Checkpoint molecules on infiltrating immune cells in colorectal tumor microenvironment

The Expression Patterns of Immune Checkpoint Molecules in Colorectal Cancer: An Analysis Based on Microsatellite Status

Recently, immunotherapy has arisen as a novel treatment approach for patients with colorectal cancer (CRC), but the effectiveness of immunotherapy varies in these patients. We hypothesized that immune checkpoint molecules (ICMs), which are the targets of immunotherapy, are often exhibited concomitantly. Our objective was to investigate the patterns of ICM expression in patients with CRC and the differences in ICM expression based on microsatellite instability status. The immunohistochemical expression of programmed cell death protein 1 (PD-1), programmed cell death ligand 1 (PD-L1), T cell immunoglobulin and mucin-domain containing-3 (TIM-3), and lymphocyte-activation gene 3 (LAG-3) in the tumor center and periphery was assessed in patients with non-metastatic colorectal cancer. We enrolled 83 patients with CRC: a total of 40 microsatellite-stable (MSS) and 43 microsatellite-instability-high (MSI-H) cancer patients. PD-L1 was more frequently expressed in the tumor center in the MSI-H patients with than that in the MSS patients (18 [41.9%] vs. 3 [7.5%], respectively; p < 0.001), and the same trend was observed for TIM-3 expression (30 [69.8%] vs. 19 [47.5%], respectively; p = 0.047). The concomitant expression of two or more ICMs was more frequently observed than no expression or the expression of a single molecule in both the MSS and MSI-H groups; a total of 34 (79.7%) patients with MSI-H cancer and 23 (57.5%) with MSS cancer showed ICM expression at the tumor center, whereas 34 (79.7%) patients with MSI-H cancer and 22 (55%) with MSS cancer showed expression at the tumor periphery. Patients with the genetic characteristics of MSI-H cancer showed higher expression levels of ICMs than those in patients with MSS cancer, and predominantly, two or more ICMs were concurrently expressed. Our findings highlight the potential efficacy of the dual-blockade approach in immunotherapy, particularly in patients with MSI-H CRC.

Applications of single-cell omics for chimeric antigen receptor T cell therapy

Chimeric antigen receptor (CAR) T cell therapy is a promising cancer treatment modality. The breakthroughs in CAR T cell therapy were, in part, possible with the help of cell analysis methods, such as single-cell analysis. Bulk analyses have provided invaluable information regarding the complex molecular dynamics of CAR T cells, but their results are an average of thousands of signals in CAR T or tumour cells. Since cancer is a heterogeneous disease where each minute detail of a subclone could change the outcome of the treatment, single-cell analysis could prove to be a powerful instrument in deciphering the secrets of tumour microenvironment for cancer immunotherapy. With the recent studies in all aspects of adoptive cell therapy making use of single-cell analysis, a comprehensive review of the recent preclinical and clinical findings in CAR T cell therapy was needed. Here, we categorized and summarized the key points of the studies in which single-cell analysis provided insights into the genomics, epigenomics, transcriptomics and proteomics as well as their respective multi-omics of CAR T cell therapy.

Construction of a 12-gene prognostic model for colorectal cancer based on heat shock protein-related genes

Some heat shock proteins (HSPs) have been shown to influence tumor prognosis, but their prognostic significance in colorectal cancer (CRC) remains unclear. This study explored the prognostic significance of HSP-related genes in CRC. Transcriptional data and clinical information of CRC patients were obtained from The Cancer Genome Atlas (TCGA) database, and a literature search was conducted to identify HSP-related genes. Using Least Absolute Selection and Shrinkage Operator (LASSO) regression and univariate/multivariate Cox regression analyses, 12 HSP-related genes demonstrating significant associations with CRC survival were successfully identified and employed to formulate a predictive risk score model. The efficacy and precision of this model were validated utilizing TCGA and Gene Expression Omnibus (GEO) datasets, demonstrating its reliability in CRC prognosis prediction. gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed significant disparities between high- and low-risk groups in chromatin remodeling biological functions and neutrophil extracellular trap formation pathways. Single sample gene set enrichment analysis (ssGSEA) further revealed differences in immune cell types and immune functional status between the two risk groups. Differential analysis showed higher expression of immune checkpoints within the low-risk group, while the high-risk group exhibited notably higher Tumor Immune Dysfunction and Exclusion (TIDE) scores. Additionally, we predicted the sensitivity of different prognosis risk patients to various drugs, providing potential drug choices for tailored treatment. Combined, our study successfully crafted a novel CRC prognostic model that can effectively predict patient survival, immune landscape, and treatment response, providing important support and guidance for CRC patient prognosis.

The exploration of mitochondrial-related features helps to reveal the prognosis and immunotherapy methods of colorectal cancer

BACKGROUND

Cancer cell survival, proliferation, and metabolism are all intertwined with mitochondria. However, a complete description of how the features of mitochondria relate to the tumor microenvironment (TME) and immunological landscape of colorectal cancer (CRC) has yet to be made. We performed subgroup analysis on CRC patient data obtained from the databases using non-negative matrix factorization (NMF) clustering. Construct a prognostic model using the mitochondrial-related gene (MRG) risk score, and then compare it to other models for accuracy. Comprehensive analyses of the risk score, in conjunction with the TME and immune landscape, were performed, and the relationship between the model and different types of cell death, radiation and chemotherapy, and drug resistance was investigated. Results from immunohistochemistry and single-cell sequencing were utilized to verify the model genes, and a drug sensitivity analysis was conducted to evaluate possible therapeutic medicines. The pan-cancer analysis is utilized to further investigate the role of genes in a wider range of malignancies.

