Using genetic markers in clinical practice David Thomas Advisor: Merck Clinical trial: Gilead and Merck

Using genetic markers in clinical practice IL28b test for chronic genotype 1 hepatitis C IL28b test for chronic genotype 2/3 hepatitis C IL28b for acute hepatitis C Future use of IL28b testing with DAA

Recovery Persistenc e

Ge, Nature, 2009; Thomas, Nature 2009; Rauch Gastroenterology 2010 Seven SNPs within a 17-kb region around IL28B gene are associated with HCV recovery

Ge, Nature, 2009 C allele associated with PegIFN and RBV in IDEAL

Clark Am J Gastro IL28b genotyping helps predict SVR in Caucasians

Clark Am J Gastro IL28b genotyping helps predict SVR in African Americans

Independent replication of the effect of genetic variation in SNPs near IL28B and SVR Ge D, et al. Nature 2009;461: Tanaka Y, et al. Nat Genet 2009;41: Suppiah V, et al. Nat Genet 2009;41: Rauch A, et al. Gastroenterology 2010; Jan 7.

Kinetics of HCV RNA decline differ early in IL28b haplotypes Genotype 1 Caucasian patients

IL28b haplotype predicts SVR in HIV/HCV coinfected patients Rallon AIDS 2010 (Pineda CID 2010, Medrano CID 2010)

Using genetic markers in clinical practice IL28b test for chronic genotype 1 hepatitis C IL28b test for chronic genotype 2/3 hepatitis C IL28b for acute hepatitis C Future use of IL28b testing with DAA

Mangia Gastro 2010 Effect of unfavorable IL28b genotype is less in Caucasian genotype 2/3 HCV infection Genotype 2, N=213; Genotype 3, N=55

Favorable IL28b genotype may be associated with relapse of genotype 3 HCV infection 281 genotype 3, Scandinavian, >11wks Rx RVR, 14 wks peg/R no RVR, 24 wks Overall SVR 80% CC relapse: o 13/64 (20%) 14wk o 7/43 (16%) 24 wk Moghaddam Hepatology 2011

Both donor and recipient IL28 status are important for outcome of IFN treatment after liver transplant Charlton Hepatology 2011

Using genetic markers in clinical practice IL28b test for chronic genotype 1 hepatitis C IL28b test for chronic genotype 2/3 hepatitis C IL28b for acute hepatitis C Future use of IL28b testing with DAA

C allele associates with higher probability of spontaneous clearance of HCV Thomas Nature 2009; Grebely Hepatology 2010; Rauch Gastro 2010

Persons with acute hepatitis C and unfavorable IL28b genotype should be treated sooner With genotype 1, interferon alfa sensitivity diminishes with time from acute infection Interferon alfa sensitivity diminishes most with genotype 1 Prioritize early treatment for T allele May not be case for HIV/HCV coinfected 1 1 Nattermann JID 2011

Using genetic markers in clinical practice IL28b test for chronic genotype 1 hepatitis C IL28b test for chronic genotype 2/3 hepatitis C IL28b for acute hepatitis C Future use of IL28b testing with DAA

EOT and SVR according to rs genotype 72 patients Telaprevir/PegIFN/RBV for total duration of 12 or 24 weeks Akuta N et al. Hepatology 2010

SPRINT-2 Treatment-Naïve Patients Stopping Rule Weeks Follow-up 24 wks TW 8-24 Undetectable Follow- up 24 wks TW 8-24 Detectable Follow-up 24 wks 8 Placebo + P/R 44 wks P/R 4 wks Follow-up 24 wks BOC + P/R 24 wks P/R 4 wks Follow-up 44 wks Placebo + P/R 20 wks BOC + P/R 44 wks P/R 4 wks Decision point for long vs. short therapy Arm 1 PR48 Control Arm 2 BOC RGT Arm 3 BOC/ PR48 Lead-in

RESPOND-2 Previous Treatment Failure Stopping Rule Weeks Placebo + P/R 44 wks P/R 4 wks Follow-up 24 wks Arm 1 PR48 Control TW 8 Undetectable BOC + P/R 32 wks P/R 4 wks Follow-up 36 wks Placebo + P/R 12 wks Follow- up 24 wks TW 8 Detectable Arm 2 BOC RGT BOC + P/R 44 wks P/R 4 wks Follow-up 24 wks Arm 3 BOC/ PR Decision point for long vs. short therapy Lead-in

consented to testing and who received 1 dose BOC or placebo (63%) Distribution of IL-28B Polymorphisms RESPOND 2 66% (259/394) SPRINT 2 62% (653/1048) TT (15%) CC (24%) CT (61%) TT (19%) CC (30%) CT (51%) SPRINT 2 team: Poordad EASL 2011

Improvement in SVR in naïve patients with boceprevir is greater with T allele SPRINT 2 team: Poordad EASL 2011

Improvement in SVR in retreated patients with boceprevir is greater with T allele RESPOND 2 team: Poordad EASL 2011

IL-28B CC polymorphism is a strong predictor of TW8 response* % Patients with undetectable HCV-RNA by TW8 CC CT + TT SPRINT-2 RESPOND-2 *Decision point for short vs. long treatment duration with RGT

Early Interferon Response (Lead-In) Further Defines Likelihood of Success For Non-CC Patients CCCTTT SPRINT-2 and RESPOND-2 combined

