Comparative Analysis and in vitro Experiments of Signatures and Prognostic Value of Immune Checkpoint Genes in Colorectal Cancer

Comprehensive analysis of signaling lymphocyte activation molecule family as a prognostic biomarker and correlation with immune infiltration in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is a common type of kidney cancer and accounts for 2-3% of all cancer cases. Furthermore, a growing number of immunotherapy approaches are being used in antitumor treatment. Signaling lymphocyte activation molecule family (SLAMF) members have been well studied in several cancers, whereas their roles in ccRCC have not been investigated. The present study comprehensively assessed the molecular mechanisms of SLAMF members in ccRCC, performed using The Cancer Genome Atlas database, with analysis of gene transcription, prognosis, biological function, clinical features, tumor-associated immune cells and the correlation with programmed cell death protein 1/programmed death-ligand 1 immune checkpoints. Simultaneously, the Tumor Immune Dysfunction and Exclusion algorithm was used to predict the efficacy of immune checkpoint blockade (ICB) therapy in patients with high and low SLAMF expression levels. The results demonstrated that all SLAMF members were highly expressed in ccRCC, and patients with high expression levels of SLAMF1, 4, 7 and 8 had a worse prognosis that those with low expression. SLAMF members were not only highly associated with immune activation but also with immunosuppressive agents. The level of immune cell infiltration was associated with the prognosis of patients with ccRCC with high SLAMF expression. Moreover, high ICB response rates were observed in patients with high expression levels of SMALF1 and 4. In summary, SLAMF members may serve as future potential biomarkers for predicting the prognosis of ccRCC and emerge as a novel immunotherapy target.

Comprehensive analysis of clinical prognosis and biological significance of CNIH4 in cervical cancer

BACKGROUND

Cornichon homolog 4 (CNIH4) belongs to the CNIH family. It functions as an oncogene in many tumors. However, CNIH4's significance in the immune landscape and its predictive potential in cervical cancer (CESC) is unexplored.

METHODS

CNIH4 levels and its effect on the survival of patients with CESC were evaluated using data retrieved from The Cancer Genome Atlas (TCGA). The oncogenic effect of CNIH4 in CESC was determined using small interfering RNA-mediated transfected cell lines and tumorigenesis experiments in animal models.

RESULTS

Higher expression of CNIH4 was found in advanced tumor and pathological stages, as well as lymph node metastasis. CNIH4 expression correlated positively with the infiltration of macrophages M2 and resting dendritic cells into the affected tissue. Additionally, functional enrichment of RNA-sequencing of CNIH4-knocked down CESC cell lines showed the association of CNIH4 to the PI3K-Akt signaling pathway. Single-sample gene set enrichment analysis highlighted several immune pathways that were elevated in the CESC samples with enhanced levels of CNIH4, including Type-I and Type-II IFN-response pathways. The impact of CNIH4 on drug sensitivity was further assessed using the GDSC database. As CNIH4 is linked to the immune landscape in CESC, this study determined a four-gene risk prediction signature utilizing CNIH4-related immunomodulators. The risk score quantified from the prediction signature was an independent predictive indicator in CESC. Receiver operating characteristic curve analysis verified the good predictive ability of the four-gene signature in TCGA-CESC cohort. Thus, the CNIH4-related model showed potential as an auxiliary TNM staging system tool.

CONCLUSION

CNIH4 may be an effective predictive biomarker for patients with cervical cancer, thus providing new ideas and research directions for CESC.

High expression of NOLC1 as an independent prognostic factor for survival in patients with colorectal cancer

BACKGROUND

As a phosphorylated protein, NOLC1 is mainly located in the nucleus and is highly expressed in a variety of tumors, participating in the regulation of cell proliferation and aging. This study further investigated the role of NOLC1 in colorectal cancer tumors, aiming to provide sufficient scientific evidence for the clinical treatment of colorectal cancer.

