International Hepatology

Genetic polymorphism and response to treatment inchronic hepatitis C: The future of personalized medicine

Tarik Asselah

Service d’Hépatologie and INSERM U773 CRB3, Beaujon Hospital, 92 110 Clichy, France

that measure the function of the genome, have afforded unique

COMMENTARY ON: Genetic variation in IL28B predicts

hepatitis C treatment-induced viral clearance. Dongliang Ge,Jacques Fellay, Alexander J. Thompson, Jason S. Simon, Kevin V.Shianna, Thomas J. Urban, Erin L. Heinzen, Ping Qiu, Arthur H.Bertelsen, Andrew J. Muir, Mark Sulkowski, John G. McHutchison,David B. Goldstei. Abstract reprinted by permission from MacmillanPublishers Ltd: Nature 200;461(7262):399–401. Copyright 2009.

Abstract: Chronic infection with hepatitis C virus (HCV) affects170 million people worldwide and is the leading cause of cirrhosisin North America. Although the recommended treatment for chronicinfection involves a 48-week course of peginterferon-2b (PegIFN-2b)or -2a (PegIFN-2a) combined with ribavirin (RBV), it is well knownthat many patients will not be cured by treatment, and that patientsof European ancestry have a significantly higher probability of beingcured than patients of African ancestry. In addition to limited effi-cacy, treatment is often poorly tolerated because of side effects thatprevent some patients from completing therapy. For these reasons,identification of the determinants of response to treatment is a highpriority. Here we report that a genetic polymorphism near the IL28Bgene, encoding interferon-3 (IFN-3), is associated with an approxi-mately twofold change in response to treatment, both amongpatients of European ancestry (P = 1.06 10–25) and African-Ameri-cans (P = 2.06 10–30). Because the genotype leading to betterresponse is in substantially greater frequency in European than Afri-can populations, this genetic polymorphism also explains approxi-mately half of the difference in response rates between African-Americans and patients of European ancestry.� 2009 Published by Elsevier B.V. on behalf of the EuropeanAssociation for the Study of the Liver.

HCV is a major cause of chronic liver disease worldwide. In addi-tion to viral and environmental behavioural factors, host geneticdiversity is thought to contribute to the spectrum of the disease[1]. In genotype 1 naïve patients, the combination of pegylatedinterferons (PEG-IFN) with ribavirin gives a sustained virologicalresponse (SVR) rate of about 50%. Because a significant number ofpatients will fail to respond or will have significant side effects, itis of major interest for both patient care and economic approachto predict non response. The sequencing of the human genome,together with the development of high-throughput technologies

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E-mail address: tarik.asselah@bjn.aphp.fr

opportunities to predict treatment response.Ge and colleagues used a genome-wide association study

(GWAS) to identify genetic variants that predict treatment out-come in chronic hepatitis C [2]. Shortly, GWAS use dense mapsof genetic markers that cover the human genome to look forallele frequency differences between cases and controls. A signif-icant frequency difference suggests that the corresponding regionof the genome contains functional DNA variants that influencethe trait of interest. The strength of the genome-wide screeningis its ability to reveal not only genes that would be expected toplay a significant role, but also genes that would not, potentiallyadding new insight into physiopathology.

In 2009, three independent GWASs reported single nucleotidepolymorphisms (SNPs) near the IL-28B (IFN-k3) region and asso-ciated with treatment response ([2–4]; Table 1). All patients wereinfected by genotype 1 and received PEG-IFN plus ribavirin. Inter-estingly, different ethnicities (European, African-American,Australian and Japanese) were included in these studies.

Ge et al. analysed 1137 patients, and they identified severalSNPs in or near the IL-28B gene on chromosome 19 that were sig-nificantly more common in responders than in non responders[2]. The genetic polymorphism was associated with an approxi-mately twofold change in SVR. Thomas and colleagues reportedthat the same IL-28B variant described by Ge et al. was also asso-ciated with HCV spontaneous clearance [5]. They genotyped thers12979860 variant in HCV cohorts comprised of individualswho spontaneously cleared the virus (n = 388) or had persistentinfection (n = 620). They showed that the C/C genotype stronglyenhances resolution of HCV infection among individuals of bothEuropean and African ancestry. Interestingly, Suppiah et al. andTanaka et al. identified rs8099917 (located �8 kb upstream ofIL-28B) as the variant the most strongly associated with SVR [3,4].

