Differential gene expression of tumor-infiltrating CD4⁺ T cells in advanced versus early stage colorectal cancer and identification of a gene signature of poor prognosis

ABSTRACT

Tumor-infiltrating lymphocytes (TILs) play indispensable roles in the progression and response to treatment of solid tumors. However, the prognostic significance of CD4⁺ TILs is not fully disclosed in cancers generally and in CRC in particular, mainly due to the existence of different functional subsets of CD4⁺ T cells. We performed transcriptomic profiling of CD4⁺ TILs isolated from CRC patients in order to identify differentially expressed genes and their functional pathways in early versus advanced disease stages. We found that in advanced stages, genes related to immune and inflammatory responses, in particular Th1-mediated immune response and cytotoxicity-mediated genes, were downregulated; while epigenetic-mediated silencing genes were upregulated. Interestingly, we identified genes, which were steadily upregulated or downregulated in CD4⁺ TILs with CRC progression from stage I to IV. Additionally, of the top 200 deregulated genes, 43 upregulated and 64 downregulated genes showed similar deregulation trends in the cancer genome atlas CRC dataset. From these 97 deregulated genes, we identified a “poor prognosis CD4 gene signature (ppCD4sig)”. Patients with high ppCD4sig score showed shorter disease-specific survival (DSS) and progression-free interval (PFI). The ppCD4sig was an independent prognostic indicator for DSS (HR = 1.73, 95% CI 1.32–2.27, P = 0.0001) and PFI (HR = 1.75, 95% CI 1.3–2.35, P = 0.0016). Additionally, patients at advanced stages and at a younger age (<55 years) were more likely to have a high ppCD4sig score. Altogether, our data provide novel insights and a unique prognostic gene signature of CD4⁺ TILs in the CRC microenvironment.

KEYWORDS:

• Colorectal cancer
• tumor-infiltrating lymphocytes
• Th1 immune response
• chromatin silencing
• predictive biomarkers

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Acknowledgments

Open Access funding was provided by the Qatar National Library.

We are grateful to patients for donating their samples. We also would like to thank the genomics core facility at Qatar Biomedical Research Institute for performing RNA-Sequencing.

Authors contributions

VN: Data curation, Methodology, Formal analysis, Investigation, Writing the original draft. RS: Data curation, Methodology, Formal analysis, Investigation, Writing-review and editing. RT and ST: Data curation, Methodology, Formal analysis, Investigation. KM, AA, MK and MN: Sample acquisition, Investigation. FA: Formal analysis, Visualization, Methodology, Writing-review and editing. EE: Conceptualization, Resources, Data curation, Software, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Methodology, Project administration, Writing-review and editing.

Disclosure of potential conflicts of interest

No potential conflicts of interest were disclosed.

Supplementary material

Supplemental data for this article can be accessed on the publisher’s website.

Additional information

Funding

This work was supported by a start-up grant [VR04] for Prof. Eyad Elkord from Qatar Biomedical Research Institute, Qatar Foundation.