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Updated: Jun 21, 2026
Visualization, Quantification, and Mapping of Immune Cell Populations in the Tumor Microenvironment
Published on: March 25, 2020
Dissecting T-cell exhaustion heterogeneity and immune ecosystem dynamics in colorectal cancer through multi-omics
Zhijing Zhang1,2, Peng Ouyang3, Kai Cui2
1Department of General Surgery, The First Affiliated Hospital of Jinan University, 613 W. Huangpu Avenue, Guangzhou, 510630, China.
Background:
Immunotherapy has shown limited efficacy in a substantial subset of CRC patients, yet the mechanisms underlying therapeutic resistance remain incompletely understood. T-cell exhaustion (TEX) in the tumor microenvironment has been identified as a pivotal driver of immune evasion and tumor progression. Dissecting its contribution to CRC is essential for the development of rational therapeutic strategies.
Methods:
We integrated scRNA-seq and bulk transcriptomic data to identify CD8⁺ T-cell exhaustion core genes via hdWGCNA and ten machine learning algorithms, constructed a multivariate Cox-based TEX score model validated across independent cohorts and immunotherapy datasets, and experimentally confirmed our findings by RT-qPCR, Western blot, and quantitative multiplex immunofluorescence in clinical CRC specimens.
Results:
Our single-cell analysis revealed a continuum of intra-tumoral CD8⁺ T-cell exhaustion states, identified a five-gene TEX score (KLF3, LMNA, SLC2A3, ARL4C, TIMP1) that predicted poor prognosis and an immunosuppressive microenvironment. Further experimental validation confirmed the differential expression and spatial co-localization with CD8⁺ T cells in clinical specimens.
Conclusions:
Our findings implicate TEX as a central mediator of immunotherapy resistance in CRC, offering a clinically actionable framework for patient stratification and therapeutic decision-making.
Insights
T-cell exhaustion (TEX) drives immunotherapy resistance in colorectal cancer (CRC). A novel five-gene TEX score predicts poor prognosis, aiding patient stratification for better treatment strategies.
Area of Science:
- Oncology
- Immunology
- Genomics
Background:
- Immunotherapy exhibits limited efficacy in a significant portion of colorectal cancer (CRC) patients.
- Mechanisms of therapeutic resistance in CRC are not fully understood.
- T-cell exhaustion (TEX) in the tumor microenvironment is a key factor in immune evasion and tumor progression.
Purpose of the Study:
- To investigate the role of T-cell exhaustion (TEX) in colorectal cancer (CRC).
- To identify core genes associated with CD8+ T-cell exhaustion.
- To develop a predictive model for immunotherapy response in CRC patients.
Main Methods:
- Integrated single-cell RNA sequencing (scRNA-seq) and bulk transcriptomic data.
- Utilized hdWGCNA and ten machine learning algorithms to identify core exhaustion genes.
- Constructed and validated a multivariate Cox-based TEX score model across independent cohorts and immunotherapy datasets.
- Experimentally validated findings using RT-qPCR, Western blot, and quantitative multiplex immunofluorescence.
Main Results:
- Identified a continuum of intra-tumoral CD8+ T-cell exhaustion states.
- Developed a five-gene TEX score (KLF3, LMNA, SLC2A3, ARL4C, TIMP1) that predicts poor prognosis.
- The TEX score correlates with an immunosuppressive tumor microenvironment.
- Confirmed differential gene expression and spatial co-localization with CD8+ T cells in clinical CRC specimens.
Conclusions:
- T-cell exhaustion (TEX) is implicated as a central mediator of immunotherapy resistance in colorectal cancer (CRC).
- The developed TEX score offers a clinically actionable framework for patient stratification.
- Findings support improved therapeutic decision-making for CRC patients undergoing immunotherapy.
