Aug 2026· Cancer Genomics & Proteomics· Vol 23, pp. 1021 - 1042· 0 citations· 54 references
Medicine
TL;DR
This study provides a systematic multi-omics characterization of immune microenvironment remodelling in CRC and identifies candidate molecular regulators that may serve as potential targets for future immunotherapy research.
Abstract
Abstract Background/Aim: Colorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality worldwide. Although immunotherapy has improved outcomes for a subset of patients, its limited efficacy in many cases highlights the need for a more comprehensive understanding of the CRC immune microenvironment. This study aimed to characterize the molecular landscape of the CRC immune microenvironment using an integrated multi-omics approach and to identify candidate regulatory molecules associated with immune remodelling. Materials and Methods: We integrated structural variation, DNA methylation, chromatin accessibility, proteomic, and phosphoproteomic data generated from an in-house CRC cohort with transcriptomic data from The Cancer Genome Atlas (TCGA). Analyses focused on 1,539 immune-related genes (IRGs) associated with CD4+ T cells, B cells, and natural killer (NK) cells. Multi-layered genomic and proteomic analyses were performed to identify altered immune-related pathways, hub genes, candidate transcription factors, and upstream kinases. Results: Higher infiltration of CD4+ T cells, B cells, and NK cells was associated with CRC. IRGs exhibited widespread alterations across genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic levels. IL10, LEP, ITGAM, and EGFR emerged as candidate hub genes. EGFR phosphorylation at S991 and T693 was significantly decreased in CRC. STAT2 and HSF1 were identified as candidate upstream transcription factors, while CDK2 emerged as a candidate upstream kinase associated with immune infiltration and immune checkpoint expression. Conclusion: This study provides a systematic multi-omics characterization of immune microenvironment remodelling in CRC and identifies candidate molecular regulators that may serve as potential targets for future immunotherapy research.
Background: Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide. Increasing evidence suggests that intestinal microbial dysbiosis contributes to colorectal tumorigenesis by reshaping host molecular signaling and the tumor immune microenvironment. However, the molecular mechanisms linking microbiome-associated alterations to host regulatory networks and disease progression remain incompletely understood. Objective: This study aimed to identify the microbiome-associated molecular regulators and immune modulators involved in colorectal cancer through an integrative multi-omics systems biology approach. Methods: Publicly available transcriptomic datasets were analyzed to identify differentially expressed genes, followed by functional enrichment, protein-protein interaction network construction, hub gene prioritization, immune infiltration profiling, survival analysis, and multi-omics characterization. Results: The identified hub genes represent hypothesis-generating host candidates for further mechanistic and clinical validation. These genes occupied key positions within host regulatory networks and were significantly associated with adverse clinical outcomes and altered CD8+ T-cell infiltration, suggesting their involvement in immune remodeling within the tumor microenvironment. Multi-omics characterization demonstrated that PTEN and SMAD4 alterations were predominantly associated with genomic deletions, whereas SMAD2 dysregulation was associated with transcriptomic and gene-dosage variation. Although the overall mutational burden of the identified hub genes was not significantly associated with disease-free survival (p = 0.878), these molecular regulators showed associations with immune-cell infiltration and CRC-related pathways. Conclusions: Collectively, our findings provide a system-level framework describing the associations between dysbiosis-relevant host pathways, CRC-related regulatory networks, and immune responses.
Huda Altoukhi, Nawal H. Siddig, N. Al-Hoshani et al.· Journal of Clinical Medicine· 0 citations
Breast cancer remains a major cause of cancer-related mortality, and exploratory computational workflows can help prioritize immune-associated markers for further investigation. Here, we used the cancer genome atlas breast invasive carcinoma (TCGA-BRCA) bulk transcriptomic data and the public single-cell dataset GSE161529 to examine associations between myeloperoxidase (MPO) expression, clinical outcomes, immune infiltration, methylation, upstream-regulator annotations, single-cell expression patterns, virtual knockdown sensitivity outputs, drug-gene interaction retrieval, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) annotation. MPO expression was lower in breast cancer tissues than in adjacent non-tumor tissues. Higher MPO expression was associated with a longer progression-free interval, whereas its associations with overall survival and disease-specific survival were not statistically significant. Receiver operating characteristic (ROC) analysis suggested tumor-normal separation within the analyzed public dataset, but this should not be interpreted as clinical diagnostic validation. Immune deconvolution and enrichment analyses indicated that MPO expression mainly tracked with immune- and myeloid-related transcriptional features, rather than establishing tumor-intrinsic regulation of the immune microenvironment. At single-cell resolution, the MPO signal was sparse, with only 85 MPO-positive cells detected before k-nearest neighbor (KNN)-based neighborhood expansion. Detectable MPO signal and MPO-associated scores were interpreted cautiously because they may be influenced by sparse expression, cell-type annotation uncertainty, dropout, doublets, or ambient RNA. In silico virtual knockdown suggested candidate immune- and inflammatory-related transcriptional changes, but these results were considered exploratory and require validation. Drug-gene interaction database (DGIdb)-based drug-gene retrieval and ADMET annotation were used only as preliminary chemical annotations and were not interpreted as therapeutic evidence. Overall, this study provides a reproducible in silico workflow for generating hypotheses about MPO-associated immune/myeloid features in breast cancer, which require external cohort validation and experimental confirmation.
Qing-Rui Li, Fei Teng, Weijia Kong et al.· Journal of Visualized Experi...· 0 citations
A seven-gene immune-related prognostic signature that, combined with clinicopathological parameters, provides a robust tool for individualized survival prediction and may guide precision management in CRC patients is developed and validated.
Background: In recent decades, the incidence of colorectal cancer (CRC) has been rising worldwide. CRC ranks second in cancer-related mortality. The identification of reliable biomarkers for early diagnosis and prognosis prediction, along with a deeper understanding of the underlying molecular events, holds substantial promise for improving patient outcomes. The tissue inhibitor of the metalloproteinase 1 (TIMP1) gene is overexpressed in various gastrointestinal malignancies and contributes to tumor progression. However, its role in regulating the CRC tumor immune microenvironment (TIME) and its potential as a clinically actionable prognostic biomarker remain unclear. Methods: To probe how TIMP1 acts as a prognosis-related candidate biomarker in colorectal carcinoma, TCGA-derived datasets were adopted to conduct Kaplan–Meier survival assessment. We also investigated the connection between the expression abundance of TIMP1 and the infiltration of immune populations and intratumoral lymphocytes; furthermore, immune checkpoint-related genes were systematically assessed across multiple tumor types via the TISIDB and TIMER2.0 platforms, with particular emphasis on CRC. We adopted the ESTIMATE scoring system to figure out how TIMP1 gene expression correlates with the phenotypic properties of the colorectal-cancer TIME. We relied on the limma toolkit for the screening of differential transcripts from high-TIMP1 and low-TIMP1 cohorts. Enrichment assessments covering Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes entries were then carried out to predict the potential biological pathways associated with TIMP1. We constructed the protein–protein interaction map for TIMP1-interacting partners via the STRING repository. To further explore TIMP1-correlated genes, we performed Venn diagram intersection analysis combined with Spearman’s correlation test. Finally, quantitative reverse-transcription PCR was then implemented to detect TIMP1 messenger-RNA abundance inside the RKO colorectal carcinoma cell line as well as normal colonic epithelial CCD-18Co cells, which offered in vitro experimental verification for our bioinformatic outcomes. Results: According to outcome data, TIMP1 transcripts were markedly up-regulated in CRC specimens and cell lines relative to normal samples. Elevated TIMP1 expression served as a poor-prognosis indicator for overall survival (hazard ratio [HR] = 0.43, 95% confidence interval [CI] = 0.29–0.64, p < 0.001) and disease-specific survival (HR = 0.39, 95% CI = 0.22–0.68, p = 0.001) among colorectal-carcinoma patients. TIMP1-high and TIMP1-low groups exhibited notable differences in immune cell infiltration (CD8+ T, macrophage, mast, neutrophil, B, monocyte, dendritic, and CD4+ T cells). TIMP1 expression was also significantly correlated with tumor-infiltrating lymphocytes, key immune checkpoint genes (e.g., CD274 [PD-L1] and CTLA4), and immunomodulatory chemokines (e.g., CCL3 and CCL5). Twelve TIMP1-interacting DEGs were selected: COL5A1, FN1, PRG4, and a cluster of nine MMPs (MMP1/2/3/7/8/9/11/13/14), all of which showed significant positive correlations with TIMP1 (r = 0.31–0.63, all p < 0.001). Conclusions: TIMP1 expression correlates with features of the tumor immune microenvironment and extracellular matrix remodeling in CRC, suggesting that TIMP1 shows potential as a candidate biomarker. However, its potential as a therapeutic target warrants further experimental investigation.
