Los Alamos Hepatitis C Immunology Database

Yusim, Karina; Richardson, Russell S.; Ning, Tao; Dalwani, Anita; Agrawal, Alka; Szinger, James; Funkhouser, Robert; Korber, Bette T.; Kuiken, Carla

doi:10.2165/00822942-200504040-00002

Cited by 67 publications

(55 citation statements)

References 26 publications

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“…The substitution R26K is a very common polymorphism found in genotype 1 isolates. 38 The two identified codons, R26 and V172, have not been described as belonging to a CTL, T helper, or antibody epitope. 38 Amino acid alignments showed a similar population structure for the 3 studied quasispecies (Fig.…”

Section: Resultsmentioning

confidence: 97%

Genetic and catalytic efficiency structure of an HCV protease quasispecies

Franco¹,

Parera²,

Aparicio³

et al. 2007

Hepatology

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The HCV nonstructural protein (NS)3/4A serine protease is not only involved in viral polyprotein processing but also efficiently blocks the retinoic-acid-inducible gen I and Toll-like receptor 3 signaling pathways and contributes to virus persistence by enabling HCV to escape the interferon antiviral response. Therefore, the NS3/4A protease has emerged as an ideal target for the control of the disease and the development of new anti-HCV agents. Here, we analyzed, at a high resolution (approximately 100 individual clones), the HCV NS3 protease gene quasispecies from three infected individuals. Nucleotide heterogeneity of 49%, 84%, and 91% were identified, respectively, which created a dense net that linked different parts of the viral population. Minority variants having mutations involved in the acquisition of resistance to current NS3/4A protease inhibitors (PIs) were also found. A vast diversity of different catalytic efficiencies could be distinguished. Importantly, 67% of the analyzed enzymes displayed a detectable protease activity. Moreover, 35% of the minority individual variants showed similar or better catalytic efficiency than the master (most abundant) enzyme. Nevertheless, and in contrast to minority variants, master enzymes always displayed a high catalytic efficiency when different viral polyprotein cleavage sites were tested. Finally, genetic and catalytic efficiency differences were observed when the 3 quasispecies were compared, suggesting that different selective forces were acting in different infected individuals. Conclusion: The rugged HCV protease quasispecies landscape should be able to react to environmental changes that may threaten its survival. (HEPATOLOGY 2007;45:899-910.)

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Section: Resultsmentioning

confidence: 97%

Genetic and catalytic efficiency structure of an HCV protease quasispecies

Franco¹,

Parera²,

Aparicio³

et al. 2007

Hepatology

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“…Five synthetic peptides, 9 to 10 amino acids in length (Mimotopes, Victoria, Australia), containing the HLA-A2 binding motif and representing widely recognized (http://hcv.lanl.gov) 7 CD8 epitopes located within nonstructural HCV proteins (NS3/1073-1081, NS3/ 1406-1415, NS4/1812-1821, NS4/1992-2000, NS5/ 2627-2635), were used to study CD8 responses. Because of the high degree of HCV variability, different sets of peptides corresponding to the prevalent sequences of different HCV genotypes (1 to 4) (www.ncbi.nlm.nih.gov/ BLAST/) 8 were synthesized and used for T cell analysis.…”

Section: Methodsmentioning

confidence: 99%

Dysfunction and functional restoration of HCV-specific CD8 responses in chronic hepatitis C virus infection

et al. 2007

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The functional impairment of HCV-specific T cell responses is believed to be an important determinant of HCV persistence, but the functional T cell defects of patients with chronic hepatitis C (CH-C) are only partially defined. CD8 responses to HLA-A2-restricted epitopes of HCV and other unrelated viruses were studied in 23 HLA-A2-positive patients both ex vivo and after in vitro culture. Degranulation capacity, intracellular perforin, and granzyme-A content and cytokine production (IFN-␥, TNF-␣) by HCV-and non-HCV-specific CD8 cells were tested both ex vivo and in vitro, whereas cytolytic activity was studied after 10 days' expansion in vitro. Memory maturation and role of exhaustion were assessed ex vivo by HCV-specific CD8 staining for CD127 and PD-1, and in vitro after peripheral blood mononuclear cells (PBMC) culture in the presence of anti-PD-L1 monoclonal antibodies. IFN-␥ production and cytolytic activity were expressed less efficiently by HCV-specific than by non-HCV specific CD8 cells derived from the same CH-C patients. The amount of stored granzyme-A within single cells was always lower in HCV-specific CD8 cells, which were less efficient also in the release of lytic granules and in the production of TNF-␣. The CD8 dysfunction was associated with high PD-1 expression by most HCV-specific CD8 cells, and PD-1/PD-L1 blockade by anti-PD-L1 antibodies in vitro was able to improve the HCVspecific CD8 function. Conclusion: Our study characterizes CD8 defects that may be important in maintaining HCV persistence; identification of strategies to correct these defects may help to define novel approaches to treat HCV infection. (HEPATOLOGY 2007;45:588 -601.) H epatitis C virus infection is a major public health problem, affecting more than 200 million people worldwide and causing chronic liver disease, with possible evolution to cirrhosis and HCC. 1 Available therapies can cure no more than 50% of infected patients, making essential the development of new therapeutic strategies for nonresponders. 1 Restoration of efficient antiviral T cell responses is one of the possible approaches to improve the efficacy of available antiviral drugs. This is suggested by the observation that HCVspecific CD4 and CD8 cells are hyporesponsive in patients with chronic hepatitis C (CH-C). 2,3 However, the functional basis of these defective T cell responses remains largely undefined.To better characterize the immune defects underlying chronic viral persistence, in this study we focused our analysis of the adaptive immune response in patients with chronic HCV infection on CD8 lymphocytes, given the central role played by these cells in the control of viral infections. Despite the low frequency of peripheral blood HCV-specific CD8 cells at this stage of infection, functional studies were carried out not only on in vitro expanded CD8 cells, but also ex vivo when HCV-specific CD8 frequencies were sufficient for a reliable analysis. This is particularly important to avoid incorrect conclusions based on the study of limited CD8 subsets s...

