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The role of IFNL4 in liver inflammation and progression of fibrosis. Genes Immun 2022; 23:111-117. [PMID: 35585257 DOI: 10.1038/s41435-022-00173-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/25/2022] [Accepted: 05/05/2022] [Indexed: 11/08/2022]
Abstract
The discovery that genetic variation within the interferon lambda locus has a profound effect on the outcome of hepatitis C virus (HCV) treatment and spontaneous clearance of HCV is one of the great triumphs of genomic medicine. Subsequently, the IFNL4 gene was discovered and proposed as the causal gene underlying this association. However, there has been a lively debate within the field concerning the causality, which has been further complicated by a change in naming. This review summarizes the genetic data available for the IFNL3/IFNl4 loci and provides an in-depth discussion of causality. We also discuss a new series of interesting data suggesting that the genetic variation at the IFNL4 loci influences the evolution of the HCV virus and the implication this relationship between our genetic makeup and virus evolution has upon our understanding of the IFNL4 system. Finally, new data support an influence of the IFNL4 gene upon liver inflammation and fibrosis that is independent of etiology, thereby linking the IFNL4 gene to some of the major liver diseases of today.
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Carrasco T, Barquín D, Ndarabu A, Fernández-Alonso M, Rubio-Garrido M, Carlos S, Makonda B, Holguín Á, Reina G. HCV Diagnosis and Sequencing Using Dried Blood Spots from Patients in Kinshasa (DRC): A Tool to Achieve WHO 2030 Targets. Diagnostics (Basel) 2021; 11:diagnostics11030522. [PMID: 33804260 PMCID: PMC8002119 DOI: 10.3390/diagnostics11030522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022] Open
Abstract
The World Health Organization has established an elimination plan for hepatitis C virus (HCV) by 2030. In Sub-Saharan Africa (SSA) access to diagnostic tools is limited, and a number of genotype 4 subtypes have been shown to be resistant to some direct-acting antivirals (DAAs). This study aims to analyze diagnostic assays for HCV based on dried blood spots (DBS) specimens collected in Kinshasa and to characterize genetic diversity of the virus within a group of mainly HIV positive patients. HCV antibody detection was performed on 107 DBS samples with Vidas® anti-HCV and Elecsys anti-HCV II, and on 31 samples with INNO-LIA HCV. Twenty-six samples were subjected to molecular detection. NS3, NS5A, and NS5B regions from 11 HCV viremic patients were sequenced. HCV seroprevalence was 12.2% (72% with detectable HCV RNA). Both Elecsys Anti-HCV and INNO-LIA HCV were highly sensitive and specific, whereas Vidas® anti-HCV lacked full sensitivity and specificity when DBS sample was used. NS5B/NS5A/NS3 sequencing revealed exclusively GT4 isolates (50% subtype 4r, 30% 4c and 20% 4k). All 4r strains harbored NS5A resistance-associated substitutions (RAS) at positions 28, 30, and 31, but no NS3 RAS was detected. Elecsys Anti-HCV and INNO-LIA HCV are reliable methods to detect HCV antibodies using DBS. HCV subtype 4r was the most prevalent among our patients. RASs found in subtype 4r in NS5A region confer unknown susceptibility to DAA.
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Affiliation(s)
- Teresa Carrasco
- Microbiology Department, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (T.C.); (D.B.); (M.F.-A.)
| | - David Barquín
- Microbiology Department, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (T.C.); (D.B.); (M.F.-A.)
| | - Adolphe Ndarabu
- Department of Internal Medicine, Centre Hospitalier Monkole, 4484 Kinshasa, Democratic Republic of the Congo; (A.N.); (B.M.)
| | - Mirian Fernández-Alonso
- Microbiology Department, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (T.C.); (D.B.); (M.F.-A.)
- ISTUN, Institute of Tropical Health, Universidad de Navarra, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Marina Rubio-Garrido
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department and Instituto Ramón y Cajal para la Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), 28034 Madrid, Spain; (M.R.-G.); (Á.H.)
| | - Silvia Carlos
- ISTUN, Institute of Tropical Health, Universidad de Navarra, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Department Preventive Medicine and Public Health, Universidad de Navarra, 31008 Pamplona, Spain
| | - Benit Makonda
- Department of Internal Medicine, Centre Hospitalier Monkole, 4484 Kinshasa, Democratic Republic of the Congo; (A.N.); (B.M.)
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department and Instituto Ramón y Cajal para la Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), 28034 Madrid, Spain; (M.R.-G.); (Á.H.)
| | - Gabriel Reina
- Microbiology Department, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (T.C.); (D.B.); (M.F.-A.)
- ISTUN, Institute of Tropical Health, Universidad de Navarra, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Correspondence: ; Tel.: +34-948-255400 (ext. 5103)
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Hashempour T, Dehghani B, Mousavi Z, Akbari T, Hasanshahi Z, Moayedi J, Yahaghi M, Davarpanah MA. Association of Mutations in the NS5A-PKRBD Region and IFNL4 Genotypes with Hepatitis C Interferon Responsiveness and its Functional and Structural Analysis. CURR PROTEOMICS 2021. [DOI: 10.2174/1570164617666200107091124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background:
The cellular antiviral responses induced by interferons require some cellular
protein kinase for its activation. Evidence indicated that a number of Hepatitis C Virus (HCV) proteins
can repress double-stranded (ds) RNA-dependent Protein Kinase (PKR) function and help HCV to escape.
However, the reports are controversial, some researchers have suggested that a region in Nonstructural
5A (NS5A) gene called Protein Kinase R-Binding Domain (PKR-BD) is associated with HCV sensitivity
to the antiviral effects of Interferon (IFN). In addition, the other factor that might be associated
with response to PEGylated-IFNα (Peg-IFNα) and Ribavirin (RBV) combination therapy, is IFNL4
genotypes.
Objective:
The aim of this study was to investigate the association between amino acid (aa) substitutions
in the NS5A region and the IFNL4 genotypes in two Single Nucleotide Polymorphism (SNP)
(rs8099917. rs12979860) in patients with HCV genotypes 1a and 3a. We also examined their response
to combination therapy and the effect of these mutations on the function and structure of PKR-BD.
Methods:
Eighty-six patients with hepatitis C were recruited and follow-up for 6 months. Several tests,
including alanine aminotransferase (ALT), aspartate aminotransferase (AST), viral load, IFNL4 genotyping,
and PKR-BD sequencing were performed. Using several well-known and trustworthy bioinformatics
tools, sequences were analyzed to define physio-chemical properties, structural features, immune
epitopes and protein-protein interaction.
Results:
Of the 86 patients, 65.1% had high viral load at baseline, 64% had CT genotype for rs12979860
and 57% had GT genotype for rs8099917. Several aa residues changes were found in the PKR-BD region.
We could not find any link between mutations in the PKR-BD region and different genotypes of IFNL4
in response to antiviral therapy. Regardless of pI, PKR-BD 1a and 3a showed similar physio-chemical
properties, and 2 phosphorylation sites and one glycosylation site were estimated for both PKR-BD 1a
and 3a. Trustworthy software were employed in order to predict B-cell epitopes, 3 regions (6-17, 26-32,
34-41) were found for both proteins, indicating a huge potential of PKR-BD protein to induce humoral
immune system. Docking analysis determined non-responder sequences in both 1a and 3a genotypes
to have higher energy value and are more compatible with PKR.
Conclusion:
To sum up, our results could not determine any significant relationship between mutations
of PKR-BD and genotypes of IFNL4 with other factors; ALT, AST, viral load. However, docking results
showed strengthened interaction between PKR-BD and PKR in non-responders that could have a
momentous impact on the illness severity.
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Affiliation(s)
- Tayebeh Hashempour
- Clinical Microbiology Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Behzad Dehghani
- Clinical Microbiology Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Mousavi
- Clinical Microbiology Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Tahereh Akbari
- Gastroenterohepatology Research Center, Department of Internal Medicine, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Zahra Hasanshahi
- Clinical Microbiology Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Javad Moayedi
- Clinical Microbiology Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Yahaghi
- Gastroenterohepatology Research Center, Department of Internal Medicine, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Mohammad Ali Davarpanah
- Gastroenterohepatology Research Center, Department of Internal Medicine, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
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Schwerk J, Negash A, Savan R, Gale M. Innate Immunity in Hepatitis C Virus Infection. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a036988. [PMID: 32341066 PMCID: PMC7849348 DOI: 10.1101/cshperspect.a036988] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Activation and viral control of the innate immune response are hallmarks of hepatitis C virus (HCV) infection and are major determinants of spontaneous clearance or progression to chronic infection and liver disease. In this review, we provide a contemporary overview of how HCV is sensed by the host cell to trigger innate immune activation and the mechanisms deployed by the virus to evade this response. Type I and III interferons (IFNs) are crucial mediators of antiviral innate immunity against HCV, and we specifically highlight the importance of IFN-λ host genetics for the outcome of HCV infection. Last, we focus on the proinflammatory responses elicited by HCV infection and describe our current understanding of how interleukin (IL)-1β signaling and cross talk between the IL-1β and IFN signaling pathways lead to sustained inflammation and increased risk of liver pathology.