Yunyi Xie, Jun Li, Zuwei Yan et al.· Genes· 0 citations
Colorectal cancer (CRC) exhibits marked cellular heterogeneity, and the cellular context of malignancy-associated epithelial programs remains incompletely defined. We integrated 2,993 CRC samples spanning bulk RNA-seq (n = 2,568; two OS/RFS cohorts), scRNA-seq (281,961 cells/152 specimens), spatial transcriptomics (n = 6), and proteomics (n = 267). Analyses included single-cell integration/annotation, GSVA/HALLMARK, interactome, pseudotime, and ligand–receptor mapping; functional CRISPR assays, EMT immunoblotting, and xenografts; TF profiling (SCENIC/JASPAR/ChIP-qPCR); and exploratory drug-response prediction (OncoPredict), cell-sensitivity assays, and docking/MD modeling. We constructed a stage-stratified single-cell atlas and resolved eleven malignant epithelial subsets, characterizing Epi_4 as late-stage–enriched with EMT, hypoxia, and inflammatory programs and adverse OS/RFS. GPRC5A marked this subset, which we define as GPRC5A+Epi; its expression rose from stage I→IV and was associated with poor outcomes across cohorts, with concordant spatial/proteomic observations. GPRC5A perturbation affected CRC proliferation, migration/invasion, EMT, and xenograft tumorigenicity, supporting a functionally important role in the tested models. SCENIC and ChIP-qPCR supported FOSL1 as an upstream regulator that occupies the GPRC5A promoter. Spatial and ligand–receptor analyses predicted close association and potentially reciprocal signaling between GPRC5A+Epi and POSTN+fibroblasts (COL1A1–SDC4, COL1A1/1A2–ITGA2/ITGB1, PPIA–BSG); concurrent high GPRC5A+Epi/POSTN+Fib signatures were associated with inferior OS/RFS. Drug-response analyses identified an association between GPRC5A status and trametinib sensitivity. Docking/MD produced a computational model of a possible trametinib–GPRC5A interaction, which remains experimentally unvalidated. GPRC5A⁺Epi is a malignancy-associated epithelial state in CRC, and GPRC5A is functionally important for malignant phenotypes in the tested models. Its inferred relationships with POSTN⁺ fibroblasts and the trametinib findings should be regarded as hypothesis-generating pending functional crosstalk, direct-binding, and therapeutic validation.
Wei-Chun Tang, Peng-Chen Xu, Sheng-Li Wang et al.· Journal of Translational Med...· 0 citations
This study integrates multi-omics datasets to identify candidate biomarkers that may influence TNBC progression and modulate therapeutic response and nominate CCND2 and KIF1A as candidate biomarkers and potential therapeutic targets in TNBC.
Roberto Aguilar, Victor Wang, Shane Deng· Journal of Immunology· 0 citations
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