Interferon (IFN)-ks, including IFN-k 1, 2 and 3 (also known asIL-29, IL-28A and IL-28B) are a newly described group of antiviralcytokines distantly related to the type I IFNs and IL-10 familymembers. The IFN-k R complex consists of a unique ligand-bind-ing chain, IFN-k R1, and an accessory chain, IL-10R2, which isshared with receptors for IL-10-related cytokines. IFN-ks bindingto its receptor activates pathways of JAK-STATs and MAPKs andinduces antiviral, antiproliferative, anti-tumor and immuneresponses (Fig. 1). IFN-k proteins seem to have lower antiviralactivity than IFN-a in vitro [6]. IFN-k1 has been shown to exhibitdose- and time-dependent HCV inhibition, to increase IFN-stimu-lated genes expression, and to enhance the antiviral efficacy of

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Cell membrane

Cytoplasm

Nucleus

IFN-stimulated genesOAS, IRF-7. PKR, IL8

Jak1Tyk2

IFN-α

INFAR-1 INFAR-2

IRF-9

STAT

2

STAT

1IRF-9

STAT

1ST

AT 2

PP

Jak-STATpathway

IFN-λ1 (IL29)IFN-λ2 (IL28A)IFN-λ3 (IL28B)

IFN λ -R1IL10 -R2

Jak1Tyk2

Antiviralactivity

Fig. 1. Interferons (IFNs) a bind a common receptor at the surface of human cells, which is known as IFN alfa receptor. IFN receptor is composed of two subunits,IFNaR1 and IFNaR2, which are associated with the Janus activated kinases (JAKs) tyrosine kinase 2 (TYK2) and JAK1, respectively. Activation of the JAKs that are associatedwith IFN-a receptor results in tyrosine phosphorylation of STAT1 and STAT2 (signal transducer and activator of transcription 1 and 2); this leads to the formation of STAT1–STAT2–IRF9 (IFN-regulatory factor 9) complex, which is known as ISGF3 (IFN-stimulated gene (ISG) factor 3) complex. This complex translocates to the nucleus and bindsIFN-stimulated response elements (ISREs) in DNA to initiate gene transcription. The interferon-k proteins induce the JAK-STAT antiviral pathway by binding to receptorsdifferent from interferon alfa. Several studies suggest that interferon-k may be important to clear HCV infection. However, although all of the identified variants in thesestudies lie in or near the IL-28B gene, none of them appear to have an obvious effect on the function of this gene. The question that remains is the biological significance ofthis genetic variant.

JOURNAL OF HEPATOLOGY

IFN-a [7]. Interestingly, it has been demonstrated that nonresponders (NR) and sustained virological responders (SVR)patients have different gene expression profiles prior to treatment[8]. The basal liver levels of expression of IFN-stimulated geneswere higher in NRs than in SVRs. In NRs, the failure to respondto exogenous PEG-IFN may indicate a blunted response to IFN.

The very impressive results from GWASs highlight the impor-tance of a better understanding of IFN signalling pathway for thediscovery of novel potential targets. Although all of the identifiedvariants in these studies lie in or near the IL-28B gene, none ofthem appear to have an obvious effect on the function of this

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gene. There are many challenges in the future. Of course, thesenew genetic predictive factors will have to compete with otherpredictors of response. The probability of SVR essentially dependson the genotype and viral load, but also on viral kinetic (rapidvirological response at 4 weeks). What will be the importanceof this genetic predictor among all others? Furthermore, will thisgenetic marker predictor be superseded by future therapies? Thedevelopment of new viral enzyme inhibitors (protease and poly-merase) is ongoing and promising results have been reportedwith two protease inhibitors (telaprevir and boceprevir) thatare currently in phase III [9]. Protease inhibitors are direct

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Table 1. Genome wide association studies and response to treatment in chronic hepatitis C.