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Sakr AA, Ahmed AE, Abd El-Maksoud MDE, Gamal A, El-Garem H, Ahmed OM. Interferon lambda 4 gene polymorphisms as a predicting tool of response to hepatitis C virus genotype 4 patients treated with Sofosbuvir and Ribavirin. INFECTION GENETICS AND EVOLUTION 2020; 86:104606. [PMID: 33127459 DOI: 10.1016/j.meegid.2020.104606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 10/07/2020] [Accepted: 10/20/2020] [Indexed: 01/04/2023]
Abstract
The relation between interferon lambda 4 gene (IFNL4) and direct acting antiviral (DAA) regimens in hepatitis C virus (HCV) infected patients is not clear. So, a single nucleotide polymorphisms (SNP) of IFNL4 gene genotypes and its relationship with Sofosbuvir (SOF) and Ribavirin (RBV) treatment response is under consideration. This study aims to investigate the relation between IFNL4 polymorphisms and clearance of HCV genotype 4 for HCV patients. Hence, the appropriate drug can be chosen for each patient. SNP genotyping assay for IFNL4 which formerly known as IL28B (rs368234815) was examined for genomic DNA. The DNA was extracted from whole blood of one hundred patients who documented to have infection with chronic HCV genotype 4 (positive PCR) and treated with SOF and RBV. Patients were diagnosed, previously, as HCV genotype 4 and classified according to drug response into two groups (responders, non-responders). All samples were compared with 50 of non-infected (negative PCR) people (control group). The TT/TT homozygous represents 48% of patients and 66% of non-infected people while the homozygous ∆G/∆G is 21% and 12%, respectively. There is significance to IFNL4 genotypes for the treatment response with the probability value p < 0.001. The percentages of the appearance of genotypes TT/TT, TT/∆G and ∆G/∆G for responders were 60%, 28% and 12%, respectively. There is no significance for gender, age, ALT and PLC to treatment response to SOF and RBV, while INR has.
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Affiliation(s)
- Amany A Sakr
- Department of Biotechnology, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Egypt.
| | - Amr E Ahmed
- Department of Biotechnology, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Egypt
| | - Mohamed D E Abd El-Maksoud
- Department of Biochemistry, Genetic Engineering and Biotechnology Research Division, National Research Centre, Dokki, Giza, Egypt
| | - Amany Gamal
- National Hepatology and Tropical Medicine Research Institute (NHTMRI), Cairo, Egypt
| | - Hasan El-Garem
- Department of Gastroenterology, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Osama M Ahmed
- Department of Zoology, Physiology Division, Faculty of Science, Beni-Suef University, Egypt
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Interferon Response in Hepatitis C Virus-Infected Hepatocytes: Issues to Consider in the Era of Direct-Acting Antivirals. Int J Mol Sci 2020; 21:ijms21072583. [PMID: 32276399 PMCID: PMC7177520 DOI: 10.3390/ijms21072583] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/04/2020] [Accepted: 04/07/2020] [Indexed: 12/16/2022] Open
Abstract
When interferons (IFNs) bind to their receptors, they upregulate numerous IFN-stimulated genes (ISGs) with antiviral and immune regulatory activities. Hepatitis C virus (HCV) is a single-stranded, positive-sense RNA virus that affects over 71 million people in the global population. Hepatocytes infected with HCV produce types I and III IFNs. These endogenous IFNs upregulate a set of ISGs that negatively impact the outcome of pegylated IFN-α and ribavirin treatments, which were previously used to treat HCV. In addition, the IFNL4 genotype was the primary polymorphism responsible for a suboptimal treatment response to pegylated IFN-α and ribavirin. However, recently developed direct-acting antivirals have demonstrated a high rate of sustained virological response without pegylated IFN-α. Herein, we review recent studies on types I and III IFN responses to in HCV-infected hepatocytes. In particular, we focused on open issues related to IFN responses in the direct-acting antiviral era.
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7
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Fang MZ, Jackson SS, O'Brien TR. IFNL4: Notable variants and associated phenotypes . Gene 2019; 730:144289. [PMID: 31846709 DOI: 10.1016/j.gene.2019.144289] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 02/06/2023]
Abstract
Interferon lambda proteins activate the JAK-STAT signalling pathway, resulting in upregulation of genes with antiviral effects. The interferon lambda family was initially thought to be redundant to the interferon alpha family, which signals through the same pathway, except for the more limited expression of the IFNLR1 receptor. However, recent studies show that interferon lambdas uniquely protect tissue barriers against a wide range of important viral infections. The interferon lambda 4 gene (IFNL4) was discovered in 2013. The IFNL4 protein is determined by the IFNL4-ΔG/TT (rs368234815) variant. The ancestral IFNL4-ΔG allele generates IFNL4, whereas IFNL4-TT causes pre-mature termination of the protein. Surprisingly, although interferons are generally antiviral proteins, the genotypes that generate the IFNL4 protein are strongly linked to impaired clearance of hepatitis C virus (HCV). IFNL4 genotype has also been linked to variation within the HCV genome, as well as risk of hepatic fibrosis, certain cancers and some infectious diseases. There has been very strong evolutionary selection against the ancestral IFNL4-ΔG allele, which is the major form in African populations, but the minor allele in Europeans and Asians. The reason for this selection and the biological mechanisms underlying observed phenotypic associations remain to be explained.
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Affiliation(s)
- Michelle Z Fang
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Dr, 6E108, MSC 9767, Bethesda, MD 20892, USA
| | - Sarah S Jackson
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Dr, 6E108, MSC 9767, Bethesda, MD 20892, USA
| | - Thomas R O'Brien
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Dr, 6E108, MSC 9767, Bethesda, MD 20892, USA.
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8
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Hsu SJ, Enkhzaya S, Lin YY, Tseng TC, Khosbayar T, Tsai CH, Wang TS, Enkhtuya D, Ivshinkhorol D, Naranzul N, Jargalsaikhan B, Amarsanaa J, Baatarkhuu O, Kao JH. Resistance-associated substitution and ledipasvir/sofosbuvir therapy in Mongolian chronic hepatitis C patients. J Formos Med Assoc 2019; 119:712-719. [PMID: 31672433 DOI: 10.1016/j.jfma.2019.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/30/2019] [Accepted: 10/03/2019] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Mongolia has the highest prevalence of hepatitis C virus (HCV) infection worldwide. Ledipasvir/sofosbuvir (LDV/SOF) was introduced to Mongolia since 2016 for HCV eradication. It has been reported that HCV resistance-associated substitutions (RASs) would affect the effectiveness of LDV/SOF in western chronic hepatitis C (CHC) patients. We thus investigated the effectiveness of LDV/SOF and the impact of RAS on the treatment outcome in Mongolian CHC patients. METHODS Patients with genotype (GT) 1b HCV infection were prospectively enrolled in Mongolia and treated with LDV/SOF for 12 weeks. The proportion of pre-treatment NS5A Y93H RAS in viral quasispecies was measured with next-generation sequencing. The endpoint of LDV/SOF effectiveness was sustained virological response at post-treatment week 12 (SVR12). RESULTS A total of 94 CHC patients were evaluated. The baseline Y93H proportion was <1% in 74 patients, 1-15% in 7, 15-50% in 2, and ≥50% in 11. All patients completed 12-week LDV/SOF treatment and the SVR rate was 90.4%. The rate of failure to achieve SVR12 for patients with Y93H < 1%, 1-15%, and ≥15% were 0%, 14.3%, and 61.5%, respectively (p for trend = 0.001). In univariable analysis, older age, baseline alanine transaminase level <40 U/mL, and a higher proportion of Y93H were associated with treatment failure. In multivariable analysis, only a higher proportion of Y93H was associated with treatment failure (p = 0.022). CONCLUSION LDV/SOF therapy achieves a high SVR rate in Mongolian CHC GT1b patients without baseline Y93H RAS. A higher proportion of Y93H may severely undermine the effectiveness of LDV/SOF.
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Affiliation(s)
- Shih-Jer Hsu
- Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan; Hepatology Medical Center, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Sukhee Enkhzaya
- Department of Infectious Disease, School of Medicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia; Department of Comprehensive Laboratory, National Center for Communicable Diseases, Ulaanbaatar, Mongolia
| | - You-Yu Lin
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tai-Chung Tseng
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Tulgaa Khosbayar
- Department of Molecular Biology and Genetics, School of BioMedicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Cheng-Hsueh Tsai
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Tzu-San Wang
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Damba Enkhtuya
- Happy Veritas Liver Diagnostic Center, Ulaanbaatar, Mongolia
| | | | - Nyamsuren Naranzul
- Department of Infectious Disease, School of Medicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Badarch Jargalsaikhan
- Department of Obstetrics and Gynecology, School of Medicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Jazag Amarsanaa
- Mongolian Association for the Study of Liver Diseases, Mongolia
| | - Oidov Baatarkhuu
- Department of Infectious Disease, School of Medicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia; Department of Comprehensive Laboratory, National Center for Communicable Diseases, Ulaanbaatar, Mongolia; Mongolian Association for the Study of Liver Diseases, Mongolia.
| | - Jia-Horng Kao
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan; Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan.
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Wu R, Geng D, Chi X, Wang X, Gao X, Xu H, Shi Y, Guan Y, Wang Y, Jin J, Ding Y, Niu J. Computational analysis of naturally occurring resistance-associated substitutions in genes NS3, NS5A, and NS5B among 86 subtypes of hepatitis C virus worldwide. Infect Drug Resist 2019; 12:2987-3015. [PMID: 31571951 PMCID: PMC6756830 DOI: 10.2147/idr.s218584] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/22/2019] [Indexed: 12/14/2022] Open
Abstract
Background and objective Direct-acting antivirals (DAA) facing resistance continue to be used in some areas worldwide. Thus, identifying hepatitis C virus (HCV) genotypes/subtypes and loci with certain prevalent resistance-associated substitutions (RASs) deserves attention. We investigated the global and regional frequencies of naturally occurring RASs among all confirmed HCV subtypes (n=86) and explored co-occurring and mutually exclusive RAS pairs within and between genes NS3, NS5A, and NS5B. Methods A total of 213,908 HCV sequences available as of July 10, 2019 were retrieved from the NCBI nucleotide database. After curation, 17,312 NS3, 8,478 NS5A, and 25,991 NS5B sequence fragments from DAA-naïve patients were screened for RASs. MEGA 6.0 was used to translate aligned nucleotide sequences into amino acid sequences, and RAS pairs were identified by hypergeometric analysis. Results RAS prevalence varied significantly among HCV subtypes. For example, D168E, highly resistanct to all protease inhibitors except voxilaprevir, was nearly absent in all subtypes except in 43.48% of GT5a sequences. RASs in NS3 exhibiting significantly different global distribution included Q80K in GT1a with the highest frequency in North America (54.49%), followed by in Europe (22.66%), Asia (6.98%), Oceania (6.62%), and South America (1.03%). The prevalence of NS3 S122G in GT1b was highest in Asia (26.6%) and lowest in Europe (2.64%). NS5A L28M, R30Q, and Y93H in GT1b, L31M in GT2b, and NS5B C316N in GT1b was most prevalent in Asia. A150V in GT3a, associated with sofosbuvir treatment failure, was most prevalent in Asia (44.09%), followed by Europe (31.19%), Oceania (24.29%), and North America (19.05%). Multiple mutually exclusive or co-occurring RAS pairs were identified, including Q80K+R155K and R155K+D168G in GT1a and L159F+C316N and R30Q (NS5A)+C316N (NS5B) in GT1b. Conclusion Our data may be of special relevance for those countries where highly effective antivirals might not be available. Considering the specific RASs prevalence will help the clinicians to make optimal treatment choices. The RASs pairs would benefit anti-HCV drug development.
