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染色体碎裂相关基因表达模式的泛癌分析表明其与肿瘤免疫及治疗药物反应相关。

Pan-cancer analysis of chromothripsis-related gene expression patterns indicates an association with tumor immune and therapeutic agent responses.

作者信息

Zhang Qin, Yang Lujie, Xiao He, Dang Zhaoqian, Kuang Xunjie, Xiong Yanli, Zhu Jianwu, Huang Zhou, Li Mengxia

机构信息

Cancer Center, Daping Hospital, Army Medical University, Chongqing, China.

出版信息

Front Oncol. 2023 Jan 24;13:1074955. doi: 10.3389/fonc.2023.1074955. eCollection 2023.

Abstract

Chromothripsis is a catastrophic event involving numerous chromosomal rearrangements in confined genomic regions of one or a few chromosomes, causing complex effects on cells the extensive structural variation. The development of whole-genome sequencing (WGS) has promoted great progress in exploring the mechanism and effect of chromothripsis. However, the gene expression characteristics of tumors undergone chromothripsis have not been well characterized. In this study, we found that the transcriptional profile of five tumor types experiencing chromothripsis is associated with an immune evasion phenotype. A gene set variation analysis (GSVA) was used to develop a CHP score, which is based on differentially expressed gene sets in the TCGA database, revealing that chromothripsis status in multiple cancers is consistent with an abnormal tumor immune microenvironment and immune cell cytotoxicity. Evaluation using four immunotherapy datasets uncovered the ability of the CHP score to predict immunotherapy response in diverse tumor types. In addition, the CHP score was found to be related to resistance against a variety of anti-tumor drugs, including anti-angiogenesis inhibitors and platinum genotoxins, while EGFR pathway inhibitors were found to possibly be sensitizers for high CHP score tumors. Univariate COX regression analysis indicated that the CHP score can be prognostic for several types of tumors. Our study has defined gene expression characteristics of tumors with chromothripsis, supporting the controversial link between chromothripsis and tumor immunity. We also describe the potential value of the CHP score in predicting the efficacy of immunotherapy and other treatments, elevating chromothripsis as a tool in clinical practice.

摘要

染色体碎裂是一种灾难性事件,涉及一条或几条染色体的受限基因组区域内的大量染色体重排,对细胞产生复杂影响以及广泛的结构变异。全基因组测序(WGS)的发展在探索染色体碎裂的机制和影响方面取得了巨大进展。然而,经历染色体碎裂的肿瘤的基因表达特征尚未得到很好的表征。在本研究中,我们发现经历染色体碎裂的五种肿瘤类型的转录谱与免疫逃逸表型相关。基因集变异分析(GSVA)用于开发基于TCGA数据库中差异表达基因集的CHP评分,揭示多种癌症中的染色体碎裂状态与异常的肿瘤免疫微环境和免疫细胞细胞毒性一致。使用四个免疫治疗数据集进行评估发现CHP评分能够预测多种肿瘤类型的免疫治疗反应。此外,发现CHP评分与对多种抗肿瘤药物的耐药性有关,包括抗血管生成抑制剂和铂类基因毒素,而表皮生长因子受体(EGFR)通路抑制剂可能是高CHP评分肿瘤的敏感剂。单因素COX回归分析表明CHP评分可对几种类型的肿瘤进行预后评估。我们的研究定义了经历染色体碎裂的肿瘤的基因表达特征,支持了染色体碎裂与肿瘤免疫之间存在争议的联系。我们还描述了CHP评分在预测免疫治疗和其他治疗疗效方面的潜在价值,提升了染色体碎裂作为临床实践工具的地位。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e7c0/9902954/6a2f00f33196/fonc-13-1074955-g001.jpg

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