- Email: [email protected]
Genetic polymorphism and response to treatment in chronic hepatitis C: The future of personalized medicine
International Hepatology
Genetic polymorphism and response to treatment in chronic hepatitis C: The future of personalized medicine Tarik Asselah Service d’Hépatologie and INSERM U773 CRB3, Beaujon Hospital, 92 110 Clichy, France
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 Macmillan Publishers Ltd: Nature 200;461(7262):399–401. Copyright 2009. Abstract: Chronic infection with hepatitis C virus (HCV) affects 170 million people worldwide and is the leading cause of cirrhosis in North America. Although the recommended treatment for chronic infection involves a 48-week course of peginterferon-2b (PegIFN-2b) or -2a (PegIFN-2a) combined with ribavirin (RBV), it is well known that many patients will not be cured by treatment, and that patients of European ancestry have a significantly higher probability of being cured than patients of African ancestry. In addition to limited efficacy, treatment is often poorly tolerated because of side effects that prevent some patients from completing therapy. For these reasons, identification of the determinants of response to treatment is a high priority. Here we report that a genetic polymorphism near the IL28B gene, encoding interferon-3 (IFN-3), is associated with an approximately twofold change in response to treatment, both among patients of European ancestry (P = 1.06 10–25) and African-Americans (P = 2.06 10–30). Because the genotype leading to better response is in substantially greater frequency in European than African populations, this genetic polymorphism also explains approximately half of the difference in response rates between AfricanAmericans and patients of European ancestry. Ó 2009 Published by Elsevier B.V. on behalf of the European Association for the Study of the Liver.
HCV is a major cause of chronic liver disease worldwide. In addition to viral and environmental behavioural factors, host genetic diversity is thought to contribute to the spectrum of the disease [1]. In genotype 1 naïve patients, the combination of pegylated interferons (PEG-IFN) with ribavirin gives a sustained virological response (SVR) rate of about 50%. Because a significant number of patients will fail to respond or will have significant side effects, it is of major interest for both patient care and economic approach to predict non response. The sequencing of the human genome, together with the development of high-throughput technologies
that measure the function of the genome, have afforded unique opportunities to predict treatment response. Ge and colleagues used a genome-wide association study (GWAS) to identify genetic variants that predict treatment outcome in chronic hepatitis C [2]. Shortly, GWAS use dense maps of genetic markers that cover the human genome to look for allele frequency differences between cases and controls. A significant frequency difference suggests that the corresponding region of the genome contains functional DNA variants that influence the trait of interest. The strength of the genome-wide screening is its ability to reveal not only genes that would be expected to play a significant role, but also genes that would not, potentially adding new insight into physiopathology. In 2009, three independent GWASs reported single nucleotide polymorphisms (SNPs) near the IL-28B (IFN-k3) region and associated with treatment response ([2–4]; Table 1). All patients were infected by genotype 1 and received PEG-IFN plus ribavirin. Interestingly, different ethnicities (European, African-American, Australian and Japanese) were included in these studies. Ge et al. analysed 1137 patients, and they identified several SNPs in or near the IL-28B gene on chromosome 19 that were significantly more common in responders than in non responders [2]. The genetic polymorphism was associated with an approximately twofold change in SVR. Thomas and colleagues reported that the same IL-28B variant described by Ge et al. was also associated with HCV spontaneous clearance [5]. They genotyped the rs12979860 variant in HCV cohorts comprised of individuals who spontaneously cleared the virus (n = 388) or had persistent infection (n = 620). They showed that the C/C genotype strongly enhances resolution of HCV infection among individuals of both European and African ancestry. Interestingly, Suppiah et al. and Tanaka et al. identified rs8099917 (located 8 kb upstream of IL-28B) as the variant the most strongly associated with SVR [3,4]. Interferon (IFN)-ks, including IFN-k 1, 2 and 3 (also known as IL-29, IL-28A and IL-28B) are a newly described group of antiviral cytokines distantly related to the type I IFNs and IL-10 family members. The IFN-k R complex consists of a unique ligand-binding chain, IFN-k R1, and an accessory chain, IL-10R2, which is shared with receptors for IL-10-related cytokines. IFN-ks binding to its receptor activates pathways of JAK-STATs and MAPKs and induces antiviral, antiproliferative, anti-tumor and immune responses (Fig. 1). IFN-k proteins seem to have lower antiviral activity than IFN-a in vitro [6]. IFN-k1 has been shown to exhibit dose- and time-dependent HCV inhibition, to increase IFN-stimulated genes expression, and to enhance the antiviral efficacy of