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Affiliation(s)
- Ruihong Wu
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Dongfeng Geng
- Centre for Reproductive Medicine, Centre for Prenatal Diagnosis, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Xiumei Chi
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Xiaomei Wang
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Xiuzhu Gao
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Hongqin Xu
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Ying Shi
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Yazhe Guan
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Yang Wang
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Jinglan Jin
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Yanhua Ding
- Phase I Clinical Research Center, The First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Junqi Niu
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
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10
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Chaturvedi N, Svarovskaia ES, Mo H, Osinusi AO, Brainard DM, Subramanian GM, McHutchison JG, Zeuzem S, Fellay J. Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes. eLife 2019; 8:e42542. [PMID: 31478832 PMCID: PMC6721370 DOI: 10.7554/elife.42542] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 05/31/2019] [Indexed: 12/21/2022] Open
Abstract
Genetic polymorphism in the interferon lambda (IFN-λ) region is associated with spontaneous clearance of hepatitis C virus (HCV) infection and response to interferon-based treatment. Here, we evaluate associations between IFN-λ polymorphism and HCV variation in 8729 patients (Europeans 77%, Asians 13%, Africans 8%) infected with various viral genotypes, predominantly 1a (41%), 1b (22%) and 3a (21%). We searched for associations between rs12979860 genotype and variants in the NS3, NS4A, NS5A and NS5B HCV proteins. We report multiple associations in all tested proteins, including in the interferon-sensitivity determining region of NS5A. We also assessed the combined impact of human and HCV variation on pretreatment viral load and report amino acids associated with both IFN-λ polymorphism and HCV load across multiple viral genotypes. By demonstrating that IFN-λ variation leaves a large footprint on the viral proteome, we provide evidence of pervasive viral adaptation to innate immune pressure during chronic HCV infection.
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Affiliation(s)
- Nimisha Chaturvedi
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | | | - Hongmei Mo
- Gilead Sciences IncFoster CityUnited States
| | | | | | | | | | | | - Jacques Fellay
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
- Precision Medicine UnitLausanne University HospitalLausanneSwitzerland
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11
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Bellocchi MC, Aragri M, Carioti L, Fabeni L, Pipitone RM, Brancaccio G, Sorbo MC, Barbaliscia S, Di Maio VC, Bronte F, Grimaudo S, Mazzucco W, Frigeri F, Cantone M, Pinto A, Perno CF, Craxì A, Gaeta GB, Di Marco V, Ceccherini-Silberstein F. NS5A Gene Analysis by Next Generation Sequencing in HCV Nosocomial Transmission Clusters of HCV Genotype 1b Infected Patients. Cells 2019; 8:E666. [PMID: 31269695 PMCID: PMC6678654 DOI: 10.3390/cells8070666] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/19/2019] [Accepted: 06/25/2019] [Indexed: 02/06/2023] Open
Abstract
Background: The aim of the study was to investigate the intra-host variability through next-generation-sequencing (NGS) of the NS5A-gene in nosocomial transmission-clusters observed in two Italian hospitals among hepatitis C virus (HCV)-genotype-1b infected patients. Methods: HCV-sequencing was performed by Sanger-sequencing (NS3 + NS5A + NS5B) and by NGS (NS5A, MiSeq-Illumina) in 15 HCV-1b infected patients [five acute with onco-hematologic-disease and 10 (4/6 acute/chronic) with β-thalassemia]. Resistance-associated-substitutions (RAS) were analysed by Geno2pheno-algorithm. Nucleotide-sequence-variability (NSV, at 1%, 2%, 5%, 10% and 15% NGS-cutoffs) and Shannon entropy were estimated. Phylogenetic analysis was performed by Mega6-software and Bayesian-analysis. Results: Phylogenetic analysis showed five transmission-clusters: one involving four HCV-acute onco-hematologic-patients; one involving three HCV-chronic β-thalassemia-patients and three involving both HCV-acute and chronic β-thalassemia-patients. The NS5A-RAS Y93H was found in seven patients, distributed differently among chronic/acute patients involved in the same transmission-clusters, independently from the host-genetic IL-28-polymorphism. The intra-host NSV was higher in chronic-patients versus acute-patients, at all cutoffs analyzed (p < 0.05). Even though Shannon-entropy was higher in chronic-patients, significantly higher values were observed only in chronic β-thalassemia-patients versus acute β-thalassemia-patients (p = 0.01). Conclusions: In nosocomial HCV transmission-clusters, the intra-host HCV quasispecies divergence in patients with acute-infection was very low in comparison to that in chronic-infection. The NS5A-RAS Y93H was often transmitted and distributed differently within the same transmission-clusters, independently from the IL-28-polymorphism.
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Affiliation(s)
| | - Marianna Aragri
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Lavinia Fabeni
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Rosaria Maria Pipitone
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, 90127 Palermo, Italy
| | - Giuseppina Brancaccio
- Infectious Diseases, Department of Mental and Physical Health and Preventive Medicine, Campania University "Luigi Vanvitelli", 80138 Naples, Italy
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Maria Chiara Sorbo
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Silvia Barbaliscia
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Velia Chiara Di Maio
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Fabrizio Bronte
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, 90127 Palermo, Italy
| | - Stefania Grimaudo
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, 90127 Palermo, Italy
| | - Walter Mazzucco
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, 90127 Palermo, Italy
| | | | - Marco Cantone
- Infectious Diseases, Department of Mental and Physical Health and Preventive Medicine, Campania University "Luigi Vanvitelli", 80138 Naples, Italy
| | - Antonio Pinto
- Hematology Department, National Cancer Institute "Fondazione Pascale", IRCCS, 80131 Naples, Italy
| | - Carlo Federico Perno
- Department of Microbiology and Clinic Microbiology, University of Milan, 20162 Milan, Italy
| | - Antonio Craxì
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, 90127 Palermo, Italy
| | - Giovanni Battista Gaeta
- Infectious Diseases, Department of Mental and Physical Health and Preventive Medicine, Campania University "Luigi Vanvitelli", 80138 Naples, Italy
| | - Vito Di Marco
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, 90127 Palermo, Italy
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12
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Hepatitis C Virus Genetic Variability, Human Immune Response, and Genome Polymorphisms: Which Is the Interplay? Cells 2019; 8:cells8040305. [PMID: 30987134 PMCID: PMC6523096 DOI: 10.3390/cells8040305] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 03/26/2019] [Accepted: 03/30/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) infection is the main cause of chronic hepatitis, affecting an estimated 150 million people worldwide. Initial exposure to HCV is most often followed by chronic hepatitis, with only a minority of individuals spontaneously clearing the virus. The induction of sustained and broadly directed HCV-specific CD4+ and CD8+ T cell responses, together with neutralizing antibodies (nAb), and specific genetic polymorphism have been associated with spontaneous resolution of the infection. However, due to its high variability, HCV is able to overwhelm the host immune response through the rapid acquisition of mutations in the epitopes targeted by T cells and neutralizing antibodies. In this context, immune-mediated pressure represents the main force in driving HCV evolution. This review summarizes the data on HCV diversity and the current state of knowledge about the contributions of antibodies, T cells, and host genetic polymorphism in driving HCV evolution in vivo.
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13
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O'Brien TR, Yang HI, Groover S, Jeng WJ. Genetic Factors That Affect Spontaneous Clearance of Hepatitis C or B Virus, Response to Treatment, and Disease Progression. Gastroenterology 2019; 156:400-417. [PMID: 30287169 DOI: 10.1053/j.gastro.2018.09.052] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) and hepatitis B virus (HBV) infections can lead to cirrhosis, end-stage liver disease, and hepatocellular carcinoma. Over the past decade, studies of individuals infected with these viruses have established genetic associations with the probability of developing a chronic infection, risk of disease progression, and likelihood of treatment response. We review genetic and genomic methods that have been used to study risk of HBV and HCV infection and patient outcomes. For example, genome-wide association studies have linked a region containing the interferon lambda genes to spontaneous and treatment-induced clearance of HCV. We review the genetic variants associated with HCV and HBV infection, and how these variants affect specific expression or activities of their products. Further studies of these variants could provide insights into risk factors for and mechanisms of chronic infection and disease progression, as well as new strategies for treatment.
