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doi: 10.1097/QAD.0000000000000052
Research Letters

IFNL4 ss469415590 variant is a better predictor than rs12979860 of pegylated interferon-alpha/ribavirin therapy failure in hepatitis C virus/HIV-1 coinfected patients

Franco, Sandraa; Aparicio, Estera; Parera, Marionaa; Clotet, Bonaventuraa,b; Tural, Cristinab; Martinez, Miguel Angela

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aFundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autonoma de Barcelona (UAB), Badalona

bFundació de la Lluita contra la Sida, Hospital Universitari Germans Trias i Pujol, Badalona, Spain.

Correspondence to Miguel Angel Martínez, Fundacio irsiCaixa, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain. Tel: +34 934656374; fax: +34 934653968; e-mail:

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A new transiently induced region (interferon-λ 4 protein; IFNL4) harbouring a dinucleotide variant ss469415590 (TT or ΔG), upstream of IFNL3 (IL28B), was recently found to be associated with hepatitis C virus (HCV) clearance. To determine the effect of IFLN4 ss469415590 variation on the HCV response to IFN-based therapy in HCV/HIV-1 coinfected patients, ss469415590 was genotyped in a cohort of 207 patients from our clinic. Treatment failure occurred in 77% of minor ΔG-allele carriers versus 48% of noncarriers, indicating that the ΔG allele was strongly associated with treatment failure. Importantly, multivariate logistic analysis revealed that ss469415590 genotype was a better predictor of treatment failure than rs12979860.

Genome-wide association studies showed that single-nucleotide polymorphisms (SNPs) nearby IL28B (principally rs12979860) are strongly associated with spontaneous [1,2] and pegylated interferon-α with ribavirin (pegIFN-α/RBV) treatment-induced clearance of HCV infection [3–5]. We and numerous other investigators confirmed the importance of IL28B SNPs in the treatment of HCV infection in HCV/HIV-1 coinfected patients [6–9]. Recently, a new transiently induced region that harbours a dinucleotide variant ss469415590 has been discovered (TT or ΔG), upstream of the interferon-λ3 protein (IFNL3) (also termed IL28B) on chromosome 19, which is in high linkage disequilibrium with rs12979860 [10]. ss469415590 (ΔG) is a frameshift variant that creates a novel gene, designated IFNL4, which is moderately similar to IFNL3 [10]. Importantly, ss469415590 may have a functional role in the innate immune response to HCV. Indeed, by using peripheral blood mononuclear cells from individuals carrying different allelic combinations of the ss469415590and rs12979860 polymorphisms, it has been shown that induction of IL28B and IFN-γ inducible protein 10 (IP-10) mRNA relies on ss469415590, but not on rs12979860, revealing that ss469415590 is the only functional variant identified so far associated with HCV clearance [11].

As there are no data about the impact of IFNL4 ss469415590 polymorphisms on treatment outcomes in HCV/HIV-1 coinfected patients, we decided to investigate the role of the ss469415590 SNP in a well characterized cohort of HCV/HIV-1 coinfected patients carrying distinct HCV genotypes and who were treated with pegIFN-α/RBV. This information may be essential to better predict the response to therapy and potentially to enable better selection of patients for treatment.

