---
title: "Multi-omics Characterization of the Immune Microenvironment in Colorectal Cancer"
id: "pubmed-42674818"
canonical_url: "https://medichelpline.com/clinical-feed/pubmed-42674818"
content_type: "clinical_feed_article"
specialty: "Oncology"
source_name: "PubMed / NCBI"
source_url: "https://pubmed.ncbi.nlm.nih.gov/42674818/"
doi: "10.21873/cgp.20614"
published_at: "2026-09-01T00:00:00.000Z"
evidence_level: "Journal Article"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Multi-omics Characterization of the Immune Microenvironment in Colorectal Cancer
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/pubmed-42674818
- **Specialty:** [Oncology](https://medichelpline.com/clinical-feed/oncology.md)
- **Primary Source:** PubMed / NCBI
- **Source URL:** [Original Journal Publication](https://pubmed.ncbi.nlm.nih.gov/42674818/)
- **DOI:** [10.21873/cgp.20614](https://doi.org/10.21873%2Fcgp.20614)
- **Published At:** 2026-09-01T00:00:00.000Z
- **Evidence Rating:** Journal Article
## Executive GIST (TL;DR)
- This study used an integrated **multi-omics** approach to profile the immune microenvironment of human **colorectal cancer** (CRC), combining in-house structural variation, DNA methylation, chromatin accessibility, proteomic, and phosphoproteomic data with TCGA transcriptomics. - Analyses focused on 1,539 immune-related genes (IRGs) associated with **CD4+ T cells**, **B cells**, and **natural killer (NK) cells** to identify molecular changes linked to immune infiltration. - The authors observed higher infiltration of CD4+ T cells, B cells, and NK cells associated with CRC samples in their analyses. - IRGs showed widespread alterations across genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic layers, indicating multilayered immune remodelling in CRC. - Four candidate **hub genes** emerged: **IL10**, **LEP**, **ITGAM**, and **EGFR**, highlighting immune regulation, metabolism, adhesion/innate immunity, and growth-factor signalling axes. - Notably, **EGFR phosphorylation** at residues **S991** and **T693** was significantly decreased in CRC samples based on phosphoproteomic data. - Candidate upstream transcription factors identified included **STAT2** and **HSF1**, implicated as regulators of altered immune-related gene expression. - **CDK2** was identified as a candidate upstream kinase associated with immune infiltration and with immune checkpoint expression changes, suggesting a possible signalling node linking cell-cycle kinases and immune regulation. - The study presents a systematic, multi-layered molecular map of immune microenvironment remodelling in CRC and proposes candidate regulatory molecules that could be explored as potential targets in future immunotherapy research. - Details such as cohort size, sample selection criteria, statistical metrics, and experimental protocols were not reported in the PubMed abstract and therefore are not available here.
## Clinical Analysis & Structured Key Points
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China.")[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#full-view-affiliation-2 "Department of Experimental Research, South China Hospital, Medical School, Shenzhen University, Shenzhen, P.R. China."), [Liewen Lin](https://pubmed.ncbi.nlm.nih.gov/?term=Lin+L&cauthor_id=42674818)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#full-view-affiliation-3 "Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People's Hospital, Second Clinical Medical College of Jinan University, Shenzhen, P.R. China."), [Yumei Chen](https://pubmed.ncbi.nlm.nih.gov/?term=Chen+Y&cauthor_id=42674818)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#full-view-affiliation-3 "Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People's Hospital, Second Clinical Medical College of Jinan University, Shenzhen, P.R. China."), [Ligang Xia](https://pubmed.ncbi.nlm.nih.gov/?term=Xia+L&cauthor_id=42674818)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#full-view-affiliation-3 "Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People's Hospital, Second Clinical Medical College of Jinan University, Shenzhen, P.R. China."), [Donge Tang](https://pubmed.ncbi.nlm.nih.gov/?term=Tang+D&cauthor_id=42674818)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#full-view-affiliation-3 "Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People's Hospital, Second Clinical Medical College of Jinan University, Shenzhen, P.R. China."), [Yong Dai](https://pubmed.ncbi.nlm.nih.gov/?term=Dai+Y&cauthor_id=42674818)[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#full-view-affiliation-4 "The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan, P.R. China.")[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#full-view-affiliation-5 "Comprehensive Health Industry Research Center, Southern University of Science and Technology Taizhou Research Institute, Taizhou, P.R. China."), [Wei Zhang](https://pubmed.ncbi.nlm.nih.gov/?term=Zhang+W&cauthor_id=42674818)[ 6 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#full-view-affiliation-6 "Department of Clinical Laboratory, Peking University Shenzhen Hospital, Shenzhen, P.R. China; w-z12@tsinghua.org.cn.")[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#full-view-affiliation-2 "Department of Experimental Research, South China Hospital, Medical School, Shenzhen University, Shenzhen, P.R. China.") Affiliations Expand ### Affiliations * 1 Department of Clinical Laboratory, Peking University Shenzhen Hospital, Shenzhen, P.R. China. * 2 Department of Experimental Research, South China Hospital, Medical School, Shenzhen University, Shenzhen, P.R. China. * 3 Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People's Hospital, Second Clinical Medical College of Jinan University, Shenzhen, P.R. China. * 4 The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan, P.R. China. * 5 Comprehensive Health Industry Research Center, Southern University of Science and Technology Taizhou Research Institute, Taizhou, P.R. China. * 6 Department of Clinical Laboratory, Peking University Shenzhen Hospital, Shenzhen, P.R. China; w-z12@tsinghua.org.cn. * PMID: **42674818** * DOI: [ 10.21873/cgp.20614 ](https://doi.org/10.21873/cgp.20614) Item in Clipboard # Multi-omics Investigations of Immune Microenvironment of Human Colorectal Cancer Hongwei Zeng et al. Cancer Genomics Proteomics. 