基于网络的鉴定与免疫沉默型癌症表型相关的关键主调控因子。
Network-based identification of key master regulators associated with an immune-silent cancer phenotype.
机构信息
Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar.
Cancer Research Department, Research Branch, Sidra Medicince, Doha, Qatar.
出版信息
Brief Bioinform. 2021 Nov 5;22(6). doi: 10.1093/bib/bbab168.
A cancer immune phenotype characterized by an active T-helper 1 (Th1)/cytotoxic response is associated with responsiveness to immunotherapy and favorable prognosis across different tumors. However, in some cancers, such an intratumoral immune activation does not confer protection from progression or relapse. Defining mechanisms associated with immune evasion is imperative to refine stratification algorithms, to guide treatment decisions and to identify candidates for immune-targeted therapy. Molecular alterations governing mechanisms for immune exclusion are still largely unknown. The availability of large genomic datasets offers an opportunity to ascertain key determinants of differential intratumoral immune response. We follow a network-based protocol to identify transcription regulators (TRs) associated with poor immunologic antitumor activity. We use a consensus of four different pipelines consisting of two state-of-the-art gene regulatory network inference techniques, regularized gradient boosting machines and ARACNE to determine TR regulons, and three separate enrichment techniques, including fast gene set enrichment analysis, gene set variation analysis and virtual inference of protein activity by enriched regulon analysis to identify the most important TRs affecting immunologic antitumor activity. These TRs, referred to as master regulators (MRs), are unique to immune-silent and immune-active tumors, respectively. We validated the MRs coherently associated with the immune-silent phenotype across cancers in The Cancer Genome Atlas and a series of additional datasets in the Prediction of Clinical Outcomes from Genomic Profiles repository. A downstream analysis of MRs specific to the immune-silent phenotype resulted in the identification of several enriched candidate pathways, including NOTCH1, TGF-$\beta $, Interleukin-1 and TNF-$\alpha $ signaling pathways. TGFB1I1 emerged as one of the main negative immune modulators preventing the favorable effects of a Th1/cytotoxic response.
一种以活跃的辅助性 T 细胞 1 (Th1)/细胞毒性应答为特征的癌症免疫表型与免疫治疗的反应性和不同肿瘤的良好预后相关。然而,在一些癌症中,这种肿瘤内免疫激活并不能提供免受进展或复发的保护。定义与免疫逃逸相关的机制对于完善分层算法、指导治疗决策以及确定免疫靶向治疗的候选者至关重要。控制免疫排斥机制的分子改变在很大程度上仍然未知。大型基因组数据集的可用性为确定肿瘤内免疫反应的关键决定因素提供了机会。我们遵循基于网络的方案来识别与免疫抗肿瘤活性差相关的转录调节剂 (TRs)。我们使用由两种最先进的基因调控网络推断技术、正则化梯度提升机和 ARACNE 组成的共识来确定 TR 调节子,以及三种独立的富集技术,包括快速基因集富集分析、基因集变异分析和虚拟富集调节子分析推断蛋白质活性,以确定影响免疫抗肿瘤活性的最重要的 TRs。这些 TRs,称为主调节剂 (MRs),分别是免疫沉默和免疫活跃肿瘤所特有的。我们在癌症基因组图谱 (The Cancer Genome Atlas) 和基因组图谱预测临床结果 (Prediction of Clinical Outcomes from Genomic Profiles repository) 中的一系列附加数据集中验证了与免疫沉默表型一致相关的 MRs。对免疫沉默表型特有的 MRs 的下游分析导致了几个富集候选途径的识别,包括 NOTCH1、TGF-$\beta $、白细胞介素-1 和 TNF-$\alpha $信号通路。TGFB1I1 作为主要的负免疫调节剂之一,阻止了 Th1/细胞毒性反应的有利作用。