METHODS AND RESULTS

We found that CRC patients based on MRG were divided into two groups with significant differences in survival outcomes and TME between groups. The predictive power of the risk score was further shown by building a prognostic model and testing it extensively in both internal and external cohorts. Multiple immune therapeutic responses and the expression of immunological checkpoints demonstrate that the risk score is connected to immunotherapy success. The correlation analysis of the risk score provide more ideas and guidance for prognostic models in clinical treatment.

CONCLUSION

The TME, immune cell infiltration, and responsiveness to immunotherapy in CRC were all thoroughly evaluated on the basis of MRG features. The comparative validation of multiple queues and models combined with clinical data ensures the effectiveness and clinical practicality of MRG features. Our studies help clinicians create individualized treatment programs for individuals with cancer.

NIFK as a potential prognostic biomarker in colorectal cancer correlating with immune infiltrates

BACKGROUND

Immune-related initiation, progress, metastasis and sensitivity to treatment associated with poor prognosis of patients with colorectal cancer (CRC). The role of Nucleolar protein interacting with the FHA domain of MKI67 (NIFK) in CRC remained to be investigated. We explore whether NIFK correlates with tumor immune infiltration and plays an important role in CRC patient prognosis.

METHODS

The data of samples involved in our study was obtained from TCGA and GEO and samples for protein expression detection and clinical information analysis were obtained from our hospital. NIFK expression, association with patient prognosis, correlation with infiltration of immune cells and its correlated genes involved in signaling pathways were analyzed using bioinformatics method along with experimental validation and clinical correlation analysis.

RESULTS

Results indicated that the expression of NIFK in tumor tissues was significantly increased compared with normal samples. colon and rectal cancer patients with high NIFK expression have poor survival compared with those with low NIFK expression. Results of cell experiments indicated that NIFK is positively correlated with cell proliferation and migration in CRC. NIFK negatively correlated with T cell CD8+, Tregs, Neutrophil and macrophage significantly. DARS and NKRF were positively correlated with NIFK and DARS correlated with CD8 + T cell, CD4 + T cell, macrophage and Neutrophil, NKRF correlated with CD8 + T cell, CD4 + T cell and macrophage in colon and rectal cancer. NIFK along with its correlated genes as DARS and NKRF were involved in Wnt, PI3K-Akt, NF-κB signaling and Intestinal immune network for lgA production.

CONCLUSIONS

Our results suggested that NIFK might be a biomarker associated with poor prognosis of CRC patients, and it would be a potential target for CRC therapy.

T Cells in Colorectal Cancer: Unravelling the Function of Different T Cell Subsets in the Tumor Microenvironment

Therapeutic options for metastatic colorectal cancer (mCRC) are very limited, and the prognosis using combination therapy with a chemotherapeutic drug and a targeted agent, e.g., epidermal growth factor receptor or tyrosine kinase, remains poor. Therefore, mCRC is associated with a poor median overall survival (mOS) of only 25-30 months. Current immunotherapies with checkpoint inhibitor blockade (ICB) have led to a substantial change in the treatment of several cancers, such as melanoma and non-small cell lung cancer. In CRC, ICB has only limited effects, except in patients with microsatellite instability-high (MSI-H) or mismatch repair-deficient (dMMR) tumors, which comprise about 15% of sporadic CRC patients and about 4% of patients with metastatic CRC. The vast majority of sporadic CRCs are microsatellite-stable (MSS) tumors with low levels of infiltrating immune cells, in which immunotherapy has no clinical benefit so far. Immunotherapy with checkpoint inhibitors requires the presence of infiltrating T cells into the tumor microenvironment (TME). This makes T cells the most important effector cells in the TME, as evidenced by the establishment of the immunoscore-a method to estimate the prognosis of CRC patients. The microenvironment of a tumor contains several types of T cells that are anti-tumorigenic, such as CD8⁺ T cells or pro-tumorigenic, such as regulatory T cells (Tregs) or T helper 17 (Th17) cells. However, even CD8⁺ T cells show marked heterogeneity, e.g., they can become exhausted, enter a state of hyporesponsiveness or become dysfunctional and express high levels of checkpoint molecules, the targets for ICB. To kill cancer cells, CD8⁺ T cells need the recognition of the MHC class I, which is often downregulated on colorectal cancer cells. In this case, a population of unconventional T cells with a γδ T cell receptor can overcome the limitations of the conventional CD8⁺ T cells with an αβT cell receptor. γδ T cells recognize antigens in an MHC-independent manner, thus acting as a bridge between innate and adaptive immunity. Here, we discuss the effects of different T cell subsets in colorectal cancer with a special emphasis on γδ T cells and the possibility of using them in CAR-T cell therapy. We explain T cell exclusion in microsatellite-stable colorectal cancer and the possibilities to overcome this exclusion to enable immunotherapy even in these "cold" tumors.