Identification and multi-omics analysis of essential coding and long non-coding genes in colorectal cancer.

ABSTRACT: 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

SUBMITTER: Li Y 

PROVIDER: S-EPMC11874739 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature