Spontaneous Control of HCV Is Associated With Expression of HLA-B*57 and Preservation of Targeted Epitopes

Chronic hepatitis C virus (HCV) infection is one of the leading causes of liver failure and liver cancer, affecting around 3% of the world's population. The extreme sequence variability of the virus resulting from error-prone replication has thwarted the discovery of a universal prophylactic vaccine. It is known that vigorous and multispecific cellular immune responses, involving both helper CD4؉ and cytotoxic CD8 ؉ T cells, are associated with the spontaneous clearance of acute HCV infection. Escape mutations in viral epitopes can, however, abrogate protective T-cell responses, leading to viral persistence and associated pathologies. Despite the propensity of the virus to mutate, there might still exist substitutions that incur a fitness cost. In this paper, we identify groups of coevolving residues within HCV nonstructural protein 3 (NS3) by analyzing diverse sequences of this protein using ideas from random matrix theory and associated methods. Our analyses indicate that one of these groups comprises a large percentage of residues for which HCV appears to resist multiple simultaneous substitutions. Targeting multiple residues in this group through vaccine-induced immune responses should either lead to viral recognition or elicit escape substitutions that compromise viral fitness. Our predictions are supported by published clinical data, which suggested that immune genotypes associated with spontaneous clearance of HCV preferentially recognized and targeted this vulnerable group of residues. Moreover, mapping the sites of this group onto the available protein structure provided insight into its functional significance. An epitope-based immunogen is proposed as an alternative to the NS3 epitopes in the peptide-based vaccine IC41. IMPORTANCEDespite much experimental work on HCV, a thorough statistical study of the HCV sequences for the purpose of immunogen design was missing in the literature. Such a study is vital to identify epistatic couplings among residues that can provide useful insights for designing a potent vaccine. In this work, ideas from random matrix theory were applied to characterize the statistics of substitutions within the diverse publicly available sequences of the genotype 1a HCV NS3 protein, leading to a group of sites for which HCV appears to resist simultaneous substitutions possibly due to deleterious effect on viral fitness. Our analysis leads to completely novel immunogen designs for HCV. In addition, the NS3 epitopes used in the recently proposed peptide-based vaccine IC41 were analyzed in the context of our framework. Our analysis predicts that alternative NS3 epitopes may be worth exploring as they might be more efficacious. Hepatitis C virus (HCV) infects more than 170 million people globally, with another 3 million people newly infected each year (1). Approximately 20% of patients spontaneously clear the virus after a period of acute viremia, while the majority of patients develop chronic disease (2, 3). Chronic HCV infection leads to liver failure and liver cancer and is t...

Section: Resultsmentioning

confidence: 63%

Statistical Linkage Analysis of Substitutions in Patient-Derived Sequences of Genotype 1a Hepatitis C Virus Nonstructural Protein 3 Exposes Targets for Immunogen Design

Quadeer

Louie

Shekhar

et al. 2014

“…Alleles such as HLA-A*03, HLA-B*27, and HLA-B*57 have been described to be associated with spontaneous resolution of HCV infection (21,27,49). It has been highlighted that these "protective" HLA class I alleles highly reproducibly select for escape mutations in the corresponding immunodominant epitopes (21,29,33). A study of the mechanisms of protection by HLA-B*27 pointed out that a rather complex pattern of 2, or sometimes even 3, substitutions is selected (8).…”

Section: Discussionmentioning

confidence: 99%

Escape from a Dominant HLA-B*15-Restricted CD8 ⁺ T Cell Response against Hepatitis C Virus Requires Compensatory Mutations outside the Epitope