E-mail address: [email protected]
Journal of Hepatology 2010 vol. 52 j 452–454
JOURNAL OF HEPATOLOGY IFN-λ1 (IL29) IFN-λ2 (IL28A) IFN-λ3 (IL28B)
IFN-α
Cell membrane
Cytoplasm
IL10 -R2
Tyk2
IFN λ -R1
Jak1
INFAR-1
Tyk2
INFAR-2
Jak1
STAT 1
P
STAT 2
STAT 2
STAT 1
IRF-9
Jak-STAT pathway
P
IRF-9
Antiviral activity
IFN-stimulated genes OAS, IRF-7. PKR, IL8
Nucleus
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 associated with 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 binds IFN-stimulated response elements (ISREs) in DNA to initiate gene transcription. The interferon-k proteins induce the JAK-STAT antiviral pathway by binding to receptors different from interferon alfa. Several studies suggest that interferon-k may be important to clear HCV infection. However, although all of the identified variants in these studies 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 of this genetic variant.
IFN-a [7]. Interestingly, it has been demonstrated that non responders (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 genes were higher in NRs than in SVRs. In NRs, the failure to respond to exogenous PEG-IFN may indicate a blunted response to IFN. The very impressive results from GWASs highlight the importance of a better understanding of IFN signalling pathway for the discovery of novel potential targets. Although all of the identified variants in these studies lie in or near the IL-28B gene, none of them appear to have an obvious effect on the function of this
gene. There are many challenges in the future. Of course, these new genetic predictive factors will have to compete with other predictors of response. The probability of SVR essentially depends on the genotype and viral load, but also on viral kinetic (rapid virological response at 4 weeks). What will be the importance of this genetic predictor among all others? Furthermore, will this genetic marker predictor be superseded by future therapies? The development of new viral enzyme inhibitors (protease and polymerase) is ongoing and promising results have been reported with two protease inhibitors (telaprevir and boceprevir) that are currently in phase III [9]. Protease inhibitors are direct
Journal of Hepatology 2010 vol. 52 j 452–454
453
International Hepatology Table 1. Genome wide association studies and response to treatment in chronic hepatitis C. References
Country
Number of patients (n)
Ethnic origin
Technology
SNP identified
Ge et al. [2]
North America
1137
African–Americans 191 European–Americans 871 Hispanics 75
Illumina Human 610 – Quad BeadChip 566,759 SNPs
rs12979860 (3 kb upstream IL-28B) linkage disequilibrium with rs8099917
Suppiah et al. [3]
Australia Europe
848
Australian 293 (training set) European 555 (validation set)
Illumina Infinium HumanHap300 or CNV370 – Quad genotyping BeadChip 311,159 SNPs
rs8099917 (8 kb upstream IL-28B) 16 others SNP identified
Tanaka et al. [4]
Japan
314
Japanese 314
Affymetrix SNP 6.0 SNP typing array 621,220 SNPs
rs8099917 (8 kb upstream IL-28B) rs12980275 rs1188122 rs8105790
antivirals and we can hypothesize that genetic markers of IFN resistance will have no effects. However, we believe that these markers will have their importance, since it is likely that IFN-based therapy will remain the backbone of the treatment in the near future as they are needed to prevent HCV resistance and subsequently to increase SVR. Furthermore it should be noted that HCV RNA encodes specific proteins that may inhibit the induction of type I IFNs. An example is the HCV NS3-4A protease which blocks dsRNA-induced IFN production by interfering with IRF-3 phosphorylation [10]. Thus, the NS3-4A protease is a dual therapeutic target whose inhibition may block viral replication and restore IRF-3 control of HCV infection. Finally, very consistent data were reported by three independent studies finding SNPs near the IL-28B (IFN-3k) region and associated with treatment response, thus opening a window for personalized medicine [2–4]. All patients were from different ethnicity origin, all infected by genotype 1, and received PEG-IFN plus ribavirin. The question that remains is the biological significance of this genetic variant. References [1] Asselah T, Bieche I, Sabbagh A, Bedossa P, Moreau R, Valla D, et al. Gene expression and hepatitis C virus infection. Gut 2009;58:846–858.
