Li Yanguo, Meng Zixing, Fan Chengjiang, Rong Hao, Xi Yang, Liao Qi
Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, China.
Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang, China.
Biochem Biophys Rep. 2025 Feb 13;41:101938. doi: 10.1016/j.bbrep.2025.101938. eCollection 2025 Mar.
Essential genes are indispensable for the survival of cancer cell. CRISPR/Cas9-based pooled genetic screens have distinguished the essential genes and their functions in distinct cellular processes. Nevertheless, the landscape of essential genes at the single cell levels and the effect on the tumor microenvironment (TME) remains limited. Here, we identified 396 essential protein-coding genes (ESPs) by integration of 8 genome-wide CRISPR loss-of-function screen datasets of colorectal cancer (CRC) cell lines and single-cell RNA sequencing (scRNA-seq) data of CRC tissues. Then, 29 essential long non-coding genes (ESLs) were predicted using Hypergeometric Test (HT) and Personalized PageRank (PPR) algorithms based on ESPs and co-expressed network constructed from scRNA-seq. CRISPR/Cas9 knockout experiment verified the effect of several ESPs and ESLs on the survival of CRC cell line. Furthermore, multi-omics features of ESPs and ESLs were illustrated by examining their expression patterns and transcription factor (TF) regulatory network at the single cell level, as well as DNA mutation and DNA methylation events at bulk level. Finally, through integrating multiple intracellular regulatory networks with cell-cell communication network (CCN), we elucidated that and are regulated by multiple CRC essential genes, and the anti-cancer drugs sunitinib can interfere the expression of them potentially. Our findings provide a comprehensive asset of CRC ESPs and ESLs, sheding light on the mining of potential therapy targets for CRC.
必需基因对于癌细胞的存活不可或缺。基于CRISPR/Cas9的基因池筛选已鉴别出不同细胞过程中的必需基因及其功能。然而，单细胞水平上必需基因的全貌以及对肿瘤微环境（TME）的影响仍然有限。在此，我们通过整合8个结直肠癌（CRC）细胞系的全基因组CRISPR功能丧失筛选数据集和CRC组织的单细胞RNA测序（scRNA-seq）数据，鉴定出396个必需蛋白质编码基因（ESPs）。然后，基于ESPs以及由scRNA-seq构建的共表达网络，使用超几何检验（HT）和个性化PageRank（PPR）算法预测了29个必需长链非编码基因（ESLs）。CRISPR/Cas9基因敲除实验验证了几个ESPs和ESLs对CRC细胞系存活的影响。此外，通过在单细胞水平检查它们的表达模式和转录因子（TF）调控网络，以及在整体水平检查DNA突变和DNA甲基化事件，阐明了ESPs和ESLs的多组学特征。最后，通过将多个细胞内调控网络与细胞间通讯网络（CCN）整合，我们阐明了[此处原文缺失部分内容]受多个CRC必需基因调控，并且抗癌药物舒尼替尼可能会干扰它们的表达。我们的研究结果提供了一份关于CRC ESPs和ESLs的综合资源，为挖掘CRC潜在治疗靶点提供了线索。
