Antigen Presentation Profiling Reveals T-cell Recognition of Lymphoma Immunoglobulin Neoantigens

Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. Such neoantigens have been implicated in response to immunotherapies including immune checkpoint blockade, yet their identification and validation remains challenging. Here we discover neoantigens in human mantle cell lymphomas using an integrated strategy for genomic and proteomic tumor antigen discovery that interrogates peptides presented within the tumor major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically identify neoantigen peptides in diagnostic tumor specimens from 17 patients. Remarkably, the 52 discovered neoantigenic peptides were invariably derived from the lymphoma immunoglobulin (Ig) heavy or light chain variable regions. Although we could identify MHC presentation of private germline polymorphic alleles, no mutated peptides were recovered from non-Ig somatically mutated genes. The immunoglobulin variable region somatic mutations were almost exclusively presented by MHC-II. We found T-cells specific for an immunoglobulin-derived neoantigen in the blood of a patient using MHC-II tetramers, and these T-cell clones expanded in frequency following tumor vaccination. These results demonstrate that an integrative approach combining MHC isolation, peptide identification and exome sequencing is an effective platform to uncover tumor neoantigens. Application of this strategy to human lymphoma implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.

癌症体细胞突变可产生新抗原（neoantigen），借此区分恶性肿瘤细胞与正常细胞。此类新抗原已被证实与包括免疫检查点阻断在内的免疫治疗应答密切相关，但其识别与验证仍颇具挑战。本研究针对人类套细胞淋巴瘤，采用整合基因组学与蛋白质组学的肿瘤抗原发现策略，对肿瘤细胞主要组织相容性复合体（major histocompatibility complex, MHC）I类与II类分子呈递的肽段进行靶向分析，以此发掘新抗原。我们将该策略应用于17例患者的诊断性肿瘤样本，系统性地识别新抗原肽段。值得注意的是，所发现的52条新抗原肽段均源自淋巴瘤免疫球蛋白（immunoglobulin, Ig）重链或轻链可变区。尽管我们能够检测到个体特异性生殖系多态性等位基因的MHC呈递现象，但并未从非Ig类体细胞突变基因中获取到突变肽段。免疫球蛋白可变区的体细胞突变肽段几乎全部由MHC-II分子呈递。我们借助MHC-II四聚体，在一名患者的血液中检测到针对免疫球蛋白衍生新抗原的特异性T细胞，且这些T细胞克隆在肿瘤疫苗接种后频率显著升高。上述结果表明，整合MHC分离、肽段鉴定与外显子组测序的一体化策略，是发掘肿瘤新抗原的有效技术平台。将该策略应用于人类淋巴瘤研究，证实免疫球蛋白新抗原可作为淋巴瘤免疫治疗的潜在靶点。