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A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus

Abstract

Chronic infection with hepatitis C virus (HCV) is a common cause of liver cirrhosis and cancer. We performed RNA sequencing in primary human hepatocytes activated with synthetic double-stranded RNA to mimic HCV infection. Upstream of IFNL3 (IL28B) on chromosome 19q13.13, we discovered a new transiently induced region that harbors a dinucleotide variant ss469415590 (TT or ΔG), which is in high linkage disequilibrium with rs12979860, a genetic marker strongly associated with HCV clearance. ss469415590[ΔG] is a frameshift variant that creates a novel gene, designated IFNL4, encoding the interferon-λ4 protein (IFNL4), which is moderately similar to IFNL3. Compared to rs12979860, ss469415590 is more strongly associated with HCV clearance in individuals of African ancestry, although it provides comparable information in Europeans and Asians. Transient overexpression of IFNL4 in a hepatoma cell line induced STAT1 and STAT2 phosphorylation and the expression of interferon-stimulated genes. Our findings provide new insights into the genetic regulation of HCV clearance and its clinical management.

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Figure 1: Identification of a novel transcribed region upstream of IFNL3.
Figure 2: Protein sequence analysis.
Figure 3: Median decrease in HCV RNA levels (log10 international units (IU)/ml) in African-American participants in the Virahep-C study during the first 28 d of treatment with pegIFN-α/RBV.
Figure 4: Analysis of the biological activity of the novel proteins.
Figure 5: Confocal imaging of IFNL4 in PHHs from liver donors with different ss469415590 genotypes.

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Acknowledgements

We thank the National Cancer Institute Sequencing Core Facility for help with RNA-seq. This research was supported by the Intramural Research Program of the US National Institutes of Health (National Cancer Institute, Division of Cancer Epidemiology and Genetics; National Institute for Diabetes, Digestive and Kidney Diseases), as well as the following grants: DA R01 013324 (J.A. and D.L.T.); ALIVE cohort, R01-DA-04334 and R01-DA-12568, and US National Institutes of Health grants R01-DA09532, R01-DA12109, R01-DA13245 and R01-DA16159 (B.R.E.); National Cancer Institute contracts N02-CP-91027 and N01-CO-12400 (B.R.E.); Substance Abuse and Mental Health Services Administration grant H79-TI12103 (B.R.E.); and the National Cancer Institute Director's Innovation Award (L.P.-O.). The Virahep-C and HALT-C studies were conducted, respectively, by the Virahep-C and HALT-C Investigators and supported by the National Institute of Diabetes and Digestive and Kidney Diseases. The data and samples from the Virahep-C and HALT-C studies reported here were supplied by the National Institute of Diabetes and Digestive and Kidney Diseases Central Repositories. This manuscript was not prepared in collaboration with the Virahep-C study group or the HALT-C study group and does not necessarily reflect the opinions or views of the Virahep-C Trial and HALT-C Trial, the National Institute of Diabetes and Digestive and Kidney Diseases Central Repositories or the National Institute of Diabetes and Digestive and Kidney Diseases. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services nor does mention of trade names, commercial products or organizations imply endorsement by the US government.

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L.P.-O. and T.R.O. conceived and supervised the project. J.A., H.L.B., B.R.E., C.D.H., T.R.M. and D.L.T. performed the clinical and epidemiological studies from which DNA samples and data were collected. L.P.-O., B.R. and R.P.D. designed the experiments. L.P.-O., B.M., W.T., H.P., H.D., D.H., P.P.-G., I.K., A.M., N.B., M.T., L.L., F.S., B.R. and R.P.D. performed experiments and analysis. T.R.O., R.M.P. and S.C. performed statistical analysis of genetic association. L.P.-O. and T.R.O. wrote the manuscript. All authors contributed to scientific discussions and approved the final manuscript.

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Correspondence to Ludmila Prokunina-Olsson or Thomas R O'Brien.

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L.P.-O., B.M., R.P.D. and T.R.O. are inventors on a patent application filed by the National Cancer Institute on the basis of these findings.

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Prokunina-Olsson, L., Muchmore, B., Tang, W. 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 45, 164–171 (2013). https://doi.org/10.1038/ng.2521

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