Baig Samina, Berikkara Assel, Khalid Ramsha, Subhan Syed A, Abbas Tanveer, Abidi Syed Hani
Department of Microbiology, University of Karachi, Karachi, Pakistan.
Dow Institute of Medical Technology, Dow University of Health Sciences, Karachi, Pakistan.
Front Microbiol. 2025 Jan 15;15:1498069. doi: 10.3389/fmicb.2024.1498069. eCollection 2024.
HCV genotypes are 30-35% polymorphic at the nucleotide level, while subtypes within the same genotype differ by nearly 20%. Although previous studies have shown the immune escape potential of several mutations within the HCV proteins, little is known about the effect of genotype/subtype-specific gene polymorphism on T-cell immunity. Therefore, this study employed several methods to examine the impact of genotype/subtype-specific polymorphisms in Core, NS3, NS5A, and NS5B sequences on T cell epitope processing and HLA-epitope interactions.
For this study, 8,942, 17,700, 14,645, and 3,277 HCV Core, NS3, NS5A, and NS5B sequences, respectively, from eight genotypes and 21 subtypes were retrieved from the Los Alamos HCV Database. Next, the NetCTL tool was employed to predict Cytotoxic T Lymphocyte (CTL) epitopes based on combined proteasomal cleavage, TAP efficacy, and HLA class I receptor binding scores. PEP-FOLD was used to model selected epitopes, followed by peptide-HLA docking using HPEPDOCK. Finally, molecular dynamics simulations were conducted for 200 ns using Desmond software to analyze differences in HLA-epitope (from different HCV genotypes) interaction kinetics and dynamics.
A total of 3,410, 8,054, 6,532, and 14,015 CTL epitopes were observed in the HCV Core, NS3, NS5A, and NS5B sequences, respectively. Significant genotype/subtype-specific variations in CTL values and docking scores were observed among NS3, NS5A, and NS5B proteins. results reveal that epitopes from genotype 6b (NS3), 6d/r (NS5B), 6o and 6 k (NS5A) exhibit higher immunogenicity than other genotypes, forming more energetically stable complexes with host receptors. These epitopes, compared to those from the same positions but different genotypes, showed binding energies of -144.24 kcal/mol, -85.30 kcal/mol, and - 43 kcal/mol, respectively. Over a 200 ns MD simulation, GT 6b and 6d/r epitopes displayed up to a 40% stronger binding energy with the HLA receptor. These findings suggest that patients infected with GT 6 may experience enhanced T cell responsiveness and broader immunogenicity.
Our study suggests that genotype/subtype-specific polymorphism in HCV may result in altered immune responses by modulating T-cell epitope processing and interaction with HLA receptors. Further experimental studies can be performed to confirm the effect of genotype/subtype-specific polymorphisms on T cell-mediated immune response.
丙型肝炎病毒（HCV）基因型在核苷酸水平上具有30%-35%的多态性，而同一基因型内的亚型差异近20%。尽管先前的研究已经显示了HCV蛋白内几种突变的免疫逃逸潜力，但关于基因型/亚型特异性基因多态性对T细胞免疫的影响知之甚少。因此，本研究采用多种方法来检测核心蛋白（Core）、非结构蛋白3（NS3）、非结构蛋白5A（NS5A）和非结构蛋白5B（NS5B）序列中基因型/亚型特异性多态性对T细胞表位加工及HLA-表位相互作用的影响。
本研究从洛斯阿拉莫斯HCV数据库中检索了分别来自8个基因型和21个亚型的8942条、17700条、14645条和3277条HCV Core、NS3、NS5A和NS5B序列。接下来，使用NetCTL工具基于蛋白酶体切割、抗原加工相关转运体（TAP）效能和HLA I类受体结合分数来预测细胞毒性T淋巴细胞（CTL）表位。使用PEP-FOLD对选定的表位进行建模，随后使用HPEPDOCK进行肽-HLA对接。最后，使用Desmond软件进行200纳秒的分子动力学模拟，以分析HLA-表位（来自不同HCV基因型）相互作用动力学和动态的差异。
在HCV Core、NS3、NS5A和NS5B序列中分别观察到3410个、8054个、6532个和14015个CTL表位。在NS3、NS5A和NS5B蛋白中观察到CTL值和对接分数存在显著的基因型/亚型特异性差异。结果显示，来自6b基因型（NS3）、6d/r基因型（NS5B）、6o基因型和6k基因型（NS5A）的表位比其他基因型表现出更高的免疫原性，与宿主受体形成能量更稳定的复合物。与来自相同位置但不同基因型的表位相比，这些表位的结合能分别为-144.24千卡/摩尔、-85.30千卡/摩尔和-43千卡/摩尔。在200纳秒的分子动力学模拟中，6b基因型和6d/r基因型的表位与HLA受体的结合能增强了40%。这些发现表明，感染6型基因型的患者可能会出现增强的T细胞反应性和更广泛的免疫原性。
我们的研究表明，HCV中的基因型/亚型特异性多态性可能通过调节T细胞表位加工以及与HLA受体的相互作用而导致免疫反应改变。可以进行进一步的实验研究来证实基因型/亚型特异性多态性对T细胞介导的免疫反应的影响。
