Department of Immunopathology, Sanquin Research, Amsterdam 1066 CX, The Netherlands.
Department of Hematopoiesis, Sanquin Research, Amsterdam 1066 CX, The Netherlands.
Proc Natl Acad Sci U S A. 2022 Jul 19;119(29):e2119736119. doi: 10.1073/pnas.2119736119. Epub 2022 Jul 8.
In the current era of T cell-based immunotherapies, it is crucial to understand which types of MHC-presented T cell antigens are produced by tumor cells. In addition to linear peptide antigens, chimeric peptides are generated through proteasome-catalyzed peptide splicing (PCPS). Whether such spliced peptides are abundantly presented by MHC is highly disputed because of disagreement in computational analyses of mass spectrometry data of MHC-eluted peptides. Moreover, such mass spectrometric analyses cannot elucidate how much spliced peptides contribute to the pool of immunogenic antigens. In this Perspective, we explain the significance of knowing the contribution of spliced peptides for accurate analyses of peptidomes on one hand, and to serve as a potential source of targetable tumor antigens on the other hand. Toward a strategy for mass spectrometry independent estimation of the contribution of PCPS to the immunopeptidome, we first reviewed methodologies to identify MHC-presented spliced peptide antigens expressed by tumors. Data from these identifications allowed us to compile three independent datasets containing 103, 74, and 83 confirmed T cell antigens from cancer patients. Only 3.9%, 1.4%, and between 0% and 7.2% of these truly immunogenic antigens are produced by PCPS, therefore providing a marginal contribution to the pool of immunogenic tumor antigens. We conclude that spliced peptides will not serve as a comprehensive source to expand the number of targetable antigens for immunotherapies.
在当前基于 T 细胞的免疫疗法时代,了解肿瘤细胞产生的哪种类型的 MHC 呈递 T 细胞抗原至关重要。除了线性肽抗原外,嵌合肽还通过蛋白酶体催化的肽拼接(PCPS)产生。由于 MHC 洗脱肽的质谱数据分析的计算分析存在分歧,因此此类拼接肽是否大量呈递 MHC 存在很大争议。此外,这种质谱分析无法阐明拼接肽对免疫原性抗原库的贡献有多少。在这篇观点文章中,我们解释了了解拼接肽的贡献对于准确分析肽组学的重要性,一方面是为了阐明其作为潜在的可靶向肿瘤抗原的来源。为了制定一种独立于质谱的策略来估计 PCPS 对免疫肽组学的贡献,我们首先回顾了鉴定肿瘤表达的 MHC 呈递拼接肽抗原的方法学。这些鉴定的数据使我们能够汇编三个独立的数据集,其中包含来自癌症患者的 103、74 和 83 种已确认的 T 细胞抗原。这些真正的免疫原性抗原中只有 3.9%、1.4%和 0%至 7.2%是由 PCPS 产生的,因此对免疫原性肿瘤抗原库的贡献微不足道。我们得出结论,拼接肽不会成为扩大免疫治疗可靶向抗原数量的全面来源。