Regeneron Pharmaceuticals Inc., Tarrytown, NY, United States.
Front Immunol. 2022 Dec 13;13:1032716. doi: 10.3389/fimmu.2022.1032716. eCollection 2022.
The presentation of virus-derived peptides by HLA class I molecules on the surface of an infected cell and the recognition of these HLA-peptide complexes by, and subsequent activation of, CD8 cytotoxic T cells provides an important mechanism for immune protection against viruses. Recent advances in proteogenomics have allowed researchers to discover a growing number of unique HLA-restricted viral peptides, resulting in a rapidly expanding repertoire of targets for immunotherapeutics (i.e. bispecific antibodies, engineered T-cell receptors (TCRs), chimeric antigen receptor T-cells (CAR-Ts)) to infected tissues. However, genomic variability between viral strains, such as Hepatitis-B virus (HBV), in combination with differences in patient HLA alleles, make it difficult to develop therapeutics against these targets. To address this challenge, we developed a novel proteogenomics approach for generating patient-specific databases that enable the identification of viral peptides based on the viral transcriptomes sequenced from individual patient liver samples. We also utilized DNA sequencing of patient samples to identify HLA genotypes and assist in target selection. Liver samples from 48 HBV infected patients, primarily from Asia, were examined to reconstruct patient-specific HBV genomes, identify regions within the human chromosomes targeted by HBV integrations and obtain a comprehensive view of HBV peptide epitopes using our HLA class-I (HLA-I) immunopeptidomics discovery platform. Two previously reported HLA associated HBV-derived peptides, HLA-A02 binder FLLTRILTI (S) from the large surface antigen and HLA-A11 binder STLPETTVVRR (C) from the capsid protein were validated by our discovery platform, but both were detected at very low frequencies. In addition, we identified and validated, using heavy peptide analogues, novel strain-specific HBV-HLA associated peptides, such as GSLPQEHIVQK (P) and variants. Overall, our novel approach can guide the development of bispecific antibody, TCR-T, or CAR-T based therapeutics for the treatment of HBV-related HCC and inform vaccine development.
病毒衍生肽由 HLA Ⅰ类分子在感染细胞表面呈递，随后被 CD8 细胞毒性 T 细胞识别和激活，为免疫保护病毒提供了重要机制。蛋白质基因组学的最新进展使研究人员能够发现越来越多独特的 HLA 限制的病毒肽，从而为免疫治疗（即双特异性抗体、工程 T 细胞受体 (TCR)、嵌合抗原受体 T 细胞 (CAR-T)）针对感染组织的靶点提供了快速扩展的 repertoire。然而，病毒株之间的基因组变异性，如乙型肝炎病毒 (HBV)，加上患者 HLA 等位基因的差异，使得针对这些靶点开发治疗方法变得困难。为了解决这一挑战，我们开发了一种新的蛋白质基因组学方法，用于生成基于从个体患者肝样本中测序的病毒转录组来识别病毒肽的患者特异性数据库。我们还利用患者样本的 DNA 测序来识别 HLA 基因型并协助目标选择。检查了来自亚洲的 48 名 HBV 感染患者的肝样本，以重建患者特异性 HBV 基因组，识别 HBV 整合靶向的人类染色体区域，并使用我们的 HLA-I (HLA-I) 免疫肽组学发现平台获得 HBV 肽表位的全面视图。我们的发现平台验证了两个先前报道的与 HLA 相关的 HBV 衍生肽，即来自大表面抗原的 HLA-A02 结合肽 FLLTRILTI (S) 和来自衣壳蛋白的 HLA-A11 结合肽 STLPETTVVRR (C)，但两者的检测频率都非常低。此外，我们使用重肽类似物鉴定和验证了新的与 HBV 相关的 HLA 相关肽，如 GSLPQEHIVQK (P) 和变体。总的来说，我们的新方法可以指导针对 HBV 相关 HCC 的双特异性抗体、TCR-T 或 CAR-T 治疗的开发，并为疫苗开发提供信息。
