Amino Acid Substitutions within HLA-B*27-Restricted T Cell Epitopes Prevent Recognition by Hepatitis Delta Virus-Specific CD8⁺T Cells

Abstract

Virus-specific CD8 T cell response seems to play a significant role in the outcome of hepatitis delta virus (HDV) infection. However, the HDV-specific T cell epitope repertoire and mechanisms of CD8 T cell failure in HDV infection have been poorly characterized. We therefore aimed to characterize HDV-specific CD8 T cell epitopes and the impacts of viral mutations on immune escape. In this study, we predicted peptide epitopes binding the most frequent human leukocyte antigen (HLA) types and assessed their HLA binding capacities. These epitopes were characterized in HDV-infected patients by intracellular gamma interferon (IFN-γ) staining. Sequence analysis of large hepatitis delta antigen (L-HDAg) and HLA typing were performed in 104 patients. The impacts of substitutions within epitopes on the CD8 T cell response were evaluated experimentally and by studies. We identified two HLA-B*27-restricted CD8 T cell epitopes within L-HDAg. These novel epitopes are located in a relatively conserved region of L-HDAg. However, we detected molecular footprints within the epitopes in HLA-B*27-positive patients with chronic HDV infections. The variant peptides were not cross-recognized in HLA-B*27-positive patients with resolved HDV infections, indicating that the substitutions represent viral escape mutations. Molecular modeling of HLA-B*27 complexes with the L-HDAg epitope and its potential viral escape mutations indicated that the structural and electrostatic properties of the bound peptides differ considerably at the T cell receptor interface, which provides a possible molecular explanation for the escape mechanism. This viral escape from the HLA-B*27-restricted CD8 T cell response correlates with a chronic outcome of hepatitis D infection. T cell failure resulting from immune escape may contribute to the high chronicity rate in HDV infection. Hepatitis delta virus (HDV) causes severe chronic hepatitis, which affects 20 million people worldwide. Only a small number of patients are able to clear the virus, possibly mediated by a virus-specific T cell response. Here, we performed a systematic screen to define CD8 epitopes and investigated the role of CD8 T cells in the outcome of hepatitis delta and how they fail to eliminate HDV. Overall the number of epitopes identified was very low compared to other hepatotropic viruses. We identified, two HLA-B*27-restricted epitopes in patients with resolved infections. In HLA-B*27-positive patients with chronic HDV infections, however, we detected escape mutations within these identified epitopes that could lead to viral evasion of immune responses. These findings support evidence showing that HLA-B*27 is important for virus-specific CD8 T cell responses, similar to other viral infections. These results have implications for the clinical prognosis of HDV infection and for vaccine development.

Genetic diversity of hepatitis D virus genotype‐1 in Europe allows classification into subtypes

“…The first set of phylogenetic analysis on the large delta antigen region indicated that all 116 isolates of our well‐characterized cohort of European patients cluster together with HDV genotype‐1 (Figure ). Then, these 116 sequences (covering L‐HDAg) from our European cohort and 621 L‐HDAg sequences from the GenBank were used to create a non‐redundant sequence dataset.…”

“…This well‐characterized cohort of patients was established to study CD8 epitopes within the HDV protein (L‐HDAg). HLA‐typing of these patients was also performed . The local ethics committees have approved this study according to the 1975 Declaration of Helsinki guidelines.…”

“…In order to obtain sequences of the L‐HDAg encoding region, cDNA products were amplified by Pfu DNA polymerases (Promega) in a two‐step nested PCR using HDV‐specific primers 891‐F, 339‐R, 912‐F and 1674‐R under the following thermal profile: 94°C for 10 minutes and a 35 cycle of 94°C for 30 seconds, 54°C for 45 seconds, and 72°C for 90 seconds and then an elongation step at 72°C for 7 minutes PCR products were purified via QIAquick ® Gel Extraction (QIAGEN) and were directly sequenced on an ABI 3730xl DNA Analyzer using internal primers, 912‐F and 1674‐R. All sequences were submitted to the GenBank, NCBI (Accession numbers: ‐ and ‐).…”

“…HLAtyping of these patients was also performed. 20 The local ethics committees have approved this study according to the 1975 Declaration of Helsinki guidelines. All patients were interviewed and informed about the study before they agreed to participate by signing a written consent.…”

Discovery and Selection of Hepatitis B Virus-Derived T Cell Epitopes for Global Immunotherapy Based on Viral Indispensability, Conservation, and HLA-Binding Strength

“…In vitro HLA binding validation. Synthetic peptides (Peptide 2.0 Inc.) of selected potential HLA binders were used in an in vitro binding assay as described previously (96). In brief, peptide exchange reactions were performed by exposure for 30 min of conditional peptide-HLA complexes (pHLA) (0.53 M) to long-wavelength UV using a 366-nm UV lamp (Camag) in the presence or absence of the indicated peptide (50 M).…”