Colorectal cancer (CRC) remains a major cause of cancer-related morbidity and mortality worldwide. Although immunotherapies have improved outcomes for a subset of patients, many cases show limited benefit. This work aimed to develop a more comprehensive molecular understanding of the immune microenvironment in human CRC by applying an integrated multi-omics strategy and to identify candidate regulatory molecules implicated in immune remodelling that could inform future immunotherapy research.
The study integrated multiple molecular layers derived from an in-house CRC cohort with publicly available transcriptomic data from The Cancer Genome Atlas (TCGA). In-house data types included structural variation, DNA methylation, chromatin accessibility, proteomic, and phosphoproteomic datasets. Analyses concentrated on a panel of 1,539 immune-related genes (IRGs) associated with three immune cell populations: CD4+ T cells, B cells, and natural killer (NK) cells. Multi-layered genomic and proteomic analyses were performed to detect altered immune-related pathways, identify hub genes, nominate candidate transcription factors, and infer upstream kinases linked to immune infiltration and immune checkpoint expression.
Analysis of the integrated datasets indicated a higher infiltration of CD4+ T cells, B cells, and NK cells associated with CRC samples. Across the 1,539 IRGs examined, widespread alterations were observed at multiple molecular levels — genomic, epigenomic (including DNA methylation and chromatin accessibility), transcriptomic, proteomic, and phosphoproteomic. This multi-layer perturbation pattern supports the conclusion that immune microenvironment remodelling in CRC is driven by coordinated changes across regulatory layers rather than by single-level alterations.
From the integrated analyses, the authors identified several candidate hub genes that stand out across molecular layers. These included IL10, LEP, ITGAM, and EGFR, representing immune-regulatory cytokine signalling, metabolic/adipokine pathways, innate immune cell adhesion/activation, and growth-factor signalling respectively. Proteomic and phosphoproteomic profiling highlighted a notable change in EGFR post-translational modification: EGFR phosphorylation at residues S991 and T693 was significantly decreased in CRC samples. The decrease in phosphorylation at these specific sites may reflect altered EGFR signalling dynamics in the tumour immune microenvironment, as captured by phosphoproteome measurements.
The multi-omics integration also yielded candidate upstream regulatory molecules. STAT2 and HSF1 were identified as putative transcription factors associated with the observed changes in immune-related gene expression. In parallel, CDK2 emerged as a candidate upstream kinase correlated with patterns of immune infiltration and with expression of immune checkpoint molecules. These nominations suggest potential mechanistic links between signalling pathways (including cell-cycle kinases) and the regulation of immune-related programs in CRC.
By mapping immune-related alterations across structural variation, epigenomics, transcriptomics, proteomics, and phosphoproteomics, this study builds a systematic molecular portrait of immune microenvironment remodelling in CRC. The identification of hub genes — notably IL10, LEP, ITGAM, and EGFR — together with altered EGFR phosphorylation and candidate regulators STAT2, HSF1, and CDK2, provides a set of prioritized molecular targets and hypotheses for follow-up functional studies. These candidate regulators may help explain variation in immune infiltration and checkpoint expression in CRC and could inform the design of combination strategies or new targets for immunotherapy research.
The summary above is based on the published abstract. Specific experimental details such as cohort size, sample selection and matching criteria, statistical methods and thresholds, validation experiments, effect sizes, and other protocol-level information were not reported in the abstract and therefore are not available here. Those details would be necessary to fully evaluate reproducibility, generalizability, and the strength of the nominated candidate regulators.
The study presents a comprehensive multi-omics characterization of immune microenvironment remodelling in colorectal cancer and nominates candidate molecular regulators — including IL10, LEP, ITGAM, EGFR, STAT2, HSF1, and CDK2 — that warrant further investigation as potential immunotherapy targets or modulators.