METHODS

We used TCGA, GEO, TNMplot, GEPIA, and other databases to explore the expression level of NOLC1 in colorectal cancer patients, as well as the correlation between the clinical characteristics of colorectal cancer patients and their expression, and conducted the prognostic analysis. Immunohistofluorescence (IHF) staining verified the analytical results. Subsequently, KEGG and GO enrichment analysis was used to identify the potential molecular mechanism of NOLC1 promoting the occurrence and development of colorectal cancer. The influence of NOLC1 expression on the immune microenvironment of colorectal cancer patients was further investigated using the TIMER database. GDSC database analysis was used to screen out possible anti-colorectal cancer drugs against NOLC1. Finally, we demonstrated the effect of NOLC1 on the activity and migration of colorectal cancer cells by Edu Cell proliferation assay and Wound Healing assay in vitro.

RESULTS

Our results suggest that NOLC1 is overexpressed in colorectal cancer, and that overexpression of NOLC1 is associated with relevant clinical features. NOLC1, as an independent risk factor affecting the prognosis of colorectal cancer patients, can lead to a poor prognosis of colorectal cancer. In addition, NOLC1 may be associated with MCM10, HELLS, NOC3L, and other genes through participating in Wnt signaling pathways and jointly regulate the occurrence and development of colorectal cancer under the influence of the tumor microenvironment and many other influencing factors. Related to NOLC1: Selumetinib, Imatinib, and targeted drugs such as Lapatinib have potential value in the clinical application of colorectal cancer. NOLC1 enhances the proliferation and migration of colorectal cancer cells.

CONCLUSIONS

High expression of NOLC1 as an independent prognostic factor for survival in patients with colorectal cancer. NOLC1 enhances the proliferation and migration of colorectal cancer cells. Further studies and clinical trials are needed to confirm the role of NOLC1 in the development and progression of colorectal cancer.

Microsatellite Instability and Immune Response: From Microenvironment Features to Therapeutic Actionability-Lessons from Colorectal Cancer

Microsatellite instability (MSI) can be found in 15-20% of all colorectal cancers (CRC) and is the key feature of a defective DNA mismatch repair (MMR) system. Currently, MSI has been established as a unique and pivotal biomarker in the diagnosis, prognosis, and treatment of CRC. MSI tumors display a strong lymphocytic activation and a shift toward a tumoral microenvironment restraining metastatic potential and ensuing in a high responsiveness to immunotherapy of MSI CRC. Indeed, neoplastic cells with an MMR defect overexpress several immune checkpoint proteins, such as programmed death-1 (PD-1) and programmed death-ligand 1(PD-L1), that can be pharmacologically targeted, allowing for the revival the cytotoxic immune response toward the tumor. This review aims to illustrate the role of MSI in the tumor biology of colorectal cancer, focusing on the immune interactions with the microenvironment and their therapeutic implications.

SLAM-family receptors come of age as a potential molecular target in cancer immunotherapy

The signaling lymphocytic activation molecule (SLAM) family receptors were discovered in immune cells for the first time. The SLAM-family receptors are a significant player in cytotoxicity, humoral immune responses, autoimmune diseases, lymphocyte development, cell survival, and cell adhesion. There is growing evidence that SLAM-family receptors have been involved in cancer progression and heralded as a novel immune checkpoint on T cells. Previous studies have reported the role of SLAMs in tumor immunity in various cancers, including chronic lymphocytic leukemia, lymphoma, multiple myeloma, acute myeloid leukemia, hepatocellular carcinoma, head and neck squamous cell carcinoma, pancreas, lung, and melanoma. Evidence has deciphered that the SLAM-family receptors may be targeted for cancer immunotherapy. However, our understanding in this regard is not complete. This review will discuss the role of SLAM-family receptors in cancer immunotherapy. It will also provide an update on recent advances in SLAM-based targeted immunotherapies.