454
[2] Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV, Urban TJ, et al. Genetic variation 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 and ribavirin 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 pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C. Nat Genet 2009;41:1105–1109. [5] Thomas DL, Thio CL, Martin MP, Qi Y, Ge D, O’Huigin C, et al. Genetic variation in IL28B and to spontaneous clearance of hepatitis C virus. Nature 2009;461:798–801. [6] Sheppard P, Kindsvogel W, Xu W, Henderson K, Schlutsmeyer S, Whitmore TE, et al. IL-28, IL-29 and their class II cytokine receptor IL-28R. Nat Immunol 2003;4:63–68. [7] Marcello T, Grakoui A, Barba-Spaeth G, Machlin ES, Kotenko SV, MacDonald MR, et al. Interferons alpha and lambda inhibit hepatitis C virus replication with distinct signal transduction and gene regulation kinetics. Gastroenterology 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 interferon plus ribavirin combination therapy in patients with chronic hepatitis C. Gut 2008;57:516–524. [9] Asselah T, Benhamou Y, Marcellin P. Protease and polymerase inhibitors for the 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 of interferon regulatory factor-3 by the hepatitis C virus serine protease. Science 2003;300:1145–1148.
Journal of Hepatology 2010 vol. 52 j 452–454
Genetic polymorphism and response to treatment in chronic hepatitis C: The future of personalized medicine Tarik Asselah Service d’Hépatologie and INSERM U773 CRB3, Beaujon Hospital, 92 110 Clichy, France
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 Macmillan Publishers Ltd: Nature 200;461(7262):399–401. Copyright 2009. Abstract: Chronic infection with hepatitis C virus (HCV) affects 170 million people worldwide and is the leading cause of cirrhosis in North America. Although the recommended treatment for chronic infection involves a 48-week course of peginterferon-2b (PegIFN-2b) or -2a (PegIFN-2a) combined with ribavirin (RBV), it is well known that many patients will not be cured by treatment, and that patients of European ancestry have a significantly higher probability of being cured than patients of African ancestry. In addition to limited efficacy, treatment is often poorly tolerated because of side effects that prevent some patients from completing therapy. For these reasons, identification of the determinants of response to treatment is a high priority. Here we report that a genetic polymorphism near the IL28B gene, encoding interferon-3 (IFN-3), is associated with an approximately twofold change in response to treatment, both among patients of European ancestry (P = 1.06 10–25) and African-Americans (P = 2.06 10–30). Because the genotype leading to better response is in substantially greater frequency in European than African populations, this genetic polymorphism also explains approximately half of the difference in response rates between AfricanAmericans and patients of European ancestry. Ó 2009 Published by Elsevier B.V. on behalf of the European Association for the Study of the Liver.