The prevalence of the ss469415590TT/ΔG substitution, as well as the rs12979860 polymorphism, was analysed in a cohort of 207 patients from our clinic with chronic HCV and HIV-1 coinfection and with a known response to treatment with peg-IFN-α/RBV at 24 weeks post-treatment. HCV genotype, HCV viral load, HIV-1 viral load, CD4+ T cell count and liver enzyme levels were determined by conventional methods as we have previously described [6,7]. The Mann–Whitney U-test, unpaired t-test and chi-squared tests were used to analyse treatment baseline covariates (GraphPad Prism, version 4.00; GraphPad Software Inc., San Diego, California, USA). A significantly higher HCV RNA viral load (log HCV RNA, IU/ml) was observed in patients who failed treatment (5.921 ± 0.04415 versus 5.684 ± 0.09192, P = 0.0093). Likewise, age and HCV genotype were significantly associated with treatment failure (43.73 ± 0.7553 versus 41.04 ± 0.5023, P = 0.0035 and 36 women out of 59 failed therapy versus 98 men out of 148, P = 0.0001, respectively). CD4+ T cell count, liver fibrosis stage, liver enzymes levels or the presence of detectable HIV-1 RNA were not significantly associated with treatment failure (data not shown). ss469415590 and rs12979860 genotyping was performed using the ABI TaqMan allelic discrimination kit and the ABI7500HT Sequence Detection System (Applied Biosystems, Foster City, California, USA). The association of ss469415590 and rs12979860 polymorphisms with response to treatment was performed by univariate and multivariate logistic regression as implemented in the SNPStats software ( [12]. ss469415590 and rs12979860 linkage disequilibrium and allele frequency were also determined with SNPStats.

ss469415590 and rs12979860 polymorphisms were in strong linkage disequilibrium (R2 = 0.95) and both had a minor allele frequency of 0.32. The ss469415590 minor allele frequency was identical to that found for Europeans in the HapMap samples (0.07 frequency in Asians, 0.32 frequency in Europeans and 0.73 frequency in Africans). We next correlated the ss469415590 and rs12979860 genotypes with the HCV peg-IFN-α/RBV treatment response. Both polymorphisms were associated with response to treatment (Table 1). However, ss469415590 had a more significant association with response to treatment [odds ratio (OR) = 3.12, 95% confidence interval (CI) = 1.1.72–5.67, P = 0.0001] than rs12979860 (OR = 2.60, 95% CI = 1.45–4.69, P = 0.0012) (Table 1). ss469415590 had also a stronger association in a multivariate model, after adjustment for age, sex, HCV RNA load and fibrosis stage (OR = 3.56, 95% CI = 1.80–7.03, P = 0.0002) than rs12979860 (OR = 2.99, 95% CI = 1.53–5.84, P = 0.001). These results demonstrate that ss469415590 is a better marker of sustained viral response (SVR) than rs12979860.

Table 1
Table 1
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Similar results were observed when samples were stratified by viral genotypes (Table 1). In patients infected with HCV genotype 1/4, the strongest association with SVR was also found for ss469415590 either in the univariate (OR = 4.69, 95% CI = 2.14–10.27, P = 0.0001 for ss469415590, OR = 4.29, 95% CI = 1.97–9.37, P = 0.0002 for rs12979860) or in the multivariate model (OR = 5.18, 95% CI = 2.11–12.71, P = 0.0002 for ss469415590, OR = 4.94, 95% CI = 2.02–12.07, P = 0.0003 for rs12979860). In patients infected with HCV genotype 3, neither ss469415590 nor rs12979860 was associated with response to treatment (OR = 0.62, 95% CI = 0.14–2.67, P = 0.51 for ss469415590, OR = 0.42, 95% CI = 0.10–1.79, P = 0.23 for rs12979860, multivariate model).

HIV-1 accelerates the course of HCV-related liver disease. SVR after peg-IFN-α/RBV therapy in HIV-1 coinfected patients reduces liver-associated complications and mortality [13]. Nevertheless, side effect rates for peg-IFN-α/RBV therapy in HIV-1 coinfected patients are very high, and premature treatment discontinuation due to serious adverse events ranges between 15% and 30%. Thus, there is a need to improve treatment strategies in this specific group of coinfected patients in order to minimize side effects and to maximize treatment success. Although promising IFN-sparing regimens are in clinical development with promising results, a clinically relevant subset of difficult-to-treat patients, such as those coinfected with HIV-1, may still require IFN in the near future. For instance, a high incidence of serious adverse events in HIV-infected patients treated with a telaprevir-based treatment regimen has been reported recently [14]. This study suggests that careful consideration of the risks and benefits of telaprevir-based therapy should be undertaken, with respect to the prospects for IFN-sparing therapy in the near future.