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Affiliation(s)
- Thomas R O'Brien
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland.
| | - Hwai-I Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Sarah Groover
- Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma
| | - Wen-Juei Jeng
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan; Liver Research Unit, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
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14
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Esposito I, Marciano S, Haddad L, Galdame O, Franco A, Gadano A, Flichman D, Trinks J. Prevalence and Factors Related to Natural Resistance-Associated Substitutions to Direct-Acting Antivirals in Patients with Genotype 1 Hepatitis C Virus Infection. Viruses 2018; 11:E3. [PMID: 30577623 PMCID: PMC6356817 DOI: 10.3390/v11010003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/14/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023] Open
Abstract
This study aimed to assess the prevalence of natural resistance-associated substitutions (RASs) to NS3, NS5A and NS5B inhibitors in 86 genotype 1 Hepatitis C Virus (HCV)-infected patients from Buenos Aires, Argentina, and to determine their effect on therapy outcome. Additionally, virological, clinical and host genetic factors were explored as predictors of the presence of baseline RASs. NS3 RASs (39.2%) were more prevalent than NS5A RASs (25%) and NS5B RASs (8.9%). In the three regions, the frequencies of RASs were significantly higher in HCV-1b than in HCV-1a. The prevalence of Y93H, L159F and Q80K were 1.3%, 6.3% and 2.5%, respectively. IFNL3 CC genotype was identified as an independent predictor of the presence of baseline RASs in NS5A and NS3 genes (p = 0.0005 and p = 0.01, respectively). Sustained virologic response was achieved by 93.3% of the patients after receiving direct-acting antivirals (DAAs), although 48.7% of them showed baseline RASs related to the DAA-regimen. Notably, the prevalence of clinically relevant RASs in the three genes was lower than that observed around the world. The baseline presence of RASs in both subtypes did not appear to affect therapy outcome. These results support the need to evaluate resistance patterns in each particular country since RASs´ prevalence significantly vary worldwide.
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Affiliation(s)
- Isabella Esposito
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), C1199ACL Buenos Aires, Argentina.
| | - Sebastián Marciano
- Sección de Hepatología, Servicio de Clínica Médica, Hospital Italiano de Buenos Aires, C1199ABB Buenos Aires, Argentina.
- Departamento de Investigación, Hospital Italiano de Buenos Aires, C1199ABB Buenos Aires, Argentina.
| | - Leila Haddad
- Sección de Hepatología, Servicio de Clínica Médica, Hospital Italiano de Buenos Aires, C1199ABB Buenos Aires, Argentina.
| | - Omar Galdame
- Sección de Hepatología, Servicio de Clínica Médica, Hospital Italiano de Buenos Aires, C1199ABB Buenos Aires, Argentina.
| | - Alejandra Franco
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), C1199ACL Buenos Aires, Argentina.
| | - Adrián Gadano
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), C1199ACL Buenos Aires, Argentina.
- Sección de Hepatología, Servicio de Clínica Médica, Hospital Italiano de Buenos Aires, C1199ABB Buenos Aires, Argentina.
- Departamento de Investigación, Hospital Italiano de Buenos Aires, C1199ABB Buenos Aires, Argentina.
| | - Diego Flichman
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, C1113AAD Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1425FQB Buenos Aires, Argentina.
| | - Julieta Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), C1199ACL Buenos Aires, Argentina.
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15
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Mylopoulou T, Papadopoulos V, Kassela K, Karakasiliotis I, Souvalidou F, Mimidis P, Veletza S, Mavromara P, Mimidis K. Relationship between antibodies to hepatitis C virus core+1 protein and treatment outcome. Ann Gastroenterol 2018; 31:593-597. [PMID: 30174396 PMCID: PMC6102464 DOI: 10.20524/aog.2018.0290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/01/2018] [Indexed: 01/02/2023] Open
Abstract
Background It has been suggested that hepatitis C virus (HCV) core+1 protein plays a crucial role in the viral life cycle, potentially affecting liver cirrhosis and the development of hepatocellular carcinoma. Methods To investigate its relationship with the outcome of HCV standard combination therapy with peginterferon-α plus ribavirin, we screened 139 consecutive HCV patients (119 with chronic HCV infection and 20 who spontaneously cleared HCV) for the presence of anti-core+1 antibodies (Abs). In addition, liver fibrosis was determined by FibroScan in all but one patients. Results Twenty-nine patients were cirrhotic (stiffness >12.5 kPa, F4 METAVIR), all of them with mild liver cirrhosis (Child-Pugh score A). Eighty-six of 139 patients were treatment-experienced with standard combination therapy. Fifty of them had achieved a sustained virological response, while 36 were non-responders. The prevalence of anti-core+1 Abs in patients with chronic HCV infection was 22.69% (27/119 patients): 18% (9/50 patients) in responders and 36.11% (13/36 patients) in non-responders (P=0.050). Five (17.24%) of the 29 cirrhotic patients and 22 (24.72%) of the 89 non-cirrhotic patients were positive for anti-core+1 Abs (P=0.405). Furthermore, the presence of anti-core+1 Abs correlated with the poor response interleukin (IL) 28B genotype TT (P=0.040). No correlation between spontaneous clearance and anti-core+1 Abs was observed (P=0.088). Conclusion The presence of anti-core+1 Abs might be correlated with the poor response IL28B TT genotype and may negatively affect the outcome of standard combination treatments in HCV patients, suggesting that core+1 may play a biological role in the course of HCV infection.
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Affiliation(s)
- Theodora Mylopoulou
- First Department of Internal Medicine, Democritus University of Thrace, Alexandroupolis (Theodora Mylopoulou, Konstantinos Mimidis), Greece
| | | | - Katerina Kassela
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens (Katerina Kassela, Penelope Mavromara), Greece
| | - Ioannis Karakasiliotis
- Laboratory of Medical Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis (Ioannis Karakasiliotis, Stavroula Veletza), Greece
| | - Fani Souvalidou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Fani Souvalidou, Panagiotis Mimidis, Penelope Mavromara), Greece
| | - Panagiotis Mimidis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Fani Souvalidou, Panagiotis Mimidis, Penelope Mavromara), Greece
| | - Stavroula Veletza
- Laboratory of Medical Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis (Ioannis Karakasiliotis, Stavroula Veletza), Greece
| | - Penelope Mavromara
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens (Katerina Kassela, Penelope Mavromara), Greece.,Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Fani Souvalidou, Panagiotis Mimidis, Penelope Mavromara), Greece
| | - Konstantinos Mimidis
- First Department of Internal Medicine, Democritus University of Thrace, Alexandroupolis (Theodora Mylopoulou, Konstantinos Mimidis), Greece
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16
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2017 KASL clinical practice guidelines management of hepatitis C: Treatment of chronic hepatitis C. Clin Mol Hepatol 2018; 24:169-229. [PMID: 30092624 PMCID: PMC6166104 DOI: 10.3350/cmh.2018.1004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 03/06/2018] [Indexed: 12/11/2022] Open
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17
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Parczewski M, Kordek J, Janczewska E, Pisula A, Łojewski W, Socha Ł, Wawrzynowicz-Syczewska M, Bociąga-Jasik M, Szymczak A, Cielniak I, Siwak E, Mularska E, Aksak-Wąs B, Urbańska A, Lübke N. Hepatitis C virus (HCV) genotype 1 NS5A resistance-associated variants are associated with advanced liver fibrosis independently of HCV-transmission clusters. Clin Microbiol Infect 2018; 25:513.e1-513.e6. [PMID: 29981869 DOI: 10.1016/j.cmi.2018.06.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 06/12/2018] [Accepted: 06/26/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The aim of the study was to characterize the differences in the frequencies of NS3 and NS5A resistance-associated variants (RAVs) among Polish therapy-naive genotype 1 (G1) hepatitis C virus (HCV)-monoinfected and human immunodeficiency virus (HIV)/HCV-coinfected patients including clustering patterns and association of RAV frequency with liver fibrosis. METHODS NS3/NS5A RAVs were identified by population sequencing in 387 directly acting antiviral treatment-naive G1-infected individuals (54 with genotype 1a (G1a) and 333 with genotype 1b (G1b)). Liver fibrosis was assessed based on histopathology or ultrasound elastography. Phylogenetic clusters were identified using maximum likelihood models. For statistics, chi-squared or two-sided Fisher's exact tests and multivariate logistic regression models were used, as appropriate. RESULTS NS3 RAVs were found in 33.33% (18/54) for G1a and 2.62% (8/297) for G1b whereas NS5A variants were present in 5.55% (3/54) G1a and 9.31% (31/333) G1b sequences. Variations in NS5A 31 and 93 codon positions were found only in G1b (4.2% (14/333) for L31I/F/M and 5.39% (17/333) for Y93H). NS5A RAVs were more frequent among patients with advanced liver fibrosis (17.17% (17/99) for F3-F4 versus 6.94% (17/245) for F0-F2; p 0.004) or liver cirrhosis (20.34% (12/59) for F4 versus 7.72% (22/285) for F0-F3; p 0.003). Liver cirrhosis (F4) was associated with higher odds ratio of the NS5A RAVs among HCV-infected patients (odds ratio 2.34, 95% CI 1.004-5.291; p 0.049). NS5A RAVs were less frequent among sequences forming clusters and pairs (5.16% (8/155) versus 11.21% (26/232); p 0.039). CONCLUSIONS Presence of NS5A RAVs correlated with progression of liver fibrosis and represents de novo selection of variants rather than transmission of drug resistance. Hence, the presence of NS5A RAVs may be a predictor for a long-lasting HCV infection.
