Microsatellite Phenotype as a Guide for Immunotherapy in Colorectal Cancer: Current Status and Future Perspectives
Abstract
1. Introduction
2. TME Alterations Across Microsatellite Phenotypes and Immunotherapy Resistance Mechanisms
2.1. MSI-H/dMMR CRC
2.1.1. Primary or Acquired Immunotherapy Resistance in MSI-H/dMMR CRC Tumors
2.1.2. Loss of Antigen Presentation
2.1.3. Upregulation/Compensatory Induction of Alternate Inhibitory Receptors and Oncogenic Signaling Pathway
2.1.4. Tumor Microenvironment (TME) Remodeling
2.2. MSS/pMMR CRC Phenotype and Resistance Mechanisms
2.3. Exception of the Dichotomy Between MSS/pMMR and MSI-H/dMMR-CRC
3. Differential Responses to ICIs in MSI-H/dMMR and MSS/pMMR CRC
3.1. ICIs in Metastatic MSI-H/dMMR CRC
3.1.1. Single-Agent PD-1 Blockade (Pembrolizumab) in Metastatic MSI-H/dMMR CRC
3.1.2. Combinational Immune Checkpoint Blockade (Nivolumab ± Ipilimumab) in Metastatic MSI-H/dMMR CRC
3.2. ICIs in Metastatic MSS/pMMR-CRC
4. Therapeutic Strategies to Enhance Immunotherapy Efficacy in MSS/pMMR CRC-Cold-to-Hot Concept
4.1. ICI Plus Chemotherapy
4.2. Double Checkpoint Inhibitory Strategy
4.3. ICI + Anti-Angiogenic Agents
4.4. ICI + Targeted Pathway Inhibitors
4.5. ICI + Radiation Therapy
4.6. Vaccines, Oncolytic Viruses, and Adoptive Cell Therapy
4.7. Bispecific Antibodies and Other Immune Modulators
5. Beyond MSI: Future Biomarkers of ICI Responsiveness in CRC Toward Precision Immunotherapy
5.1. Clinically Validated Biomarkers
5.2. Emerging Biomarkers
5.2.1. TMB
5.2.2. Polymerase ε and Polymerase δ (POLE/POLD1) Mutations
5.2.3. PD-L1 Expression
5.2.4. Circulating Tumor DNA(ctDNA) and Immunotherapy Response
5.2.5. Microbiome Composition
6. Emerging and Future Directions in CRC Treatment Management
7. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
| APM | Antigen Presentation Machinery |
| B2M | β2-microglobulin |
| BiTEs | Bispecific T-cell Engagers |
| CAFs | Cancer-Associated Fibroblasts |
| CAR-T | Chimeric Antigen Receptor T cells |
| CEA | Carcinoembryonic Antigen |
| CIMP | CpG Island Methylator Phenotype |
| CRC | Colorectal Cancer |
| CTLA-4 | Cytotoxic T-Lymphocyte-Associated Protein 4 |
| ctDNA | Circulating Tumor DNA |
| DCs | Dendritic Cells |
| dMMR | Deficient Mismatch Repair |
| DNA | Deoxyribonucleic Acid |
| EGFR | Epidermal Growth Factor Receptor |
| FDA | Food and Drug Administration |
| FOLFIRI | Folinic Acid + Fluorouracil + Irinotecan |
| FOLFOX | Folinic Acid + Fluorouracil + Oxaliplatin |
| HLA | Human Leukocyte Antigen |
| ICI/ICIs | Immune Checkpoint Inhibitor(s) |
| IFN-γ | Interferon-gamma |
| ITIM | Immunoreceptor Tyrosine-based Inhibitory Motif |
| ITSM | Immunoreceptor Tyrosine-based Switch Motif |
| JAK | Janus Kinase |
| LAG-3 | Lymphocyte Activation Gene-3 |
| MAPK | Mitogen-Activated Protein Kinase |
| mCRC | Metastatic Colorectal Cancer |
| MDSCs | Myeloid-Derived Suppressor Cells |
| MHC-I | Major Histocompatibility Complex Class I |
| MHC-II | Major Histocompatibility Complex Class II |
| MLH1 | MutL Homolog 1 |
| MMR | Mismatch Repair |
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| Feature | MSI-H/dMMR (Immune-Hot) | MSS/pMMR (Immune-Cold) |
|---|---|---|
| TMB/neoantigens | ↑ TMB ↑ neoantigen load | ↓ TMB ↓ neoantigens |
| Immune infiltration | ↑ Dense CD8+ T cells, NK cells, Th1 cells | ↓ Poor effector T-cell infiltration enriched suppressive cells, MDSCs, Tregs, TAMs (M2) |
| Inflammation | Active IFN-γ signaling, CXCL9/10 production | ↓ |
| Immune checkpoints | ↑ PD-1/PD-L1 expression | ↓ |
| TME profile | Inflamed, immune-active | Immunosuppressive, immune-cold |
| Main resistance mechanisms | ↑ T-cell exhaustion, B2M/JAK mutations, immunoediting (in subsets) | ↑ WNT/β-catenin, MAPK, TGF-β signaling, stromal exclusion, VEGF-driven suppression |
| Key suppressive factors | ↑ MDSCs, Tregs, TAMs (M2) | ↑ Desmoplasia, MDSCs, Tregs, TAMs (M2) |
| Response to ICIs | ↑ Strong | ↓ Poor |