HCV is a major cause of chronic liver disease worldwide. In addition to viral and environmental behavioural factors, host genetic diversity is thought to contribute to the spectrum of the disease [1]. In genotype 1 naïve patients, the combination of pegylated interferons (PEG-IFN) with ribavirin gives a sustained virological response (SVR) rate of about 50%. Because a significant number of patients will fail to respond or will have significant side effects, it is of major interest for both patient care and economic approach to predict non response. The sequencing of the human genome, together with the development of high-throughput technologies
that measure the function of the genome, have afforded unique opportunities to predict treatment response. Ge and colleagues used a genome-wide association study (GWAS) to identify genetic variants that predict treatment outcome in chronic hepatitis C [2]. Shortly, GWAS use dense maps of genetic markers that cover the human genome to look for allele frequency differences between cases and controls. A significant frequency difference suggests that the corresponding region of the genome contains functional DNA variants that influence the trait of interest. The strength of the genome-wide screening is its ability to reveal not only genes that would be expected to play a significant role, but also genes that would not, potentially adding new insight into physiopathology. In 2009, three independent GWASs reported single nucleotide polymorphisms (SNPs) near the IL-28B (IFN-k3) region and associated with treatment response ([2–4]; Table 1). All patients were infected by genotype 1 and received PEG-IFN plus ribavirin. Interestingly, different ethnicities (European, African-American, Australian and Japanese) were included in these studies. Ge et al. analysed 1137 patients, and they identified several SNPs in or near the IL-28B gene on chromosome 19 that were significantly more common in responders than in non responders [2]. The genetic polymorphism was associated with an approximately twofold change in SVR. Thomas and colleagues reported that the same IL-28B variant described by Ge et al. was also associated with HCV spontaneous clearance [5]. They genotyped the rs12979860 variant in HCV cohorts comprised of individuals who spontaneously cleared the virus (n = 388) or had persistent infection (n = 620). They showed that the C/C genotype strongly enhances resolution of HCV infection among individuals of both European and African ancestry. Interestingly, Suppiah et al. and Tanaka et al. identified rs8099917 (located 8 kb upstream of IL-28B) as the variant the most strongly associated with SVR [3,4]. Interferon (IFN)-ks, including IFN-k 1, 2 and 3 (also known as IL-29, IL-28A and IL-28B) are a newly described group of antiviral cytokines distantly related to the type I IFNs and IL-10 family members. The IFN-k R complex consists of a unique ligand-binding chain, IFN-k R1, and an accessory chain, IL-10R2, which is shared with receptors for IL-10-related cytokines. IFN-ks binding to its receptor activates pathways of JAK-STATs and MAPKs and induces antiviral, antiproliferative, anti-tumor and immune responses (Fig. 1). IFN-k proteins seem to have lower antiviral activity than IFN-a in vitro [6]. IFN-k1 has been shown to exhibit dose- and time-dependent HCV inhibition, to increase IFN-stimulated genes expression, and to enhance the antiviral efficacy of
E-mail address: [email protected]
Journal of Hepatology 2010 vol. 52 j 452–454
JOURNAL OF HEPATOLOGY IFN-λ1 (IL29) IFN-λ2 (IL28A) IFN-λ3 (IL28B)
IFN-α
Cell membrane
Cytoplasm
IL10 -R2
Tyk2
IFN λ -R1
Jak1
INFAR-1
Tyk2
INFAR-2
Jak1
STAT 1
P
STAT 2
STAT 2
STAT 1
IRF-9
Jak-STAT pathway
P
IRF-9
Antiviral activity
IFN-stimulated genes OAS, IRF-7. PKR, IL8
Nucleus
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 associated with 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 binds IFN-stimulated response elements (ISREs) in DNA to initiate gene transcription. The interferon-k proteins induce the JAK-STAT antiviral pathway by binding to receptors different from interferon alfa. Several studies suggest that interferon-k may be important to clear HCV infection. However, although all of the identified variants in these studies 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 of this genetic variant.