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Affiliation(s)
- M Parczewski
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland.
| | - J Kordek
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | | | | | - W Łojewski
- Department of Infectious Diseases, Regional Hospital in Zielona Gora, Zielona Góra, Poland
| | - Ł Socha
- Department of Infectious Diseases, Hepatology and Liver Transplantation, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - M Wawrzynowicz-Syczewska
- Department of Infectious Diseases, Hepatology and Liver Transplantation, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - M Bociąga-Jasik
- Department of Infectious Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - A Szymczak
- Department of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Wrocław Medical University, Wrocław, Poland
| | - I Cielniak
- Hospital for Infectious Diseases, HIV Out-Patient's Clinic, Warsaw, Poland
| | - E Siwak
- Hospital for Infectious Diseases, HIV Out-Patient's Clinic, Warsaw, Poland
| | - E Mularska
- Hospital for Infectious Diseases, Chorzów, Poland
| | - B Aksak-Wąs
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - A Urbańska
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - N Lübke
- Institute of Virology, Heinrich-Heine-University Düsseldorf, University Hospital, Düsseldorf, Germany
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18
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Forni D, Cagliani R, Pontremoli C, Pozzoli U, Vertemara J, De Gioia L, Clerici M, Sironi M. Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV. Front Microbiol 2018; 9:854. [PMID: 29765366 PMCID: PMC5938362 DOI: 10.3389/fmicb.2018.00854] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/13/2018] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) belongs to the Hepacivirus genus and is genetically heterogeneous, with seven major genotypes further divided into several recognized subtypes. HCV origin was previously dated in a range between ∼200 and 1000 years ago. Hepaciviruses have been identified in several domestic and wild mammals, the largest viral diversity being observed in bats and rodents. The closest relatives of HCV were found in horses/donkeys (equine hepaciviruses, EHV). However, the origin of HCV as a human pathogen is still an unsolved puzzle. Using a selection-informed evolutionary model, we show that the common ancestor of extant HCV genotypes existed at least 3000 years ago (CI: 3192–5221 years ago), with the oldest genotypes being endemic to Asia. EHV originated around 1100 CE (CI: 291–1640 CE). These time estimates exclude that EHV transmission was mainly sustained by widespread veterinary practices and suggest that HCV originated from a single zoonotic event with subsequent diversification in human populations. We also describe a number of biologically important sites in the major HCV genotypes that have been positively selected and indicate that drug resistance-associated variants are significantly enriched at positively selected sites. HCV exploits several cell-surface molecules for cell entry, but only two of these (CD81 and OCLN) determine the species-specificity of infection. Herein evolutionary analyses do not support a long-standing association between primates and hepaciviruses, and signals of positive selection at CD81 were only observed in Chiroptera. No evidence of selection was detected for OCLN in any mammalian order. These results shed light on the origin of HCV and provide a catalog of candidate genetic modulators of HCV phenotypic diversity.
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Affiliation(s)
- Diego Forni
- Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy
| | - Rachele Cagliani
- Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy
| | - Chiara Pontremoli
- Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy
| | - Jacopo Vertemara
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Don C. Gnocchi Foundation Onlus, IRCCS, Milan, Italy
| | - Manuela Sironi
- Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy
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Huang Y, Li MH, Hou M, Xie Y. Peginterferon alfa-2a for the treatment of chronic hepatitis C in the era of direct-acting antivirals. Hepatobiliary Pancreat Dis Int 2017; 16:470-479. [PMID: 28992878 DOI: 10.1016/s1499-3872(17)60044-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/23/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND The availability of novel direct-acting antivirals (DAAs) represents a new era of curative hepatitis C virus (HCV) treatment, with over 95% of patients infected with HCV genotype 1 achieving sustained virological response (SVR). Nevertheless, the majority of patients globally are unable to access these treatments because of cost and infrastructure constraints and, thus, remain untreated and uncured. DATA SOURCE Relevant articles of peginterferon (PegIFN)-based treatments in HCV and sofosbuvir-based treatments, simeprevir, daclatasvir/asunaprevir, ritonavir-boosted paritaprevir/ombitasvir/dasabuvir, and grazoprevir/elbasvir, were searched in PubMed database, including general population and special population. RESULTS PegIFN in combination with ribavirin remains an important and relevant option for some patients, achieving SVR rates of up to 79% in genotype 1 and 89% in genotype 2 or 3 infections, which increases for patients with favorable IL28B genotypes. Triple therapy of DAA plus PegIFN/ribavirin is effective in treating difficult-to-cure patients infected with HCV genotype 3 or with resistance-associated variants. Owing to its long history in HCV management, the efficacy, tolerability and long-term outcomes associated with PegIFN alfa-2a are well established and have been validated in large-scale studies and in clinical practice for many populations. Furthermore, emerging data show that IFN-induced SVR is associated with lower incidences of hepatocellular carcinoma compared with DAAs. On the contrary, novel DAAs have yet to be studied in special populations, and long-term outcomes, particularly tumor development and recurrence in patients with cirrhosis and/or hepatocellular carcinoma, and reactivation of HBV in dually infected patients, are still unclear. CONCLUSION In this interferon-free era, PegIFN-based regimens remain a safe and effective option for selected HCV patients.
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Affiliation(s)
- Yan Huang
- Shanghai Roche Pharmaceuticals Ltd., Shanghai 201203, Beijing, China
| | - Ming-Hui Li
- Liver Disease Center, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Min Hou
- Shanghai Roche Pharmaceuticals Ltd., Shanghai 201203, Beijing, China
| | - Yao Xie
- Liver Disease Center, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.
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20
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Chen JH, Zeng Z, Zhang XX, Zhang Y, Zhang RW, Wang S, Wu CH, Yu M, Liu D, Xi HL, Zhou YX, An YY, Xu XY. Efficacy and safety of combined directly acting antivirals for treatment of Chinese chronic hepatitis C patients in a real-world setting. World J Gastroenterol 2017; 23:4072-4079. [PMID: 28652660 PMCID: PMC5473126 DOI: 10.3748/wjg.v23.i22.4072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/16/2017] [Accepted: 04/12/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To assess the efficacy and safety of combined directly acting antivirals (DAAs) for the treatment of Chinese chronic hepatitis C (CHC) patients in a real-world setting.
METHODS Hospitalized CHC patients who were treated with DAAs at Peking University First Hospital between January 2015 and December 2016 were enrolled. Samples and clinical data were collected at 0 wk, 2 wk, 4 wk, 8 wk, 12 wk, or 24 wk during DAAs treatment and at 4 wk, 12 wk, and 24 wk after the end of treatment.
RESULTS Fifty-four patients who underwent DAAs treatment were included in our study, of whom 83.3% (45/54) achieved rapid virological response at 2 wk after treatment initiation (RVR 2) and 94.4% (51/54) achieved sustained virological response at 24 wk after the end of treatment (SVR 24). Serum creatinine and uric acid levels at the end of treatment were significantly increased compared with baseline levels (83.6 ± 17.9 vs 88.8 ± 19.4, P01 < 0.001; 320.8 ± 76.3 vs 354.5 ± 87.6, P01 < 0.001), and no significant improvements were observed at 24w after the end of treatment (83.6 ± 17.9 vs 86.8 ± 19.1, P02 = 0.039; 320.8 ± 76.3 vs 345.9 ± 89.4, P02 = 0.001). The total frequency of adverse events (AEs) during treatment was 33.3% (18/54), with major AEs being fatigue (16.7%), headache (7.4%), anorexia (7.4%), and insomnia (5.6%).
CONCLUSION Though based in a small cohort of patients, the abnormal changes in renal function indices and relative high frequency of AEs during combined DAAs treatment should be taken as a note of caution.
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21
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Ansari MA, Pedergnana V, L C Ip C, Magri A, Von Delft A, Bonsall D, Chaturvedi N, Bartha I, Smith D, Nicholson G, McVean G, Trebes A, Piazza P, Fellay J, Cooke G, Foster GR, Hudson E, McLauchlan J, Simmonds P, Bowden R, Klenerman P, Barnes E, Spencer CCA. Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus. Nat Genet 2017; 49:666-673. [PMID: 28394351 PMCID: PMC5873514 DOI: 10.1038/ng.3835] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/10/2017] [Indexed: 12/11/2022]
Abstract
Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. We use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals chronically infected with HCV, predominately genotype 3. We show that both HLA alleles and interferon lambda innate immune system genes drive viral genome polymorphism, and that IFNL4 genotypes determine HCV viral load through a mechanism that is dependent on a specific polymorphism in the HCV polyprotein. We highlight the interplay between innate immune responses and the viral genome in HCV control.
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Affiliation(s)
- M Azim Ansari
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Oxford Martin School, University of Oxford, Oxford, UK.,Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Vincent Pedergnana
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Camilla L C Ip
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Andrea Magri
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Annette Von Delft
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - David Bonsall
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Nimisha Chaturvedi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Istvan Bartha
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - David Smith
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | | | - Gilean McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Amy Trebes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Graham Cooke
- Wright-Fleming Institute, Imperial College London, London, UK
| | | | | | - Emma Hudson
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Chris C A Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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22
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Trinks J, Caputo M, Hulaniuk ML, Corach D, Flichman D. Hepatitis C virus pharmacogenomics in Latin American populations: implications in the era of direct-acting antivirals. Pharmgenomics Pers Med 2017; 10:79-91. [PMID: 28405170 PMCID: PMC5378445 DOI: 10.2147/pgpm.s125452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In recent years, great progress has been made in the field of new therapeutic options for hepatitis C virus (HCV) infection. The new direct-acting antiviral agents (DAAs) represent a great hope for millions of chronically infected individuals because their use may lead to excellent cure rates with fewer side effects. In Latin America, the high prevalence of HCV genotype 1 infection and the significant association of Native American ancestry with risk predictive single-nucleotide polymorphisms (SNPs) in IFNL4 and ITPA genes highlight the need to implement new treatment regimens in these populations. However, the universal accessibility to DAAs is still not a reality in the region as their high cost is one of the major, although not the only, limiting factors for their broad implementation. Therefore, under these circumstances, could the assessment of host genetic markers be a useful tool to prioritize DAA treatment until global access to these new drugs can be achieved? This review will summarize the scientific evidences and the potential implications of HCV pharmacogenomics in this rapidly evolving era of anti-HCV drug development.
