Designed neopeptides activate antitumor immune response

Purpose: The low mutational load of some cancers is considered one reason for the difficulties to develop effective tumor vaccines. To overcome this problem, we developed a strategy to design neopeptides through single amino acid mutations to enhance their immunogenicity. Experimental Design: Exome- and RNA sequencing as well as in silico HLA-binding predictions to autologous HLA molecules were used to identify candidate neopeptides. Subsequently, in silico HLA-anchor placements were used to deduce putative T cell receptor contacts of peptides. Single amino acids of TCR contacting residues were then mutated by amino acid replacements. Overall, 175 peptides were synthesized and sets of 25 each containing both peptides designed to bind to HLA class I and II molecules applied in the vaccination. Upon development of a tumor recurrence, the tumor-infiltrating lymphocytes (TILs) were characterized in detail both at the bulk and clonal level. Results: The immune response of peripheral blood T cells to vaccine peptides, including natural peptides and designed neopeptides, gradually increased with repetitive vaccination, but remained low. In contrast, at the time of tumor recurrence, CD8+ TILs and CD4+ TILs responded to 45% and 100% respectively of the vaccine peptides. Further, TIL-derived CD4+ T cell clones showed strong responses and tumor cell lysis not only against the designed neopeptide but also against the unmutated natural peptides of the tumor. Conclusions: Turning tumor self-peptides into foreign antigens by introduction of designed mutations is a promising strategy to induce strong intratumoral CD4+ T cell responses in a cold tumor like glioblastoma.

研究目的：部分癌症的低突变负荷被认为是开发有效肿瘤疫苗的难点之一。为破解这一困境，我们开发了一种通过单氨基酸突变设计新表位肽（neopeptide）的策略，以增强其免疫原性。实验设计：我们采用外显子组测序与RNA测序，结合针对自体人类白细胞抗原（HLA）分子的计算机辅助HLA结合预测，筛选候选新表位肽。随后，通过计算机分析HLA锚定位点，推导肽段潜在的T细胞受体（TCR）结合残基，并对TCR结合位点的单个氨基酸进行替换突变。本研究共合成175条肽段，以每25条为一组，每组包含分别靶向HLA I类与II类分子的肽段，用于疫苗制备。当患者出现肿瘤复发时，我们从细胞群体与克隆层面详细表征了肿瘤浸润淋巴细胞（TILs）。研究结果：外周血T细胞对疫苗肽段（包括天然肽段与设计的新表位肽）的免疫应答随重复疫苗接种逐渐增强，但整体水平仍较低。与之形成鲜明对比的是，在肿瘤复发时，CD8阳性肿瘤浸润淋巴细胞与CD4阳性肿瘤浸润淋巴细胞分别对45%和100%的疫苗肽段产生应答。进一步研究发现，源自TIL的CD4阳性T细胞克隆不仅对设计的新表位肽产生强烈应答，还可介导肿瘤细胞裂解，且识别靶点涵盖肿瘤的未突变天然肽段。研究结论：通过引入设计性突变将肿瘤自身肽段转化为外源抗原，是在胶质母细胞瘤这类冷肿瘤中诱导强烈瘤内CD4阳性T细胞应答的极具前景的策略。