IFN-a [7]. Interestingly, it has been demonstrated that non responders (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 genes were higher in NRs than in SVRs. In NRs, the failure to respond to exogenous PEG-IFN may indicate a blunted response to IFN. The very impressive results from GWASs highlight the importance of a better understanding of IFN signalling pathway for the discovery of novel potential targets. Although all of the identified variants in these studies lie in or near the IL-28B gene, none of them appear to have an obvious effect on the function of this
gene. There are many challenges in the future. Of course, these new genetic predictive factors will have to compete with other predictors of response. The probability of SVR essentially depends on the genotype and viral load, but also on viral kinetic (rapid virological response at 4 weeks). What will be the importance of this genetic predictor among all others? Furthermore, will this genetic marker predictor be superseded by future therapies? The development of new viral enzyme inhibitors (protease and polymerase) is ongoing and promising results have been reported with two protease inhibitors (telaprevir and boceprevir) that are currently in phase III [9]. Protease inhibitors are direct
Journal of Hepatology 2010 vol. 52 j 452–454
453
International Hepatology Table 1. Genome wide association studies and response to treatment in chronic hepatitis C. References
Country
Number of patients (n)
Ethnic origin
Technology
SNP identified
Ge et al. [2]
North America
1137
African–Americans 191 European–Americans 871 Hispanics 75
Illumina Human 610 – Quad BeadChip 566,759 SNPs
rs12979860 (3 kb upstream IL-28B) linkage disequilibrium with rs8099917
Suppiah et al. [3]
Australia Europe
848
Australian 293 (training set) European 555 (validation set)
Illumina Infinium HumanHap300 or CNV370 – Quad genotyping BeadChip 311,159 SNPs
rs8099917 (8 kb upstream IL-28B) 16 others SNP identified
Tanaka et al. [4]
Japan
314
Japanese 314
Affymetrix SNP 6.0 SNP typing array 621,220 SNPs
rs8099917 (8 kb upstream IL-28B) rs12980275 rs1188122 rs8105790
antivirals and we can hypothesize that genetic markers of IFN resistance will have no effects. However, we believe that these markers will have their importance, since it is likely that IFN-based therapy will remain the backbone of the treatment in the near future as they are needed to prevent HCV resistance and subsequently to increase SVR. Furthermore it should be noted that HCV RNA encodes specific proteins that may inhibit the induction of type I IFNs. An example is the HCV NS3-4A protease which blocks dsRNA-induced IFN production by interfering with IRF-3 phosphorylation [10]. Thus, the NS3-4A protease is a dual therapeutic target whose inhibition may block viral replication and restore IRF-3 control of HCV infection. Finally, very consistent data were reported by three independent studies finding SNPs near the IL-28B (IFN-3k) region and associated with treatment response, thus opening a window for personalized medicine [2–4]. All patients were from different ethnicity origin, all infected by genotype 1, and received PEG-IFN plus ribavirin. The question that remains is the biological significance of this genetic variant. References [1] Asselah T, Bieche I, Sabbagh A, Bedossa P, Moreau R, Valla D, et al. Gene expression and hepatitis C virus infection. Gut 2009;58:846–858.
454
[2] Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV, Urban TJ, et al. Genetic variation 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 and ribavirin 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 pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C. Nat Genet 2009;41:1105–1109. [5] Thomas DL, Thio CL, Martin MP, Qi Y, Ge D, O’Huigin C, et al. Genetic variation in IL28B and to spontaneous clearance of hepatitis C virus. Nature 2009;461:798–801. [6] Sheppard P, Kindsvogel W, Xu W, Henderson K, Schlutsmeyer S, Whitmore TE, et al. IL-28, IL-29 and their class II cytokine receptor IL-28R. Nat Immunol 2003;4:63–68. [7] Marcello T, Grakoui A, Barba-Spaeth G, Machlin ES, Kotenko SV, MacDonald MR, et al. Interferons alpha and lambda inhibit hepatitis C virus replication with distinct signal transduction and gene regulation kinetics. Gastroenterology 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 interferon plus ribavirin combination therapy in patients with chronic hepatitis C. Gut 2008;57:516–524. [9] Asselah T, Benhamou Y, Marcellin P. Protease and polymerase inhibitors for the 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 of interferon regulatory factor-3 by the hepatitis C virus serine protease. Science 2003;300:1145–1148.
Journal of Hepatology 2010 vol. 52 j 452–454