| Category | Therapeutic Strategy | Examples | Current Status in MSI-H/dMMR CRC | Actions/Limitations |
|---|---|---|---|---|
| MSI-H/dMMR CRC | ||||
| SOC | PD-1 blockade | Pembrolizumab | Approved first-line treatment for metastatic MSI-H/dMMR CRC | Durable responses due to high TMB, abundant neoantigens, and inflamed TME |
| Guideline-supported options | PD-1 ± CTLA-4 blockade | Nivolumab ± Ipilimumab | Recommended for mCRC in selected cases | Enhances T-cell activation and improves response durability |
| Strategy | Approaches | Development Stage | Evidence | Main Objective |
|---|---|---|---|---|
| ICI + Chemotherapy | FOLFOX/FOLFIRI + PD-1/PD-L1 inhibitors | Clinical | Mixed | Enhance antigen release and immune activation |
| Dual Checkpoint Blockade | Botensilimab + Balstilimab | Clinical | Engouraging | Simultaneous activation of innate and adaptive immunity |
| ICI + Anti-Angiogenic Therapy | Bevacizumab-, Regorafenib-, or Fruquintinib-based combinations | Clinical | Promising | Normalize vasculature and reduce immune suppression |
| ICI + Targeted Therapy | MEK, EGFR, or TGF-β inhibitors | Clinical | Overcome tumor-intrinsic immune resistance | |
| ICI + Radiotherapy | PD-1/PD-L1 inhibitor combinations | Clinical | Promote antigen release and immune priming | |
| Vaccines and Oncolytic Viruses | Neoantigen vaccines, viral therapies | Early clinical development | Exploratory | Generate tumor-specific immune responses |
| Adoptive Cell Therapy | CAR-T cells, TCR-engineered T cells, TILs | Early clinical development | Enhance antigen-specific T-cell activity | |
| Bispecific Antibodies (BiTEs) | Cibisatamab and related agents | Early clinical development | Redirect T cells toward tumor cells | |
| Other Immune Modulators | OX40, 4-1BB, LAG-3, TIM-3 targeting agents | Early clinical development | Augment anti-tumor immune responses |
| Clinical Setting | Indications | Recommendations | Key Considerations |
|---|---|---|---|
| Universal MSI/MMR Testing | All newly diagnosed CRC cases | MMR immunohistochemistry (IHC) and/or PCR/NGS-based MSI testing | Identifies MSI-H/dMMR tumors and supports Lynch syndrome screening |
| Stage II MSI-H/dMMR CRC | Localized disease | Individualized adjuvant treatment decisions | Favorable prognosis; limited benefit from adjuvant 5-FU-based chemotherapy |
| Metastatic MSI-H/dMMR CRC | Advanced disease | First-line PD-1 blockade (e.g., pembrolizumab); nivolumab ± ipilimumab in selected cases | Potential for durable responses; monitor immune-related adverse events |
| Metastatic MSS/pMMR CRC | Advanced disease | Prioritize clinical trial enrollment | Standard chemotherapy and targeted therapies remain the backbone of treatment |
| Lynch Syndrome | Suspected or confirmed hereditary disease | Genetic counseling and surveillance programs | Family screening, risk assessment, and cancer prevention |
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Koustas, E.; Trifylli, E.-M.; Oraiopoulos, V.; Karamouzis, M.V.; Sarantis, P. Microsatellite Phenotype as a Guide for Immunotherapy in Colorectal Cancer: Current Status and Future Perspectives. Genes 2026, 17, 674. https://doi.org/10.3390/genes17060674
Koustas E, Trifylli E-M, Oraiopoulos V, Karamouzis MV, Sarantis P. Microsatellite Phenotype as a Guide for Immunotherapy in Colorectal Cancer: Current Status and Future Perspectives. Genes. 2026; 17(6):674. https://doi.org/10.3390/genes17060674
Chicago/Turabian StyleKoustas, Evangelos, Eleni-Myrto Trifylli, Vaios Oraiopoulos, Michalis V. Karamouzis, and Panagiotis Sarantis. 2026. "Microsatellite Phenotype as a Guide for Immunotherapy in Colorectal Cancer: Current Status and Future Perspectives" Genes 17, no. 6: 674. https://doi.org/10.3390/genes17060674
APA StyleKoustas, E., Trifylli, E.-M., Oraiopoulos, V., Karamouzis, M. V., & Sarantis, P. (2026). Microsatellite Phenotype as a Guide for Immunotherapy in Colorectal Cancer: Current Status and Future Perspectives. Genes, 17(6), 674. https://doi.org/10.3390/genes17060674

