简介：随着最近批准PD-1抑制剂nivolumab和CTLA-4抑制剂ipilimumab的组合，免疫疗法已成为恶性胸膜间皮瘤(MPM)的一线治疗选择。尽管具有高突变负担的肿瘤通常对免疫疗法有反应，但据报道MPM的突变负担非常低，这与其他与致癌物暴露有关的肿瘤不一致。我们先前证明了染色体重排很常见，并且在MPM中具有新抗原潜力。在这里，我们调查了免疫疗法治疗的MPM患者的染色体重排是否与生存相关。Introduction:Immunotherapy has emerged as a frontline treatment option for malignant pleural mesothelioma (MPM) with the recent approval of the combination of the PD-1 inhibitor nivolumab and the CTLA-4 inhibitor ipilimumab. Whereas tumors with high mutation burdens are typically responsive to immunotherapy, MPM reportedly has a very low mutation burden, which is inconsistent with other tumors related to carcinogen exposures. We previously demonstrated that chromosomal rearrangements are common and have neoantigenic potential in MPM. Herein we investigated whether chromosomal rearrangements are associated with survival in patients with MPM treated with immunotherapy.

方法：在单独使用nivolumab(NCT29908324)或nivolumab和ipilimumab(NCT30660511)联合治疗之前，从患者(n=44)获得至少一行治疗后进行性MPM的胸膜活检。进行RNA和全基因组测序。通过生物信息学软件包SVAtools检测到的染色体重排连接点用于估计对独特转录本的影响。通过使用归一化的基因表达数据和Molecular Signature Database中的gene Ontology数据集中的ssGSEA算法来确定每个样品中的抗原呈递。使用cox模型估计免疫治疗后总体存活的相关性。基于组间明确的分离，使用1.5年的总体存活结果来区分治疗后具有持久存活益处和不具有持久存活益处的患者。根据1.5年的临界值，使用接受手术特征的区域(AUROC)确定与免疫治疗后患者生存的任意关联。

Methods：Pleural biopsies of progressive MPM after at least one line of therapy were obtained from patients (n=44) prior to treatment with nivolumab alone (NCT29908324) or the combination of nivolumab and ipilimumab (NCT30660511). RNA and whole genome sequencing were performed. The junctions of chromosomal rearrangements, detected by a bioinformatics package SVAtools, were used to estimate the impact on unique transcripts. Antigen presentation in each sample was determined by using normalized gene expression data and the ssGSEA algorithm in the Gene Ontology dataset in Molecular Signature Database. Associations with overall survival following immunotherapy were estimated using cox models. Based on a clear separation between groups, an overall survival outcome of 1.5 years was used to distinguish patients with and without durable survival benefit following treatment. Area under receiving operating characteristic (AUROC) was used to determine any associations with patients’ survival after immunotherapy based on the 1.5-year cutoff.

结果：虽然连接计数本身并不能预测总生存期或1.5年生存率，但我们使用多个抗原呈递基因组鉴定了抗原呈递和连接计数之间的统计学显着相互作用。例如，代表“调节抗原加工和肽抗原呈递”的基因集显示出与连接的高度显着相互作用(p=0.0026)，并可预测总体存活率(p=0.003)。这种相互作用还预测了1.5年或更长的生存期，AUROC为0.82。虽然具有高表达抗原呈递基因组的肿瘤中的连接计数与改善的存活结果相关，但具有低表达抗原呈递基因组的肿瘤中的高连接计数与较差的存活相关。

Results:While junction counts by themselves did not predict overall survival or ³ 1.5-year survival, we identified statistically significant interactions between antigen presentation and junctions counts using multiple antigen presentation gene sets. For example, a gene set representing the “regulation of antigen processing and presentation of peptide antigen” demonstrated a highly significant interaction with junctions (p=0.0026) and was predictive of overall survival (p=0.003). This interaction also predicted 1.5-year or greater survival with an AUROC of 0.82. While junction counts in tumors with high expression of antigen presentation gene sets were associated with improved survival outcomes, high junction counts in tumors with low expression of antigen presentation gene sets were associated with worse survival.

结论：在保留抗原呈递的情况下，染色体重排与免疫治疗改善的生存结果相关。相反，在缺乏有效抗原呈递的情况下，染色体重排与较差的存活结果相关。随着最近批准nivolumab和ipilimumab联合用于MPM的一线治疗，我们的方法可能有助于确定哪些患者将从一线免疫检查点抑制剂中获益最多。

Conclusion:In the context of preserved antigen presentation, chromosomal rearrangements are associated with improved survival outcomes with immunotherapy. In contrast, in the absence of effective antigen presentation, chromosomal rearrangements were associated with poor survival outcomes. With the recent approval of the combination of nivolumab and ipilimumab for the frontline treatment of MPM, our approach might be useful to identify patients who would benefit the most with frontline immune checkpoint inhibitors.