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Affiliation(s)
- Julieta Trinks
- Basic Science and Experimental Medicine Institute (ICBME), University Institute of the Italian Hospital of Buenos Aires
- Scientific and Technological National Research Council (CONICET)
| | - Mariela Caputo
- Scientific and Technological National Research Council (CONICET)
- Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica
| | - María L Hulaniuk
- Basic Science and Experimental Medicine Institute (ICBME), University Institute of the Italian Hospital of Buenos Aires
| | - Daniel Corach
- Scientific and Technological National Research Council (CONICET)
- Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica
| | - Diego Flichman
- Scientific and Technological National Research Council (CONICET)
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
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23
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Murakawa M, Asahina Y, Kawai-Kitahata F, Nakagawa M, Nitta S, Otani S, Nagata H, Kaneko S, Asano Y, Tsunoda T, Miyoshi M, Itsui Y, Azuma S, Kakinuma S, Tanaka Y, Iijima S, Tsuchiya K, Izumi N, Tohda S, Watanabe M. Hepatic IFNL4 expression is associated with non-response to interferon-based therapy through the regulation of basal interferon-stimulated gene expression in chronic hepatitis C patients. J Med Virol 2017; 89:1241-1247. [PMID: 28036111 DOI: 10.1002/jmv.24763] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 12/16/2016] [Accepted: 12/16/2016] [Indexed: 12/27/2022]
Abstract
Single nucleotide polymorphisms (SNPs) within or near interferon lambda 4 (IFNL4) gene located upstream of IFNL3 are associated with response to anti-HCV therapy both in interferon (IFN)-based and IFN-free regimens. IFNL4 encodes IFNλ4, a newly discovered type III IFN, and its expression is controlled by rs368234815-TT/ΔG, which is in strong linkage disequilibrium (LD) with other tag SNPs within or near IFNL4 such as rs12979860 and rs8099917. Intrahepatic expression levels of IFN-stimulated genes (ISGs) affect the responsiveness to IFNα and are also associated with IFNL4 genotype. However, IFNL4 expressions and its role in intrinsic antiviral innate immunity remain unclear. This study evaluated the effect of IFNL4 on intrahepatic ISG expression and investigated its relationship with treatment outcomes in liver samples obtained from 49 chronic hepatitis C patients treated with pegylated (PEG)-IFN/ribavirin therapy. IFNL4 mRNA was detected in 11 of 22 patients with IFNL4-unfavorable SNPs but not in patients with favorable genotypes. IFNL4 expression was associated with non-response to PEG-IFN/ribavirin therapy. Intrahepatic expression of antiviral ISGs (ISG15 and MX1) was significantly higher in IFNL4-unfavorable patients with detectable IFNL4 mRNA than in patients with undetectable IFNL4 mRNA, whereas the expression of suppressive ISGs (RNF125, SOCS1, SOCS3, and RNF11) was lower in patients with detectable IFNL4 mRNA. In summary, intrahepatic expression of IFNL4 was associated with increased antiviral ISG expression and decreased suppressive ISG expression at baseline, resulting in poor responsiveness to IFNα-based therapy in HCV infection.
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Affiliation(s)
- Miyako Murakawa
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Clinical Laboratory, Medical Hospital, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuhiro Asahina
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Liver Disease Control, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fukiko Kawai-Kitahata
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Mina Nakagawa
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sayuri Nitta
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoshi Otani
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroko Nagata
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shun Kaneko
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yu Asano
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoyuki Tsunoda
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masato Miyoshi
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuhiro Itsui
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishin Azuma
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sei Kakinuma
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Clinical Laboratory, Medical Hospital, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuhito Tanaka
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Sayuki Iijima
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kaoru Tsuchiya
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo, Japan
| | - Namiki Izumi
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo, Japan
| | - Shuji Tohda
- Department of Liver Disease Control, Tokyo Medical and Dental University, Tokyo, Japan
| | - Mamoru Watanabe
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
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24
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Eltahla AA, Leung P, Pirozyan MR, Rodrigo C, Grebely J, Applegate T, Maher L, Luciani F, Lloyd AR, Bull RA. Dynamic evolution of hepatitis C virus resistance-associated substitutions in the absence of antiviral treatment. Sci Rep 2017; 7:41719. [PMID: 28139734 PMCID: PMC5282498 DOI: 10.1038/srep41719] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/28/2016] [Indexed: 01/01/2023] Open
Abstract
Resistance against new hepatitis C virus (HCV) antivirals is an area of increasing interest. Resistance-associated substitutions (RASs) have been identified in treatment-naïve individuals, but pressures driving treatment-independent RAS emergence are poorly understood. We analysed the longitudinal evolution of RASs in twelve participants with early acute HCV infections. Full-genome deep sequences were analysed for changes in RAS frequency within NS3, NS5A and NS5B-coding regions over the course of the infection. Emergence of RASs relevant only to the polymerase non-nucleoside inhibitors (NNI) was detected, and these lay within CD8+ T-cell epitopes. Conversely, the loss of NNI RASs over time appeared likely to be driven by viral fitness constraints. These results highlight the importance of monitoring CD8+ T cell epitope-associated RASs in populations with dominant HLA types.
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Affiliation(s)
- Auda A. Eltahla
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
| | - Preston Leung
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
| | - Mehdi R. Pirozyan
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
| | - Chaturaka Rodrigo
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
| | - Jason Grebely
- The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Tanya Applegate
- The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Lisa Maher
- The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Fabio Luciani
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
| | - Andrew R. Lloyd
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
| | - Rowena A. Bull
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
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25
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Lasfar A, Zloza A, de la Torre A, Cohen-Solal KA. IFN-λ: A New Inducer of Local Immunity against Cancer and Infections. Front Immunol 2016; 7:598. [PMID: 28018361 PMCID: PMC5156659 DOI: 10.3389/fimmu.2016.00598] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 11/30/2016] [Indexed: 12/11/2022] Open
Abstract
IFN-λ is the newly established type III IFN with unique immunomodulatory functions. In contrast to the IFN-α/β family and to some extent IFN-γ, IFN-λ is apparently acting in specific areas of the body to activate resident immune cells and induces a local immunity, instrumental in preventing particular infections and also keeping transformed cells under control. Mucosal areas of lung and gastrointestinal tracts are now under scrutiny to elucidate the immune mechanisms triggered by IFN-λ and leading to viral protection. New evidence also indicates the crucial role of IFN-λ in promoting innate immunity in solid cancer models. Based on its unique biological activities among the IFN system, new immunotherapeutic approaches are now emerging for the treatment of cancer, infection, and autoimmune diseases. In the present review, we highlight the recent advances of IFN-λ immunomodulatory functions. We also discuss the perspectives of IFN-λ as a therapeutic agent.
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Affiliation(s)
- Ahmed Lasfar
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Andrew Zloza
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA; Section of Surgical Oncology Research, Department of Surgery, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Andrew de la Torre
- Department of Surgery, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA; St Joseph's Medical Center, Paterson, NJ, USA
| | - Karine A Cohen-Solal
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA; Section of Surgical Oncology Research, Department of Surgery, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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26
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Aiken T, Garber A, Thomas D, Hamon N, Lopez R, Konjeti R, McCullough A, Zein N, Fung J, Askar M, John BV. Donor IFNL4 Genotype Is Associated with Early Post-Transplant Fibrosis in Recipients with Hepatitis C. PLoS One 2016; 11:e0166998. [PMID: 27875564 PMCID: PMC5119817 DOI: 10.1371/journal.pone.0166998] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/07/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND AND AIMS Early post-transplant hepatic fibrosis is associated with poor outcomes and may be influenced by donor/recipient genetic factors. The rs368234815 IFNL4 polymorphism is related to the previously described IL28B polymorphism, which predicts etiology-independent hepatic fibrosis. The aim of this study was to identify the impact of donor and/or recipient IFNL4 genotype on early fibrosis among patients transplanted for hepatitis C (HCV). METHODS Clinical data were collected for 302 consecutive patients transplanted for HCV. 116 patients who had available liver biopsies and donor/recipient DNA were included. 28% of these patients with stage 2 fibrosis or greater were compared to patients without significant post-transplant fibrosis with respect to clinical features as well as donor/recipient IFNL4 genotype. RESULTS The IFNL4 TT/TT genotype was found in 26.0% of recipients and 38.6% of donors. Patients who developed early post-transplant fibrosis had a 3.45 adjusted odds of having donor IFNL4 TT/TT genotype (p = 0.012). Donor IFNL4 TT/TT genotype also predicted decreased overall survival compared to non-TT/TT genotypes (p = 0.016). CONCLUSIONS Donor IFNL4 TT/TT genotype, a favorable predictor of spontaneous HCV clearance pre-transplant, is associated with increased early post-transplant fibrosis and decreased survival.
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Affiliation(s)
- Taylor Aiken
- Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Ari Garber
- Digestive Diseases Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Dawn Thomas
- Allogen Laboratories, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Nicole Hamon
- Allogen Laboratories, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Rocio Lopez
- Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Rajesh Konjeti
- Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States of America
| | - Arthur McCullough
- Digestive Diseases Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Nizar Zein
- Digestive Diseases Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - John Fung
- Digestive Diseases Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Medhat Askar
- Transplant Immunology, Baylor University Medical Center, Dallas, Texas, United States of America
| | - Binu V. John
- Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States of America
- Gastroenterology and Hepatology, Hunter Holmes McGuire VA Medical Center, Richmond, Virginia, United States of America
- * E-mail:
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27
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Hong M, Schwerk J, Lim C, Kell A, Jarret A, Pangallo J, Loo YM, Liu S, Hagedorn CH, Gale M, Savan R. Interferon lambda 4 expression is suppressed by the host during viral infection. J Exp Med 2016; 213:2539-2552. [PMID: 27799623 PMCID: PMC5110018 DOI: 10.1084/jem.20160437] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/10/2016] [Accepted: 10/04/2016] [Indexed: 01/21/2023] Open
Abstract
Interferon (IFN) lambdas are critical antiviral effectors in hepatic and mucosal infections. Although IFNλ1, IFNλ2, and IFNλ3 act antiviral, genetic association studies have shown that expression of the recently discovered IFNL4 is detrimental to hepatitis C virus (HCV) infection through a yet unknown mechanism. Intriguingly, human IFNL4 harbors a genetic variant that introduces a premature stop codon. We performed a molecular and biochemical characterization of IFNλ4 to determine its role and regulation of expression. We found that IFNλ4 exhibits similar antiviral activity to IFNλ3 without negatively affecting antiviral IFN activity or cell survival. We show that humans deploy several mechanisms to limit expression of functional IFNλ4 through noncoding splice variants and nonfunctional protein isoforms. Furthermore, protein-coding IFNL4 mRNA are not loaded onto polyribosomes and lack a strong polyadenylation signal, resulting in poor translation efficiency. This study provides mechanistic evidence that humans suppress IFNλ4 expression, suggesting that immune function is dependent on other IFNL family members.