Design of the ADVANCE Study of Telaprevir in Treatment Naïve HCV genotype 1 Patients

Differences between ADVANCE cohort and those typed

Improvement in SVR in Caucasian naive patients with telaprevir is greater with T allele ADVANCE TEAM, Jacobson EASL 2011

REALIZE (retreatment) Study Design Weeks 72 T12/PR48 Peg-IFN + RBV TVR + Peg-IFN + RBV Pbo + Peg-IFN + RBV n=212 Follow-up SVR assessment TVR + Peg-IFN + RBV Peg-IFN + RBV Lead-in T12/PR48 n=210 Follow-up Pbo + Peg-IFN + RBV Pbo/PR48 Pbo + Peg-IFN + RBV Peg-IFN + RBV n=105 Follow-up

SVR Rates by IL28B Genotype and Prior Response Prior relapsers Patients achieving SVR (%) Prior partial responders Prior null responders CCCT TT CCCT TT CCCT TT Pooled T12/PR48 (n=209) Pbo/PR48 (n=52) Pooled T12/PR48 (n=79) Pbo/PR48 (n=20) Pooled T12/PR48 (n=134) Pbo/PR48 (n=33) 51/58 4/12100/117 6/3029/34 3/105/81/5 33/57 2/1010/14 0/5 4/1027/92 1/1810/32 1/15 n/N= n/a Pol et al EASL 2011

Viral Breakthrough Rates by IL28B Genotype and Prior Response Viral breakthrough defined as confirmed HCV RNA increase >1 log 10 from the lowest level during a considered treatment phase, or confirmed HCV RNA >100 IU/mL in patients who previously reached <25 IU/mL during the considered treatment phase Patients with viral breakthrough (%) Prior relapsers Prior partial responders Prior null responders CCCT TT CCCT TT CCCT TT Pooled T12/PR48 (n=209) Pbo/PR48 (n=52) Pooled T12/PR48 (n=79) Pbo/PR48 (n=20) Pooled T12/PR48 (n=134) Pbo/PR48 (n=33) 1/580/12 2/117 4/300/34 0/10 1/8 1/5 9/57 1/101/14 0/5 5/1044/92 2/1816/321/15 n/N= n/a

Relapse Rates by IL28B Genotype and Prior Response Patients with viral relapse (%) Prior relapsers Prior partial responders Prior null responders CCCT TT CCCT TT CCCT TT Pooled T12/PR48 (n=209) Pbo/PR48 (n=52) Pooled T12/PR48 (n=79) Pbo/PR48 (n=20) Pooled T12/PR48 (n=134) Pbo/PR48 (n=33) 2/566/10 8/112 12/182/33 2/5 1/7 0/1 10/44 0/23/130/511/40 2/34/141/2 n/N= Relapse was defined as having confirmed detectable HCV RNA levels during the entire follow-up period (relapse Week 72) n/a

IL28b C allele use is even less clear beyond boceprevir and telaprevir May play a role with IFN sparing DAA o HCV protease may inhibit and its inhibition may have larger effect with C allele More potent regimens will mask the IL28b difference

More potent HCV regimens will overwhelm IL28b C allele advantage Pilar investigators Aerssens EASL 2011

Clinical Applications of IL28b Testing in HCV genotype 1 infection IL28b testing provides information that is useful for estimating treatment response but not generally necessary for care of HCV infected persons IL28b genotype discriminates less as treatment potency improves and will someday be unhelpful

Clinical Applications of IL28b Testing in HCV genotype 1 infection Timing of treatment of acute infection o Start sooner for unfavorable genotype Timing of treatment for chronic infection o Delay for unfavorable genotype and low disease stage Not to withhold HCV protease inhibitor Staging (CC noninvasive to detect cirrhosis) Transplant: ?? IL28b favorable liver for IL28b unfavorable recipient

SNPs on chromosome 20 strongly associated with Hb decline at week 4 Hemoglobin change at week 4 of PegIFN/RBV: > 3 g/dL and < 10 g/dL Anemia occurred in 9.1 – 11% of the population Among European Americans – rs had genome wide significance; P = o Weaker among African and Hispanic Americans Inosine triphosphatase (ITPA) gene o 2 gene mutation cause ITPA deficiency

Predicted ITPA deficiency is associated with less Hb decline at treatment week 4

Population Frequency of ITPA deficiency

Protective mechanism of ITPA deficiency is not known but does not impact SVR RBV metabolism differs in nucleated and non-nucleated cells RBV-TP accumulates deplete ATP hemolysis Potential mechanism(s) o Accumulation of ITP modifies the ratio of RBV-TP and ATP Inosine- MP phospha te Page T; Connor JD. Int J Biochem; 1990;22:379; Homma et al Clin Gastro Hepatol 2004;2:337; Bierau J et al. Future medicine 2007;8:1221

SNP at ribavirin transporter gene influences SVR post pegIFN and ribavirin Morello JID 2010

Clinical application of ITPA testing Not commercially available in USA Might inform RBV dose Might inform patient counseling Might inform timing of rEPO

Personalized Medicine for Hepatitis C IL28b gives important information on likelihood of spontaneous clearance and SVR Future applications of ITPA and other discoveries are changing