Open Access

Revolutionizing prognostic predictions in colorectal cancer: Macrophage‑driven transcriptional insights from single‑cell RNA sequencing and gene co‑expression network analysis

  • Authors:
    • Yang Feng
    • Zhuo Cheng
    • Jingyuan Gao
    • Tao Huang
    • Jun Wang
    • Qian Tang
    • Ke Pu
    • Chang Liu
  • View Affiliations

  • Published online on: October 3, 2024     https://doi.org/10.3892/ol.2024.14721
  • Article Number: 587
  • Copyright: © Feng et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )
Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )


Abstract

Tumor‑associated macrophages have become important biomarkers for cancer diagnosis, prognosis and therapy. The dynamic changes in macrophage subpopulations significantly impact the outcomes of cancer immunotherapy. Hence, identifying additional macrophage‑related biomarkers is essential for enhancing prognostic predictions in colorectal cancer (CRC) immunotherapy. CRC single‑cell RNA sequencing (scRNA‑seq) data was obtained from the Gene Expression Omnibus (GEO) database. The data were processed, normalized and clustered using the ‘Seurat’ package. Cell types within each cluster were annotated using the ‘SingleR’ package. Weighted gene co‑expression network analysis identified modules corresponding to specific cell types. A non‑negative matrix factorization algorithm was employed to segregate different clusters based on the selected module. Differentially expressed genes (DEGs) were identified across various clusters and a prognostic model was constructed using lasso regression and Cox regression analyses. The robustness of the model was validated using The Cancer Genome Atlas (TCGA) database and GEO microarrays. Additionally, the prognosis, immune characteristics and response to immune checkpoint inhibitor (ICI) therapy were individually analyzed. The scRNA‑seq data from GSE200997, consisting of 23 samples, were analyzed. Dimensionality reduction and cluster identification allowed the isolation of the primary myeloid cell subpopulations. The macrophage‑related brown module was identified, which was further divided into two clusters. Using the DEGs from these clusters, a prognostic model was developed, comprising five macrophage‑related genes. The robustness of the model was confirmed using microarray datasets GSE17536, GSE38832 and GSE39582, as well as TCGA cohort. Patients classified as high‑risk by the present model exhibited poorer survival rates, lower tumor mutation burden, reduced microsatellite instability, lower tumor purity, more severe tumor immune dysfunction and exclusion, and less benefit from ICIs therapy compared with low‑risk patients. The present prognostic model shows promise as a biomarker for risk stratification and predicting therapeutic efficacy in patients with CRC. However, further well‑designed prospective studies are necessary to validate the findings.
View Figures
View References

Related Articles

Journal Cover

December-2024
Volume 28 Issue 6

Print ISSN: 1792-1074
Online ISSN:1792-1082

Sign up for eToc alerts

Recommend to Library

Copy and paste a formatted citation
x
Spandidos Publications style
Feng Y, Cheng Z, Gao J, Huang T, Wang J, Tang Q, Pu K and Liu C: Revolutionizing prognostic predictions in colorectal cancer: Macrophage‑driven transcriptional insights from single‑cell RNA sequencing and gene co‑expression network analysis. Oncol Lett 28: 587, 2024.
APA
Feng, Y., Cheng, Z., Gao, J., Huang, T., Wang, J., Tang, Q. ... Liu, C. (2024). Revolutionizing prognostic predictions in colorectal cancer: Macrophage‑driven transcriptional insights from single‑cell RNA sequencing and gene co‑expression network analysis. Oncology Letters, 28, 587. https://doi.org/10.3892/ol.2024.14721
MLA
Feng, Y., Cheng, Z., Gao, J., Huang, T., Wang, J., Tang, Q., Pu, K., Liu, C."Revolutionizing prognostic predictions in colorectal cancer: Macrophage‑driven transcriptional insights from single‑cell RNA sequencing and gene co‑expression network analysis". Oncology Letters 28.6 (2024): 587.
Chicago
Feng, Y., Cheng, Z., Gao, J., Huang, T., Wang, J., Tang, Q., Pu, K., Liu, C."Revolutionizing prognostic predictions in colorectal cancer: Macrophage‑driven transcriptional insights from single‑cell RNA sequencing and gene co‑expression network analysis". Oncology Letters 28, no. 6 (2024): 587. https://doi.org/10.3892/ol.2024.14721