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“…We then assessed the coverage of known HCV CTL epitopes downloaded from the Los Alamos HCV Immunology Database (Yusim et al, 2005; http://www. hcv.lanl.gov) (Supplementary Material S2, available in JGV Online).…”

Section: Coverage Of Known Ctl Epitopesmentioning

confidence: 99%

“…The second most frequent variant (27 % coverage), which is present both in H77 and in the three-mosaic cocktail, has a V9I mutation in the HLA-A2 anchor residue, thus potentially abrogating HLA-A2 binding. Thus, whilst H77 contains a probable escape variant, the three-mosaic cocktail can potentially prime immune responses to the reactive epitope.We then assessed the coverage of known HCV CTL epitopes downloaded from the Los Alamos HCV Immunology Database (Yusim et al, 2005; http://www. hcv.lanl.gov) (Supplementary Material S2, available in JGV Online).…”

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confidence: 99%

Genotype 1 and global hepatitis C T-cell vaccines designed to optimize coverage of genetic diversity

Yusim

Fischer

Yoon

et al. 2010

Journal of General Virology

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Immunological control of hepatitis C virus (HCV) is possible and is probably mediated by host T-cell responses, but the genetic diversity of the virus poses a major challenge to vaccine development. We considered monovalent and polyvalent candidates for an HCV vaccine, including natural, consensus and synthetic 'mosaic' sequence cocktails. Mosaic vaccine reagents were designed using a computational approach first applied to and demonstrated experimentally for human immunodeficiency virus type 1 (HIV-D). Mosaic proteins resemble natural proteins, but are assembled from fragments of natural sequences via a genetic algorithm and optimized to maximize the coverage of potential T-cell epitopes (all 9-mers) found in natural sequences and to minimize the inclusion of rare 9-mers to avoid vaccine-specific responses. Genotype 1-specific and global vaccine cocktails were evaluated. Among vaccine candidates considered, polyvalent mosaic sequences provided the best coverage of both known and potential epitopes and had the fewest rare epitopes. A global vaccine based on conserved proteins across genotypes may be feasible, as a five-antigen mosaic cocktail provided 90, 77 and 70 % coverage of the Core, NS3 and NS4 proteins, respectively; protein coverage diminished with increased protein variability, dropping to 38 % for NS2. For the genotype 1-specific vaccine, the H77 prototype vaccine sequence matched only 50 % of the potential epitopes in the population, whilst a polyprotein three-antigen mosaic cocktail increased potential epitope coverage to 83 %. More than 75 % coverage of all HCV proteins was achieved with a three-antigen mosaic cocktail, suggesting that genotype-specific vaccines could also include the more variable proteins. INTRODUCTIONAn estimated 170 million people are infected with hepatitis C virus (HCV) worldwide (Armstrong et al., 2000;Lauer & Walker, 2001). Acute HCV infection leads to chronic infection in 70-80 % of infected individuals (Alter et al., 1999;Conry-Cantilena et al., 1996) and can result in liver cirrhosis, liver failure and hepatocellular carcinoma (Lauer & Walker, 2001). The current treatment with pegylated alpha interferon and the nucleoside analogue ribavirin has improved clinical outcomes (Davis et al., 1998;Fried et al., 2002; Manns et al., 2001;Zeuzem et al., 2000), but is expensive and requires sophisticated medical management, which is out of reach for the majority of infected people. Development of a prophylactic vaccine to prevent the spread of HCV infection remains paramount.Several findings indicate that immunological control of HCV is possible. In humans and chimpanzees, spontaneous eradication of HCV can occur during acute infection (Cooper et al., 1999; Gerlach et al., 1999Gerlach et al., , 2003Lechner et al., 2000; Thimme et al., 2001). Spontaneously cleared HCV infection reduced the likelihood of developing a chronic infection in continuously exposed drug users (Mehta et al., 2002). Reinfection after initial clearance had a shorter duration and a lower peak viraemia in the ch...

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Los Alamos Hepatitis C Immunology Database

Cited by 67 publications

References 26 publications

Genetic and catalytic efficiency structure of an HCV protease quasispecies

Genetic and catalytic efficiency structure of an HCV protease quasispecies

Dysfunction and functional restoration of HCV-specific CD8 responses in chronic hepatitis C virus infection

Genotype 1 and global hepatitis C T-cell vaccines designed to optimize coverage of genetic diversity

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