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Affiliation(s)
- MeeAe Hong
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Johannes Schwerk
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Chrissie Lim
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Alison Kell
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Abigail Jarret
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Joseph Pangallo
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Yueh-Ming Loo
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Shuanghu Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84112
| | - Curt H Hagedorn
- Department of Medicine, University of Arkansas for Medical Sciences and the Central Arkansas Veterans Healthcare System, Little Rock, AR 72205
- Genetics Program, University of Arkansas for Medical Sciences and the Central Arkansas Veterans Healthcare System, Little Rock, AR 72205
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Ram Savan
- Department of Immunology, University of Washington, Seattle, WA 98109
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28
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Effects of Resistance-Associated NS5A Mutations in Hepatitis C Virus on Viral Production and Susceptibility to Antiviral Reagents. Sci Rep 2016; 6:34652. [PMID: 27703205 PMCID: PMC5050404 DOI: 10.1038/srep34652] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/16/2016] [Indexed: 12/13/2022] Open
Abstract
Direct-acting antivirals (DAAs) for hepatitis C virus (HCV) have potent anti-HCV effects but may provoke resistance-associated variants (RAVs). In this study, we assessed the characteristics of these RAVs and explored efficacious anti-HCV reagents using recombinant HCV with NS5A from a genotype 1b strain. We replaced the NS5A of JFH1 with that of Con1 (JFH1/5ACon1) and introduced known NS5A inhibitor resistance mutations (L31M, L31V, L31I and Y93H) individually or in combination. Susceptibilities against anti-HCV reagents were also investigated. RAVs with Y93H exhibited high extracellular core antigen levels and infectivity titers. Variants with any single mutation showed mild to moderate resistance against NS5A inhibitors, whereas variants with double mutations at both L31 and Y93 showed severe resistance. The variants with mutations exhibited similar levels of susceptibility to interferon (IFN)-α, IFN-λ1, IFN-λ3 and Ribavirin. Variants with the Y93H mutation were more sensitive to protease inhibitors compared with JFH1/5ACon1. In conclusion, the in vitro analysis indicated that the Y93H mutation enhanced infectious virus production, suggesting advantages in the propagation of RAVs with this mutation. However, these RAVs were susceptible to protease inhibitors. Thus, a therapeutic regimen that includes these reagents is a promising means to eradicate these RAVs.
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29
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Heim MH, Bochud PY, George J. Host - hepatitis C viral interactions: The role of genetics. J Hepatol 2016; 65:S22-S32. [PMID: 27641986 DOI: 10.1016/j.jhep.2016.07.037] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 07/29/2016] [Accepted: 07/29/2016] [Indexed: 12/15/2022]
Abstract
Hepatitis C virus (HCV) is a major cause of chronic viral hepatitis that can lead to cirrhosis and hepatocellular carcinoma. Only a minority of patients can clear the virus spontaneously. Elimination of HCV during acute infection correlates with a rapid induction of innate, especially interferon (IFN)-induced genes, and a delayed induction of adaptive immune responses. There is a strong association between genetic variants in the IFNλ (IL28B) locus with the rate of spontaneous clearance. Individuals with the ancestral IFNλ4 allele capable of producing a fully active IFNλ4 are paradoxically not able to clear HCV in the acute phase and develop chronic hepatitis C (CHC) with more than 90% probability. In the chronic phase of HCV infection, the wild-type IFNλ4 genotype is strongly associated with an induction of hundreds of classical type I/type III IFN stimulated genes in hepatocytes. However, the activation of the endogenous IFN system in the liver is ineffective in clearing HCV, and is even associated with impaired therapeutic responses to pegylated (Peg)IFNα containing treatments. While the role of genetic variation in the IFNλ locus to the outcome of CHC treatment has declined, it is clear that variation not only at this locus, but also at other loci, modulate clinically important liver phenotypes, including inflammation, fibrosis progression and the development of hepatocellular cancer. In this review, we summarize current knowledge about the role of genetics in the host response to viral hepatitis and the potential future evolution of knowledge in understanding host-viral interactions.
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Affiliation(s)
- Markus H Heim
- Division of Gastroenterology and Hepatology, University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland; Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031 Basel, Switzerland.
| | - Pierre-Yves Bochud
- Infectious Diseases Service, University Hospital and University of Lausanne, Rue du Bugnon 46, 1011 Lausanne-CHUV, Switzerland.
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia.
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30
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Peiffer KH, Sommer L, Zeuzem S, Sarrazin C. Reply. Hepatology 2016; 64:1378-9. [PMID: 26946328 DOI: 10.1002/hep.28536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 03/03/2016] [Indexed: 12/07/2022]
Affiliation(s)
- Kai-Henrik Peiffer
- J. W. Goethe University, Department of Gastroenterology and Hepatology, Frankfurt, Germany
| | - Lisa Sommer
- J. W. Goethe University, Department of Gastroenterology and Hepatology, Frankfurt, Germany
| | - Stefan Zeuzem
- J. W. Goethe University, Department of Gastroenterology and Hepatology, Frankfurt, Germany
| | - Christoph Sarrazin
- J. W. Goethe University, Department of Gastroenterology and Hepatology, Frankfurt, Germany
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Pedergnana V, Smith D, Klenerman P, Barnes E, Spencer CCA, Ansari MA. Interferon lambda 4 variant rs12979860 is not associated with RAV NS5A Y93H in hepatitis C virus genotype 3a. Hepatology 2016; 64:1377-8. [PMID: 26945900 PMCID: PMC5042047 DOI: 10.1002/hep.28533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/10/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Vincent Pedergnana
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - David Smith
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | | | - Paul Klenerman
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Eleanor Barnes
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Chris C. A. Spencer
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - M. Azim Ansari
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom,Oxford Martin SchoolUniversity of OxfordOxfordUnited Kingdom
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Walker A, Kaiser R, Bartenschlager R, Timm J. Genotypic resistance testing of HCV - is there a clinical need? GMS INFECTIOUS DISEASES 2016; 4:Doc05. [PMID: 30671319 PMCID: PMC6301723 DOI: 10.3205/id000023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Persistent infections with the hepatitis C virus (HCV) pose a profound global public health burden. In the past 5 years treatment of chronic hepatitis C has dramatically changed. Novel direct-acting antivirals (DAAs) specifically inhibiting viral enzymes or factors that are essential for the viral replication cycle have been developed and licensed for hepatitis C therapy. These novel drugs target the viral NS3/4A protease, the NS5B RNA-dependent RNA-polymerase or the replication factor NS5A. Combinations of DAAs against these targets are highly efficacious achieving virus elimination in the majority of treated patients. In countries where affordable, this rapid clinical development virtually replaced earlier interferon (IFN)-α based therapy that had been in use as standard of care for the last 25 years. With the approval of DAAs for the treatment of chronic hepatitis C the question emerged whether resistance-associated substitutions (RASs) might be of clinical relevance. Here, we discuss the available evidence for the possible benefit of resistance genotyping prior to therapy to optimize treatment of chronic hepatitis C.
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Affiliation(s)
- Andreas Walker
- Institute for Virology, Heinrich-Heine-University, University Hospital, Düsseldorf, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany.,German Center for Infection Research, Heidelberg University, Heidelberg, Germany
| | - Jörg Timm
- Institute for Virology, Heinrich-Heine-University, University Hospital, Düsseldorf, Germany
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De Re V, De Zorzi M, Caggiari L, Lauletta G, Tornesello ML, Fognani E, Miorin M, Racanelli V, Quartuccio L, Gragnani L, Russi S, Pavone F, Ghersetti M, Costa EG, Casarin P, Bomben R, Mazzaro C, Basaglia G, Berretta M, Vaccher E, Izzo F, Buonaguro FM, De Vita S, Zignego AL, De Paoli P, Dolcetti R. HCV-related liver and lymphoproliferative diseases: association with polymorphisms of IL28B and TLR2. Oncotarget 2016; 7:37487-37497. [PMID: 27183918 PMCID: PMC5122326 DOI: 10.18632/oncotarget.9303] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/19/2016] [Indexed: 12/29/2022] Open
Abstract
To explore the relationship between innate immunity and hepatitis C Virus (HCV) in determining the risk of cirrhosis (CIR), hepatocellular carcinoma (HCC), mixed cryoglobulinemia syndrome (MCS) and non-Hodgkin lymphoma (NHL), we investigated the impact of the toll-like receptor-2 (TLR2) and interleukin-28B (IL28B) genetic variants. TLR2 -174 del variant was associated with TLR2 expression and with specific downstream molecules that drive the expression of different interleukins; rs12979860 Il28B was important in response to interferon-treatment and in spontaneous clearance of HCV. The risk for liver and lymphoproliferative diseases in HCV progression was clarified by stratifying 862 HCV-positive patients into groups based on liver (CIR, HCC) and lymphoproliferative HCV-related diseases (MCS, NHL) and compared with chronic HCV (CHC) infection. Analysis of TLR2-IL28B haplotypes showed an association of wild type haplotype with the lymphoproliferative diseases (OR 1.77, p = 0.029) and a slight increase in HCV viral load (HR 1.38, p = 0.054). Wild type haplotype (TLR2 ins/ins- IL28B C/C) was also found associated with older age in patients with an hepatic diseases (in CIR and in HCC p = 0.038 and p = 0.020, respectively) supporting an effect of innate immunity in the liver disease progression. TLR2 and IL28B polymorphisms in combination showed a role in the control of HCV viral load and different HCV disease progression.
