A comprehensive in silico analysis for identification of therapeutic epitopes in HPV16, 18, 31 and 45 oncoproteins

Human papillomaviruses (HPVs) are a group of circular double-stranded DNA viruses, showing severe tropism to mucosal tissues. A subset of HPVs, especially HPV16 and 18, are the primary etiological cause for several epithelial cell malignancies, causing about 5.2% of all cancers worldwide. Due to the high prevalence and mortality, HPV-associated cancers have remained as a significant health problem in human society, making an urgent need to develop an effective therapeutic vaccine against them. Achieving this goal is primarily dependent on the identification of efficient tumor-associated epitopes, inducing a robust cell-mediated immune response. Previous information has shown that E5, E6, and E7 early proteins are responsible for the induction and maintenance of HPV-associated cancers. Therefore, the prediction of major histocompatibility complex (MHC) class I T cell epitopes of HPV16, 18, 31 and 45 oncoproteins was targeted in this study. For this purpose, a two-step plan was designed to identify the most probable CD8+ T cell epitopes. In the first step, MHC-I and II binding, MHC-I processing, MHC-I population coverage and MHC-I immunogenicity prediction analyses, and in the second step, MHC-I and II protein-peptide docking, epitope conservation, and cross-reactivity with host antigens’ analyses were carried out successively by different tools. Finally, we introduced five probable CD8+ T cell epitopes for each oncoprotein of the HPV genotypes (60 epitopes in total), which obtained better scores by an integrated approach. These predicted epitopes are valuable candidates for in vitro or in vivo therapeutic vaccine studies against the HPV-associated cancers. Additionally, this two-step plan that each step includes several analyses to find appropriate epitopes provides a rational basis for DNA- or peptide-based vaccine development.

人乳头瘤病毒（Human papillomaviruses, HPVs）是一类环状双链DNA病毒，对黏膜组织具有显著嗜性。其中部分亚型，尤其是HPV16与HPV18，是多种上皮细胞恶性肿瘤的主要致病原，全球范围内约5.2%的癌症由其引发。鉴于HPV相关癌症高流行率与高致死率的特征，该类癌症始终是人类社会面临的重大公共卫生难题，因此亟需开发针对此类疾病的有效治疗性疫苗。而实现这一目标的核心在于筛选高效的肿瘤相关表位，以诱导强烈的细胞介导免疫应答。已有研究表明，E5、E6及E7早期蛋白参与了HPV相关癌症的诱导与维持过程。因此，本研究以预测HPV16、18、31及45型癌蛋白的主要组织相容性复合体（major histocompatibility complex, MHC）I类T细胞表位为目标。为此，我们设计了两步策略以筛选最具潜力的CD8+ T细胞表位：第一步开展MHC-I/II结合能力、MHC-I抗原加工过程、MHC-I群体覆盖率及MHC-I免疫原性预测分析；第二步依次通过不同工具完成MHC-I/II蛋白质-肽段对接、表位保守性及与宿主抗原交叉反应性分析。最终，本研究为每一种HPV基因型的癌蛋白筛选出5个潜在CD8+ T细胞表位（共计60个表位），这些表位经整合分析后获得了更优的评分。上述预测表位可作为抗HPV相关癌症体外或体内治疗性疫苗研究的优质候选靶点。此外，本研究采用的两步策略（每一步均包含多项表位筛选分析）可为DNA疫苗或肽段疫苗的理性开发提供科学依据。