簡介：隨著最近批準PD-1抑製劑nivolumab和CTLA-4抑製劑ipilimumab的組合，免疫療法已成為惡性胸膜間皮瘤(MPM)的一線治療選擇。盡管具有高突變負擔的腫瘤通常對免疫療法有反應，但據報道MPM的突變負擔非常低，這與其他與致癌物暴露有關的腫瘤不一致。我們先前證明了染色體重排很常見，並且在MPM中具有新抗原潛力。在這裏，我們調查了免疫療法治療的MPM患者的染色體重排是否與生存相關。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：在單獨使用nivolumab(NCT29908324)或nivolumab和ipilimumab(NCT30660511)聯合治療之前，從患者(n=44)獲得至少一行治療後進行性MPM的胸膜活檢。進行RNA和全基因組測序。通過生物信息學軟件包SVAtools檢測到的染色體重排連接點用於估計對獨特轉錄本的影響。通過使用歸一化的基因表達數據和Molecular Signature Database中的gene Ontology數據集中的ssGSEA算法來確定每個樣品中的抗原呈遞。使用cox模型估計免疫治療後總體存活的相關性。基於組間明確的分離，使用1.5年的總體存活結果來區分治療後具有持久存活益處和不具有持久存活益處的患者。根據1.5年的臨界值，使用接受手術特征的區域(AUROC)確定與免疫治療後患者生存的任意關聯。

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.

結果：雖然連接計數本身並不能預測總生存期或1.5年生存率，但我們使用多個抗原呈遞基因組鑒定了抗原呈遞和連接計數之間的統計學顯著相互作用。例如，代表“調節抗原加工和肽抗原呈遞”的基因集顯示出與連接的高度顯著相互作用(p=0.0026)，並可預測總體存活率(p=0.003)。這種相互作用還預測了1.5年或更長的生存期，AUROC為0.82。雖然具有高表達抗原呈遞基因組的腫瘤中的連接計數與改善的存活結果相關，但具有低表達抗原呈遞基因組的腫瘤中的高連接計數與較差的存活相關。

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.

結論：在保留抗原呈遞的情況下，染色體重排與免疫治療改善的生存結果相關。相反，在缺乏有效抗原呈遞的情況下，染色體重排與較差的存活結果相關。隨著最近批準nivolumab和ipilimumab聯合用於MPM的一線治療，我們的方法可能有助於確定哪些患者將從一線免疫檢查點抑製劑中獲益最多。

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.