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Affiliation(s)
- Valli De Re
- Bio-Proteomics Facility/ Cancer Bioimmunotherapy, Department of Translational Research, Centro di Riferimento Oncologico (CRO), National Cancer Institute, Aviano, Italy
| | - Mariangela De Zorzi
- Bio-Proteomics Facility/ Cancer Bioimmunotherapy, Department of Translational Research, Centro di Riferimento Oncologico (CRO), National Cancer Institute, Aviano, Italy
| | - Laura Caggiari
- Bio-Proteomics Facility/ Cancer Bioimmunotherapy, Department of Translational Research, Centro di Riferimento Oncologico (CRO), National Cancer Institute, Aviano, Italy
| | - Gianfranco Lauletta
- Liver Unit, Division of Internal Medicine and Clinical Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Medical School, Bari, Italy
| | - Maria Lina Tornesello
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori “Fondazione G. Pascale” - IRCCS, Napoli, Italy
| | - Elisa Fognani
- Interdepartmental Center for Systemic Manifestations of Hepatitis Virus MASVE, Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Marta Miorin
- Cytogenetics and Molecular Biology Unit, Santa Maria degli Angeli Hospital Pordenone, Pordenone, Italy
| | - Vito Racanelli
- Immunology Section, Department of Biomedical Sciences and Human Oncology, University of Bari Medical School, Bari, Italy
| | - Luca Quartuccio
- Clinic of Rheumatology, Department of Medical and Biological Sciences, University Hospital “Santa Maria della Misericordia”, Udine, Italy
| | - Laura Gragnani
- Interdepartmental Center for Systemic Manifestations of Hepatitis Virus MASVE, Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Sabino Russi
- Liver Unit, Division of Internal Medicine and Clinical Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Medical School, Bari, Italy
| | - Fabio Pavone
- Liver Unit, Division of Internal Medicine and Clinical Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Medical School, Bari, Italy
| | - Michela Ghersetti
- Internal Medicine-Liver Unit, Santa Maria degli Angeli Hospital Pordenone, Pordenone, Italy
| | - Elena Garlatti Costa
- Internal Medicine-Liver Unit, Santa Maria degli Angeli Hospital Pordenone, Pordenone, Italy
| | - Pietro Casarin
- Internal Medicine-Liver Unit, Santa Maria degli Angeli Hospital Pordenone, Pordenone, Italy
| | - Riccardo Bomben
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico (CRO), National Cancer Institute, Aviano, Italy
| | - Cesare Mazzaro
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico (CRO), National Cancer Institute, Aviano, Italy
| | - Giancarlo Basaglia
- Microbiology-Immunology and Virology Unit, Centro di Riferimento Oncologico (CRO), National Cancer Institute, Aviano, Italy
| | - Massimiliano Berretta
- Medical Oncology, Centro di Riferimento Oncologico (CRO), National Cancer Institute, Aviano, Italy
| | - Emanuela Vaccher
- Medical Oncology, Centro di Riferimento Oncologico (CRO), National Cancer Institute, Aviano, Italy
| | - Francesco Izzo
- Hepatobiliary Unit, Istituto Nazionale Tumori “Fondazione G. Pascale” - IRCCS, Napoli, Italy
| | - Franco Maria Buonaguro
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori “Fondazione G. Pascale” - IRCCS, Napoli, Italy
| | - Salvatore De Vita
- Clinic of Rheumatology, Department of Medical and Biological Sciences, University Hospital “Santa Maria della Misericordia”, Udine, Italy
| | - Anna Linda Zignego
- Interdepartmental Center for Systemic Manifestations of Hepatitis Virus MASVE, Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Paolo De Paoli
- Scientific Directorate, Centro di Riferimento Oncologico (CRO), National Cancer Institute, Aviano, Italy
| | - Riccardo Dolcetti
- Cancer Bio-Immunotherapy, Department of Translational Research, Centro di Riferimento Oncologico (CRO), National Cancer Institute, Aviano, Italy
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
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Investigation of NS3 Protease Resistance-Associated Variants and Phenotypes for the Prediction of Treatment Response to HCV Triple Therapy. PLoS One 2016; 11:e0156731. [PMID: 27281344 PMCID: PMC4900565 DOI: 10.1371/journal.pone.0156731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/18/2016] [Indexed: 12/14/2022] Open
Abstract
Triple therapy of chronic hepatitis C virus (HCV) infection with boceprevir (BOC) or telaprevir (TVR) leads to virologic failure in many patients which is often associated with the selection of resistance-associated variants (RAVs). These resistance profiles are of importance for the selection of potential rescue treatment options. In this study, we sequenced baseline NS3 RAVs population-based and investigated the sensitivity of NS3 phenotypes in an HCV replicon assay together with clinical factors for a prediction of treatment response in a cohort of 165 German and Swiss patients treated with a BOC or TVR-based triple therapy. Overall, the prevalence of baseline RAVs was low, although the frequency of RAVs was higher in patients with virologic failure compared to those who achieved a sustained virologic response (SVR) (7% versus 1%, P = 0.06). The occurrence of RAVs was associated with a resistant NS3 quasispecies phenotype (P<0.001), but the sensitivity of phenotypes was not associated with treatment outcome (P = 0.2). The majority of single viral and host predictors of SVR was only weakly associated with treatment response. In multivariate analyses, low AST levels, female sex and an IFNL4 CC genotype were independently associated with SVR. However, a combined analysis of negative predictors revealed a significantly lower overall number of negative predictors in patients with SVR in comparison to individuals with virologic failure (P<0.0001) and the presence of 2 or less negative predictors was indicative for SVR. These results demonstrate that most single baseline viral and host parameters have a weak influence on the response to triple therapy, whereas the overall number of negative predictors has a high predictive value for SVR.
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Nguyen LT, Hall N, Sheerin D, Carr M, De Gascun CF. Naturally occurring HCV NS5A/B inhibitor resistance-associated mutations to direct-acting antivirals. Antivir Ther 2016; 21:447-53. [PMID: 26789637 DOI: 10.3851/imp3025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND Direct-acting antivirals (DAAs) have significantly improved the treatment response in HCV chronic infection with higher potency and better tolerance. We established the prevalence of naturally occurring NS5A and NS5B inhibitor resistance-associated mutations (RAMs) in HCV genotype (GT)-1 chronically infected individuals in Ireland. METHODS In a multicentre cohort study, employing sequencing-based analysis, the presence of RAMs was determined in the HCV NS5A (n=119) and the NS5B (n=60). RESULTS Naturally occurring RAMs in NS5A (M28V, R30Q, L31I, P58S, E62D and Y93H) were identified in 14.3% (17/119) of cases. Notably, the major RAM Y93H was found in 15.2% (7/46) of GT-1b versus none (0/73) in GT-1a (P=0.0009). The frequency of Y93H present in IFNL3 rs12979860 CC major homozygotes (30%, 3/10) was higher than in the non-CC group (11.1%, 4/36). GT-1b-infected individuals harbouring Y93H had significantly higher viral loads than those without this mutation (P=0.006). Additionally, two novel insertions in GT-1a and GT-1b were identified in the NS5A interferon sensitivity-determining region. In NS5B, only minor pre-existing RAMs (L159F, C316N and I434M) were detected in 10% (6/60) of samples. The proportion of individuals harbouring multiple RAMs in different DAA target regions was low. CONCLUSIONS RAMs to novel DAAs were infrequent in the DAA-naive population in the present study. The NS5A Y93H substitution was the only significant RAM identified. Given the low frequency of multiple RAMs in NS3, NS5A and NS5B regions and the unclear impact of pre-existing Y93H on the response in combination therapies, the role of pre-treatment RAM analysis in treatment-naive individuals requires further investigation.
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Affiliation(s)
- Linh Thuy Nguyen
- Ireland Vietnam Blood-Borne Virus Initiative, Dublin, Ireland and Hanoi, Vietnam.
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Ahmed A, Felmlee DJ. Mechanisms of Hepatitis C Viral Resistance to Direct Acting Antivirals. Viruses 2015; 7:6716-29. [PMID: 26694454 PMCID: PMC4690891 DOI: 10.3390/v7122968] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/24/2015] [Accepted: 12/08/2015] [Indexed: 12/28/2022] Open
Abstract
There has been a remarkable transformation in the treatment of chronic hepatitis C in recent years with the development of direct acting antiviral agents targeting virus encoded proteins important for viral replication including NS3/4A, NS5A and NS5B. These agents have shown high sustained viral response (SVR) rates of more than 90% in phase 2 and phase 3 clinical trials; however, this is slightly lower in real-life cohorts. Hepatitis C virus resistant variants are seen in most patients who do not achieve SVR due to selection and outgrowth of resistant hepatitis C virus variants within a given host. These resistance associated mutations depend on the class of direct-acting antiviral drugs used and also vary between hepatitis C virus genotypes and subtypes. The understanding of these mutations has a clear clinical implication in terms of choice and combination of drugs used. In this review, we describe mechanism of action of currently available drugs and summarize clinically relevant resistance data.
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Affiliation(s)
- Asma Ahmed
- Plymouth University, Peninsula School of Medicine and Dentistry, Plymouth PL6 8BU, UK.
| | - Daniel J Felmlee
- Plymouth University, Peninsula School of Medicine and Dentistry, Plymouth PL6 8BU, UK.
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