Tumor tissue microorganisms are closely associated with tumor immune subtypes

Studies have found that different immune subtypes are present in the same tumor. Different tumor subtypes have different tumor microenvironments (TME). This means that the efficacy of immunotherapy in actual applications will, therefore, have different results. Existing tumor immune subtype studies have mostly focused on immune cells, stromal cells, genes and molecules without considering the presence of microbes. Some studies have shown that microflora can strongly promote many gastrointestinal cancers. The microbiome has, therefore, become an important biomarker and regulatory factor of cancer progression and therapeutic responses. In addition, the presence of microflora can strongly regulate the host immune system, indirectly affecting tumor growth. Taken together, it is important to study the relationships that develop among tumor tissue microorganisms, tumor immune subtype, and the TME. In this study, correlations between microbial abundance, immune cell infiltration, immune gene expression and tumor immune subtype were studied. To accomplish this, tissue microorganisms and immune cell ratios with significant differences between the different cancers were obtained by comparing 203 gastric cancer and intestinal cancer samples. Two immune subtypes of intestinal samples were obtained by K-means clustering algorithm and tissue microorganisms, immune cell ratios and immune-related genes with significant differences between different immune subtypes were screened through Wilcoxon rank sum test. The results showed that Clostridioides difficile, Aspergillus fumigatus, Yarrowia lipolytica, and Fusarium pseudograminearum were all closely associated with the identified tumor immune subtypes. Our open-source software is freely available from GitHub at https://github.com/gutmicrobes/IMM-subtype.git.

Prognostic Value and Correlation With Tumor Immune Infiltration of a Novel Metabolism-Related Gene Signature in Pancreatic Cancer

Background

Energy metabolism has been considered as one of the novel features of neoplasms. This study aimed to establish the prognostic signature for pancreatic cancer (PC) based on metabolism-related genes (MRGs).

Methods

We obtained MRGs from the Molecular Signatures Database (MSigDB) and gene sequence data in the Cancer Genome Atlas (TCGA) databases. Then, differentially expressed MRGs (DE-MRGs) were identified utilizing the R software. We built the prognostic model via multivariate Cox regression. Moreover, external validation of the prognostic signature was also performed. Nomogram was created to predict the overall survival (OS). Next, this study analyzed the prognostic value, clinical relationship, and metabolism-related signaling pathways of the prognostic signature. The role in tumor infiltration was further evaluated. Eventually, the expression level of the three MRGs along with the function of NT5E was validated.

Results

Twenty-two MRGs were chosen, eight of which were identified to be most significantly correlated with the prognosis of PC. Meanwhile, a 3-MRG prognostic signature was established, and we verified this prognostic model in two separate external cohorts. What is more, the nomogram was used to predict 1-/2-/3-year OS of PC patients. In addition, the immune cell infiltration and expression of immune checkpoint were significantly influenced by the risk score. Finally, three MRGs were highly expressed in PC cell lines, and NT5E was associated with the proliferation and migration ability of PC.

Conclusion

To sum up, the study established and validated a 3-MRG prognostic signature for PC, and the signature could be utilized to predict the prognosis and assist the individualized clinical management of patients with PC.

Association analysis of B7-H3 and B7-H4 gene single nucleotide polymorphisms in susceptibility to ankylosing spondylitis in eastern Chinese Han population

This study was conducted to describe the association between the genetic variation of the recently identified immune checkpoint molecules B7-H3 and B7-H4, and the susceptibility to ankylosing spondylitis (AS). Two single nucleotide polymorphisms (SNPs) of B7-H3 gene and three SNPs of B7-H4 gene were genotyped in 649 AS patients and 646 age- and sex-matched healthy controls. Allele, genotype frequencies and different inheritance models were performed to calculate odds ratios (ORs) and 95% confidence intervals (CIs), and the demographic and clinical parameters of patients were recorded. Our data indicated that B7-H4 rs10801935 and rs3738414 polymorphisms were correlated with AS susceptibility. In the stratification analyses, the minor A allele and GA genotype of B7-H4 rs3738414 increased the risk of AS in male patients (OR = 1.244, 95%CI = 1.026-1.508; OR = 1.453, 95%CI = 1.120-1.886, respectively). However, the association did not reach statistical significance after Bonferroni correction. Furthermore, haplotype analysis revealed that B7-H4 haplotype block TAG was a risk factor for the onset of AS (OR = 1.190, 95%CI = 1.020-1.389). These findings suggested that B7-H4 gene polymorphism may contribute to AS susceptibility in eastern Chinese Han population.