2026 Sep-Oct. Show details Display options Display options Format Abstract PubMed PMID Cancer Genomics Proteomics Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Cancer+Genomics+Proteomics%22%5Bjour%5D&sort=date&sort_order=desc) * [ Search in NLM Catalog ](https://www.ncbi.nlm.nih.gov/nlmcatalog?term=%22Cancer+Genomics+Proteomics%22%5BTitle+Abbreviation%5D) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42674818/) . 2026 Sep-Oct;23(5):1021-1042. doi: 10.21873/cgp.20614. ### Authors [Hongwei Zeng](https://pubmed.ncbi.nlm.nih.gov/?term=Zeng+H&cauthor_id=42674818)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#short-view-affiliation-1 "Department of Clinical Laboratory, Peking University Shenzhen Hospital, Shenzhen, P.R. China.")[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#short-view-affiliation-2 "Department of Experimental Research, South China Hospital, Medical School, Shenzhen University, Shenzhen, P.R. China."), [Liewen Lin](https://pubmed.ncbi.nlm.nih.gov/?term=Lin+L&cauthor_id=42674818)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#short-view-affiliation-3 "Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People's Hospital, Second Clinical Medical College of Jinan University, Shenzhen, P.R. China."), [Yumei Chen](https://pubmed.ncbi.nlm.nih.gov/?term=Chen+Y&cauthor_id=42674818)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#short-view-affiliation-3 "Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People's Hospital, Second Clinical Medical College of Jinan University, Shenzhen, P.R. China."), [Ligang Xia](https://pubmed.ncbi.nlm.nih.gov/?term=Xia+L&cauthor_id=42674818)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#short-view-affiliation-3 "Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People's Hospital, Second Clinical Medical College of Jinan University, Shenzhen, P.R. China."), [Donge Tang](https://pubmed.ncbi.nlm.nih.gov/?term=Tang+D&cauthor_id=42674818)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#short-view-affiliation-3 "Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People's Hospital, Second Clinical Medical College of Jinan University, Shenzhen, P.R. China."), [Yong Dai](https://pubmed.ncbi.nlm.nih.gov/?term=Dai+Y&cauthor_id=42674818)[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#short-view-affiliation-4 "The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan, P.R. China.")[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#short-view-affiliation-5 "Comprehensive Health Industry Research Center, Southern University of Science and Technology Taizhou Research Institute, Taizhou, P.R. China."), [Wei Zhang](https://pubmed.ncbi.nlm.nih.gov/?term=Zhang+W&cauthor_id=42674818)[ 6 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#short-view-affiliation-6 "Department of Clinical Laboratory, Peking University Shenzhen Hospital, Shenzhen, P.R. China; w-z12@tsinghua.org.cn.")[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42674818/#short-view-affiliation-2 "Department of Experimental Research, South China Hospital, Medical School, Shenzhen University, Shenzhen, P.R. China.") ### Affiliations * 1 Department of Clinical Laboratory, Peking University Shenzhen Hospital, Shenzhen, P.R. China. * 2 Department of Experimental Research, South China Hospital, Medical School, Shenzhen University, Shenzhen, P.R. China. * 3 Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People's Hospital, Second Clinical Medical College of Jinan University, Shenzhen, P.R. China. * 4 The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan, P.R. China. * 5 Comprehensive Health Industry Research Center, Southern University of Science and Technology Taizhou Research Institute, Taizhou, P.R. China. * 6 Department of Clinical Laboratory, Peking University Shenzhen Hospital, Shenzhen, P.R. China; w-z12@tsinghua.org.cn. * PMID: **42674818** * DOI: [ 10.21873/cgp.20614 ](https://doi.org/10.21873/cgp.20614) Item in Clipboard Cite Display options Display options Format Abstract PubMed PMID ## 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. **Keywords:** Immune microenvironment; colorectal cancer; drug targets; multi-omics; phosphoproteome. Copyright © 2026 International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved. [PubMed Disclaimer](https://pubmed.ncbi.nlm.nih.gov/disclaimer/) ## MeSH terms * Colorectal Neoplasms* / genetics Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Colorectal+Neoplasms%2Fgenetics%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Colorectal+Neoplasms) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42674818/) * Colorectal Neoplasms* / immunology Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Colorectal+Neoplasms%2Fimmunology%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Colorectal+Neoplasms) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42674818/) * Colorectal Neoplasms* / metabolism Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Colorectal+Neoplasms%2Fmetabolism%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Colorectal+Neoplasms) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42674818/) * Colorectal Neoplasms* / pathology Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Colorectal+Neoplasms%2Fpathology%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Colorectal+Neoplasms) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42674818/) * Gene Expression Regulation, Neoplastic Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Gene+Expression+Regulation%2C+Neoplastic%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Gene+Expression+Regulation%2C+Neoplastic) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42674818/) * Genomics / methods Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Genomics%2Fmethods%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Genomics) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42674818/) * Humans Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Humans%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Humans) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42674818/) * Multiomics Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Multiomics%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Multiomics) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42674818/) * Proteomics* / methods Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Proteomics%2Fmethods%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in
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