Research Paper Volume 15, Issue 23 pp 14422—14444
Integrative analysis of single-cell and bulk RNA seq to reveal the prognostic model and tumor microenvironment remodeling mechanisms of cuproptosis-related genes in colorectal cancer
- 1 Clinical School, Wannan Medical College, Wuhu 241000, Anhui, P.R. China
- 2 Department of Microbiology and Immunology, Wannan Medical College, Wuhu 241000, Anhui, P.R. China
- 3 Department of Nuclear Medicine, Yijishan Hospital of Wannan Medical College, Wuhu 241000, Anhui, P.R. China
Received: July 28, 2023 Accepted: November 3, 2023 Published: December 8, 2023
https://doi.org/10.18632/aging.205324How to Cite
Copyright: © 2023 Chu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Abstract
Background: Recently, there has been a great deal interest in cuproptosis, a form of programmed cell death that is mediated by copper. The specific mechanism through which cuproptosis-related genes impact the development of colorectal cancer (CRC) remains unknown.
Methods: Here, we combined bulk RNA-seq with scRNA-seq to investigate the CRGs functions within CRC. A number of 61 cuproptosis-related genes were chosen for further investigation. Nine prognostic CRGs were identified by Lasso-Cox. The RiskScore was created and the patients have been separated into two different groups, low- and high-RiskScore group. The CIBERSORT, ESTIMATE, MCP-counter, TIDE, and IPS have been employed to score the TME, and GSVA and GSEA were utilized to evaluate the pathway within the both groups. Further, we used cell communication analysis to explore the tumor microenvironment remodeling mechanisms of the COX17 and DLAT based on scRNA-seq. Finally, we used IHC and qPCR to validate the expression of COX17 and DLAT.
Results: AOC3, CCS, CDKN2A, COX11, COX17, COX19, DLD, DLAT, and PDHB have been recognized as prognostic CRGs in CRC. The high-risk group exhibited the worst prognosis, an immune-deficient phenotype, and were more resistant to ICB treatment. Further, scRNA-seq analysis revealed that elevated expression of COX17 in CD4-CXCL13Tfh could contribute to the immune evasion while DLAT had the opposite effect, reversing T cell exhaustion and inducing pyroptosis to boost CD8-GZMKT infiltration.
Conclusions: The current investigation has developed a prognostic framework utilizing cuproptosis-related genes that is highly effective in predicting prognosis, TME type, and response to immunotherapy in CRC patients. Furthermore, our study reveals a novel finding that elevated levels of COX17 expression within CD4-CXCL13 T cells in CRC mediates T cell exhaustion and Treg infiltration, while DLAT has been found to facilitate the anti-tumor immunity activation through the T cell exhaustion reversal and the induction of pyroptosis.
Abbreviations
CRC: Colorectal cancer; TIICs: Tumor-infiltrating immune cells; LASSO: Least absolute shrinkage and selection operator; ROC: Receiver operating characteristic; GSEA: Gene set enrichment analysis; GSVA: Gene set variation analysis; TME: Tumor microenvironment; GEO: Gene Expression Omnibus; TCGA: The Cancer Genome Atlas; OS: Overall survival; MsigDB: Molecular Signature Database; ROC: Receiver operation characteristic; scRNA-seq: single cell RNA-seq; GO: The Gene Ontology; KEGG: The Kyoto Encyclopedia of Genes and Genomes; MSI: Microsatellite Instability; dMMR: MisMatch Repair-deficient; MSS: Microsatellite stability.