References Country Number ofpatients (n)

Ethnic origin Technology SNP identified

Ge et al. [2] NorthAmerica

1137 African–Americans 191 Illumina Human 610– Quad BeadChip 566,759 SNPs

rs12979860(�3 kb upstream IL-28B)linkage disequilibrium withrs8099917

European–Americans 871Hispanics 75

Suppiah et al. [3] AustraliaEurope

848 Australian 293 (training set) Illumina InfiniumHumanHap300 orCNV370 – Quad genotypingBeadChip �311,159 SNPs

rs8099917(�8 kb upstream IL-28B)16 others SNP identified

European 555 (validation set)

Tanaka et al. [4] Japan 314 Japanese 314 Affymetrix SNP 6.0SNP typing array�621,220 SNPs

rs8099917(�8 kb upstream IL-28B)rs12980275rs1188122rs8105790

International Hepatology

antivirals and we can hypothesize that genetic markers of IFNresistance will have no effects. However, we believe that thesemarkers will have their importance, since it is likely thatIFN-based therapy will remain the backbone of the treatmentin the near future as they are needed to prevent HCV resistanceand subsequently to increase SVR. Furthermore it should benoted that HCV RNA encodes specific proteins that may inhibitthe induction of type I IFNs. An example is the HCV NS3-4A pro-tease which blocks dsRNA-induced IFN production by interferingwith IRF-3 phosphorylation [10]. Thus, the NS3-4A protease is adual therapeutic target whose inhibition may block viral replica-tion and restore IRF-3 control of HCV infection.

Finally, very consistent data were reported by three indepen-dent studies finding SNPs near the IL-28B (IFN-3k) region andassociated with treatment response, thus opening a window forpersonalized medicine [2–4]. All patients were from differentethnicity origin, all infected by genotype 1, and receivedPEG-IFN plus ribavirin. The question that remains is the biologicalsignificance of this genetic variant.

References

[1] Asselah T, Bieche I, Sabbagh A, Bedossa P, Moreau R, Valla D, et al. Geneexpression and hepatitis C virus infection. Gut 2009;58:846–858.

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[2] Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV, Urban TJ, et al. Geneticvariation in IL28B predicts hepatitis C treatment-induced viral clearance.Nature 2009;461:399–401.

[3] Suppiah V, Moldovan M, Ahlenstiel G, Berg T, Weltman M, Abate ML, et al.IL28B is associated with response to chronic hepatitis C interferon-alpha andribavirin therapy. Nat Genet 2009;41:1100–1104.

[4] Tanaka Y, Nishida N, Sugiyama M, Kurosaki M, Matsuura K, Sakamoto N,et al. Genome-wide association of IL28B with response to pegylatedinterferon-alpha and ribavirin therapy for chronic hepatitis C. Nat Genet2009;41:1105–1109.

[5] Thomas DL, Thio CL, Martin MP, Qi Y, Ge D, O’Huigin C, et al. Geneticvariation in IL28B and to spontaneous clearance of hepatitis C virus. Nature2009;461:798–801.

[6] Sheppard P, Kindsvogel W, Xu W, Henderson K, Schlutsmeyer S, WhitmoreTE, et al. IL-28, IL-29 and their class II cytokine receptor IL-28R. Nat Immunol2003;4:63–68.

[7] Marcello T, Grakoui A, Barba-Spaeth G, Machlin ES, Kotenko SV, MacDonaldMR, et al. Interferons alpha and lambda inhibit hepatitis C virus replicationwith distinct signal transduction and gene regulation kinetics. Gastroenter-ology 2006;131:1887–1898.

[8] Asselah T, Bieche I, Narguet S, Sabbagh A, Laurendeau I, Ripault MP, et al.Liver gene expression signature to predict response to pegylated interferonplus ribavirin combination therapy in patients with chronic hepatitis C. Gut2008;57:516–524.

[9] Asselah T, Benhamou Y, Marcellin P. Protease and polymerase inhibitors forthe treatment of hepatitis C. Liver Int 2009;29:57–67.

[10] Foy E, Li K, Wang C, Sumpter Jr R, Ikeda M, Lemon SM, et al. Regulation ofinterferon regulatory factor-3 by the hepatitis C virus serine protease.Science 2003;300:1145–1148.

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