Ruhl

Chhatwal

Strathmann

et al. 2012

Self Cite

Antiviral CD8 ؉ T cells are a key component of the adaptive immune system against hepatitis C virus (HCV).For the development of immune therapies, it is essential to understand how CD8 ؉ T cells contribute to clearance of infection and why they fail so often. A mechanism for secondary failure is mutational escape of the virus. However, some substitutions in viral epitopes are associated with fitness costs and often require compensatory mutations. We hypothesized that compensatory mutations may point toward epitopes under particularly strong selection pressure that may be beneficial for vaccine design because of a higher genetic barrier to escape. We previously identified two HLA-B*15-restricted CD8 ؉ epitopes in NS5B (LLRHHNMVY 2450-2458 and SQRQKKVTF 2466-2474 ), based on sequence analysis of a large HCV genotype 1b outbreak. Both epitopes are targeted in about 70% of HLA-B*15-positive individuals exposed to HCV. Reproducible selection of escape mutations was confirmed in an independent multicenter cohort in the present study. Interestingly, mutations were also selected in the epitope flanking region, suggesting that compensatory evolution may play a role. Covariation analysis of sequences from the database confirmed a significant association between escape mutations inside one of the epitopes (H2454R and M2456L) and substitutions in the epitope flanking region (S2439T and K2440Q). Functional analysis with the subgenomic replicon Con1 confirmed that the primary escape mutations impaired viral replication, while fitness was restored by the additional substitutions in the epitope flanking region. We concluded that selection of escape mutations inside an HLA-B*15 epitope requires secondary substitutions in the epitope flanking region that compensate for fitness costs.A ntiviral CD8 ϩ T cells are one of the key components of the adaptive immune system against hepatitis C virus (HCV). During acute infection, HCV-specific CD8 ϩ T cells are activated in the majority of patients (24, 38). Nevertheless, viral persistence is observed in 50 to 80% of patients. These patients with chronic HCV infection are at risk of progressive liver disease and liver cancer. For the development of immune therapies against HCV, it is essential to understand how CD8 ϩ T cells contribute to clearance of infection and why they fail so often. Different mechanisms for CD8 ϩ T cell failure have been described. The proposed mechanisms include primary failure by lack or impairment of priming of specific CD8 ϩ T cells upon HCV infection, as well as secondary failure after the initial priming (reviewed in reference 40). Studies of patients with acute HCV infection suggest that CD8 ϩ T cells are activated in most patients, irrespective of the outcome of infection (6), which supports an important role for secondary failure of HCV-specific CD8 ϩ T cells.Upon transition from acute to chronic HCV infection, the frequency of specific CD8 ϩ T cells declines (6). Moreover, CD8 ϩ T cells from patients with chronic HCV infection produce fewer cytokines and p...

“…The CD8 ϩ T cell response against the epitope IPFYGKAI 1373-1380 was also studied in a patient with acute HCV genotype 1a infection. The patient was previously reported in a study on the impact of HLA-B*57 on HCV infection outcome (30) and was also HLA-B*51 positive. Interestingly, here, the response was detectable by week 11 after infection but became completely undetectable in an IFN-␥ enzyme-linked immunospot (ELISpot) assay by week 47 (Fig.…”

Section: Cd8mentioning

confidence: 85%

Distinct Escape Pathway by Hepatitis C Virus Genotype 1a from a Dominant CD8 ⁺ T Cell Response by Selection of Altered Epitope Processing

Walker

Skibbe

Steinmann

et al. 2016

Self Cite

Antiviral CD8؉ T cells are a key component of the adaptive immune response against HCV, but their impact on viral control is influenced by preexisting viral variants in important target epitopes and the development of viral escape mutations. Immunodominant epitopes highly conserved across genotypes therefore are attractive for T cell based prophylactic vaccines. Here, we characterized the CD8 ؉ T cell response against the highly conserved HLA-B*51-restricted epitope IPFYGKAI 1373-1380 located in the helicase domain of NS3 in people who inject drugs (PWID) exposed predominantly to HCV genotypes 1a and 3a. Despite this epitope being conserved in both genotypes, the corresponding CD8 ؉ T cell response was detected only in PWID infected with genotype 3a and HCV-RNA negative PWID, but not in PWID infected with genotype 1a. In genotype 3a, the detection of strong CD8؉ T cell responses was associated with epitope variants in the autologous virus consistent with immune escape. Analysis of viral sequences from multiple cohorts confirmed HLA-B*51-associated escape mutations inside the epitope in genotype 3a, but not in genotype 1a. Here, a distinct substitution in the N-terminal flanking region located 5 residues upstream of the epitope (S1368P; P ‫؍‬ 0.00002) was selected in HLA-B*51-positive individuals. Functional assays revealed that the S1368P substitution impaired recognition of target cells presenting the endogenously processed epitope. The results highlight that, despite an epitope being highly conserved between two genotypes, there are major differences in the selected viral escape pathways and the corresponding T cell responses. IMPORTANCE HCV is able to evolutionary adapt to CD8؉ T cell immune pressure in multiple ways. Beyond selection of mutations inside targeted epitopes, this study demonstrates that HCV inhibits epitope processing by modification of the epitope flanking region under T cell immune pressure. Selection of a substitution five amino acids upstream of the epitope underlines that efficient antigen presentation strongly depends on its larger sequence context and that blocking of the multistep process of antigen processing by mutation is exploited also by HCV. The pathways to mutational escape of HCV are to some extent predictable but are distinct in different genotypes. Importantly, the selected escape pathway of HCV may have consequences for the destiny of antigen-specific CD8 ؉ T cells. Based on phylogenetic analysis, hepatitis C virus (HCV) can be classified into at least seven genotypes and multiple subtypes that differ up to 20% at the amino acid level (1). The HCV genotypes have distinct epidemiological characteristics, they are associated with different transmission risk factors, and their frequencies in a population are regionally different. In Europe and North America the HCV genotypes 1 and 3 are most common (2, 3). Since routine screening via nucleic acid amplification for HCV eliminated the risk for infection through blood products, the most important risk group for incident HC...