains elements linked to biochemical fxns DNA variants linked to disease lie within or near non-coding fxnl DNA elements 75% of the genome is transcribed at some point in cells Genes that are highly interlaced with overlapping transcripts are synthesized from both DNA strands this has implications for the definition of a gene Doubled the number of known recognition sites for DNA binding proteins Chromosome loops & twists enable communication between distal elements Ecker et al, Nature 489, 52-55, 2012

14 Why Learn about Genetics and Genomics? Understanding of disease pathogenesis Define risk of disease Disease classification/definition Prognostic implications Optimize treatment strategies - timing of OLTx, mechanism-specific therapy Prevention strategies (eg DILD, ALD) Design and personalize new treatments Determine risk to children & family members

15 Simple Mendelian Disorders a1-antitrypsin Deficiency Alagille s Syndrome Cystic Fibrosis Haemochromatosis Hepatic Porphyrias Glycogen Storage Diseases PFIC & BRIC Wilson s Disease

16 Complex Traits Alcoholic Liver Disease Non-alcoholic fatty liver Hepatitis B & C Infection Autoimmune Hepatitis Primary Biliary Cirrhosis Primary Sclerosing Cholangitis

17 Common Complex Disease Have a Significant Genetic Component Disease Heritability (%) Asthma 60 Blood pressure Bone mineral density Cervical and lumbar disc degeneration Insulin-dependent diabetes (IDDM) 70 Obesity Osteoarthritis Rheumatoid arthritis 60 Ulcerative colitis 50 MacGregor et al. Trends in Genetics 16, 131(2000).

18 Finding Disease Genes and Variants Candidate Gene Approach Genotype with SNPs in known genes to accelerate disease association studies Whole Genome Scans Genotype with SNPs in predicted but uncharacterized genes

19 Finding the gene hypothesis-free Whole genome SNP scanning Use SNP map to scan whole genome in cases and controls >2.7 million SNPs in current database Requires high throughput genotyping technology Used to be restricted to pharma companies, but no longer - especially at Mount Sinai!

20 Impact of Genomics on Hepatitis and Liver Disease Response to alpha IF in HCV Genetic Risk of fibrosis progression in HCV Pharmacogenomics and drug toxicity

21 3 kb 60 Mb A Polymorphism on Chromosome 19 Predicts SVR: IL- 28B IL28B gene IFN Lambda-3 gene 19q13.13 Polymorphism rs Chromosome 19 Ge D, et al. Nature. 2009;461: Chromosome 19 graphic courtesy of Oak Ridge National Laboratory. Available at: Accessed on: October 21, 2009.

22 IL-28B CC genotype is associated with SVR Ge et al, Nature, 2009

23 Evolving Paradigms for Predicting Response to IFN-based Rx for HCV Genetics emerges! Genotype 2/3 No advanced fibrosis Low viral load Younger age <40 years Female Weight Lack of steatosis No insulin resistance Adherence Rapid viral response (RVR) Ribavirin dosage Race/ethnicity IL-28B Anemia 2011-present Race/ethnicity low viral load absence of cirrhosis statin use IL-28B Genotype 1a/1b On treatment viral response Lead-in ervr McHutchison JG, et al. N Engl J Med Manns MP, et al. Lancet Patton HM, et al. J Hepatol. 2004; Poynard T, et al. Lancet

24 Impact of Genomics on HCV Progression Host, not Viral Factors Correlate with Fibrosis Progression in HCV No correlation between either HCV viral load or genotype and fibrosis progression Gender, alcohol use, and other risks contribute, but don t explain all the differences SNPs may correlate with fibrosis progression in humans

25 Patients with HCV have Variable Fibrosis Progression F METAVIR Rapid N=1157 Intermediate Duration in years Slow fibroser Poynard et al. Lancet 1997; 349: 825

26 SNPs Associated with Cirrhosis Risk Score (CRS) Predictors Public ID Gene (Chr) Risk Genotype or Phenotype P valuea (Univariate) ORs (95%CI) SNP1b AZIN1 (Chr8) GG ( ) SNP2 rs TLR4 (Chr9) CC ( ) SNP3 rs TRPM5 (Chr11) CT, CC ( ) SNP4 rs none (Chr15) 242 AG,AA ( ) SNP5 rs none (Chr1) GG ( ) SNP6 rs none (Chr3) AG, AA ( ) SNP7 rs AQP2 (Chr12) GG ( ) Huang H, et al. Hepatology, 2007

27 Equal Stratification of Risk in Placebo and Rx Groups is Critical Low Placebo Group Medium Unequal stratification! HCV patients High Rx Group Low, medium and high refer to fibrosis stage or progression rate

28 Selection of Patients with High Fibrosis Progression Rate will Optimize Antifibrotic Clinical Trials Low Placebo Group Medium HCV patients High Rx Group Low, medium and high refer to fibrosis progression rate

29 SNPs Associated with Fibrosis Risk - Implications 1. Potential to predict disease progression and refine Rx 2. Possible correlation of liver fibrosis SNPs with progression in other organs, including kidney, lung, & pancreas 3. Discovery of new genes mechanistically linked to pathogenesis

30 Using SNP information to Uncover New Biology Predictors Public ID Gene (Chr) Risk Genotype or Phenotype P valuea (Univariate) ORs (95%CI) SNP1b AZIN1 (Chr8) GG ( ) SNP2 rs TLR4 (Chr9) CC ( ) SNP3 rs TRPM5 (Chr11) CT, CC ( ) SNP4 rs none (Chr15) 242 AG,AA ( ) SNP5 rs none (Chr1) GG ( ) SNP6 rs none (Chr3) AG, AA ( ) SNP7 rs AQP2 (Chr12) GG ( ) Huang H, et al. Hepatology, 2007

31 Toll-Like Receptors (TLRs) TLR4 LPS A family of mammalian transmembrane pattern-recognition receptors Recognize structural components unique to bacteria, fungi and viruses Signal and activate inflammatory responses Two well-known SNPs correlate with SLOWER fibrosis progression: Asp299Gly Thr399Ile Beutler B. Nature 2004,430(6996):

32 Prediction: Genomics Will Personalize Health Care

33 What Is Personalized Medicine? Use medications and other treatments that would work best for each individual Avoid medications that would cause an individual to have adverse side effects Predict which illnesses an individual was likely to get and design a personalized health care plan to prevent or detect these diseases early New York Times Magazine, Sunday, November 6, 2005.

34 Genetic Differences in Drug Metabolism The First Frontier of Personalized Medicine Pharmacogenomics To determine efficacy and dosing of drugs To predict risk of toxicity

35 Personalized Medicine - Genetic Definition of Subpopulations With Different Response Profiles

36 Drug Induced Liver Injury Network (DILIN)

37 Summary & Predictions Genetics and Genomics in Hepatitis and Liver Disease Genomic information will profoundly improve our ability to predict: Disease risk and progression rates Response to therapies Drug-related liver toxicities The demand for integrating genomic information will require: Big data platforms to integrate genomic and EMR data Software systems to insert decision-support guidance based on these data at the point-of-care The need to assimilate these approaches will be driven by: Insurers who seek to prevent disease and optimize Rx to reduce costs Entrepreneurs and businesses with novel IT and technology solutions Academic medical centers who can ride the wave (e.g. Mount Sinai) The public, and patients & their families, NOT by providers