To our knowledge, this is the only study to analyse the association of IFNL4 (ss469415590) genotype variants and response to peg-IFN-α/RBV therapy in HCV/HIV-1 coinfected patients. Our results indicate that IFNL4 can be a better predictor to IFN-based treatment response than IFNL3 (IL28B) associated variants in HCV/HIV-1 coinfected patients. IFN-α is not only used to treat HCV infection. IFN-α has been used to treat hepatitis B virus infection or some types of cancer. Recently, it has been shown that pegIFN-α may be an effective therapy for the treatment of refractory AIDS-associated Kaposi's sarcoma [15]. IFNL4 genotype may be a useful tool to select patients for IFN-α-based therapies.

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This study was supported by grants from the Spanish Ministry of Science and Innovation (BFU2010-15194 and SAF2010-21617).

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Conflicts of interest

There are no conflicts of interest.

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1. Rauch A, Kutalik Z, Descombes P, Cai T, Di Iulio J, Mueller T, et al. Genetic variation in IL28B is associated with chronic hepatitis C and treatment failure: a genome-wide association study. Gastroenterology 2010; 138:1338–1345.

2. Thomas DL, Thio CL, Martin MP, Qi Y, Ge D, O’Huigin C, et al. Genetic variation in IL28B and spontaneous clearance of hepatitis C virus. Nature 2009; 461:798–801.

3. 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.

4. 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.

5. 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.

6. Aparicio E, Parera M, Franco S, Perez-Alvarez N, Tural C, Clotet B, Martinez MA. IL28B SNP rs8099917 is strongly associated with pegylated interferon-alpha and ribavirin therapy treatment failure in HCV/HIV-1 coinfected patients. PLoS One 2010; 5:e13771.

7. de Castellarnau M, Aparicio E, Parera M, Franco S, Tural C, Clotet B, Martinez MA. Deciphering the interleukin 28B variants that better predict response to pegylated interferon-alpha and ribavirin therapy in HCV/HIV-1 coinfected patients. PLoS One 2012; 7:e31016.

8. Pineda JA, Caruz A, Rivero A, Neukam K, Salas I, Camacho A, et al. Prediction of response to pegylated interferon plus ribavirin by IL28B gene variation in patients coinfected with HIV and hepatitis C virus. Clin Infect Dis 2010; 51:788–795.

9. Rallon NI, Naggie S, Benito JM, Medrano J, Restrepo C, Goldstein D, et al. Association of a single nucleotide polymorphism near the interleukin-28B gene with response to hepatitis C therapy in HIV/hepatitis C virus-coinfected patients. AIDS 2010; 24:F23–F29.

10. Prokunina-Olsson L, Muchmore B, Tang W, Pfeiffer RM, Park H, Dickensheets H, et al. A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. Nat Genet 2013; 45:164–171.

11. Bibert S, Roger T, Calandra T, Bochud M, Cerny A, Semmo N, et al. IL28B expression depends on a novel TT/-G polymorphism which improves HCV clearance prediction. J Exp Med 2013; 210:1109–1116.

12. Sole X, Guino E, Valls J, Iniesta R, Moreno V. SNPStats: a web tool for the analysis of association studies. Bioinformatics 2006; 22:1928–1929.

13. Berenguer J, Alvarez-Pellicer J, Martin PM, Lopez-Aldeguer J, Von-Wichmann MA, Quereda C, et al. Sustained virological response to interferon plus ribavirin reduces liver-related complications and mortality in patients coinfected with human immunodeficiency virus and hepatitis C virus. Hepatology 2009; 50:407–413.

14. Cachay ER, Wyles DL, Torriani FJ, Ballard C, Colwell B, Lin JC, et al. High incidence of serious adverse events in HIV-infected patients treated with a telaprevir-based hepatitis C virus treatment regimen. AIDS 2013; [Epub ahead of print].

15. Rokx C, van der Ende ME, Verbon A, Rijnders BJ. Peginterferon alfa-2a for AIDS-associated Kaposi's sarcoma: experience with 10 patients. Clin Infect Dis 2013; [Epub ahead of print].

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