Identifying immune cells-related phenotype to predict immunotherapy and clinical outcome in gastric cancer

m6A regulator-mediated methylation modifications define the immune infiltration characteristics of the tumor microenvironment in prostate adenocarcinoma

Prostate adenocarcinoma (PRAD) persists as the predominant non-cutaneous malignancy diagnosed in males, which is a primary contributor to cancer-related mortality globally. It is reported that the progression of prostate adenocarcinoma is associated with various factors, including genetics, age, obesity, etc. Contemporary research indicates that epigenetic inheritance is a leading factor in the initiation and progression of cancer. RNA methylation modification is the most prevalent form of RNA modification, with N6-methyladenosine (m6A) representing the most common modification on mRNA and lncRNAs. However, the biological mechanisms underpinning this association in prostate adenocarcinoma and its correlation with patients' prognostic survival outcomes remain elusive. Our study elucidates the roles of the tumor microenvironment (TME) and genetic mutations during the initiation and progression of prostate adenocarcinoma. Additionally, we stratify prostate adenocarcinoma into distinct subtypes based on m6A scoring. This approach enhances our comprehension of the functional role of m6A in the development of prostate adenocarcinoma, offering novel insights into the clinical strategies and understanding the biological significance between prostate adenocarcinoma and m6A modification.

Maturity and density of tertiary lymphoid structures associate with tumor metastasis and chemotherapy response

Background

Tertiary Lymphoid Structures (TLSs) are abnormal clusters of immune cells that form in tissues not normally associated with the immune system, usually in cases of long-lasting inflammation, like cancer. TLSs have been suggested as a potential prognostic indicator in various cancer types.

Methods

We retrospectively enrolled 223 gastric cancer (GC) patients who had surgical resections in this study. We utilized hematoxylin and eosin (HE) staining to detect the presence, abundance, and maturity of TLSs. In serial sections, we used immunohistochemistry to examine the cellular composition of TLSs.

Results

The pathological review identified TLSs in 95.1% of the tumors, lymphoid aggregates in 79.8%, primary follicles in 45.7%, and lymphoid aggregates in 95.1% of the cases. Based on Kaplan-Meier curves, the maturation and abundance of TLSs contributed to longer disease-free survival (DFS) and overall survival (OS). In addition, the density of TLSs was strongly associated with the occurrence of tumor metastases and the response to adjuvant chemotherapy.

Conclusions

We validated the prognostic value of TLSs in GC patients in both independent cohorts, and the maturity and density of TLS correlated with tumor metastasis. In addition, TLS may reflect sustained antitumor potency, which has important implications for adjuvant chemotherapy.

New insights into immune cells in cancer immunotherapy: from epigenetic modification, metabolic modulation to cell communication

Cancer is one of the leading causes of death worldwide, and more effective ways of attacking cancer are being sought. Cancer immunotherapy is a new and effective therapeutic method after surgery, radiotherapy, chemotherapy, and targeted therapy. Cancer immunotherapy aims to kill tumor cells by stimulating or rebuilding the body's immune system, with specific efficiency and high safety. However, only few tumor patients respond to immunotherapy and due to the complex and variable characters of cancer immune escape, the behavior and regulatory mechanisms of immune cells need to be deeply explored from more dimensions. Epigenetic modifications, metabolic modulation, and cell-to-cell communication are key factors in immune cell adaptation and response to the complex tumor microenvironment. They collectively determine the state and function of immune cells through modulating gene expression, changing in energy and nutrient demands. In addition, immune cells engage in complex communication networks with other immune components, which are mediated by exosomes, cytokines, and chemokines, and are pivotal in shaping the tumor progression and therapeutic response. Understanding the interactions and combined effects of such multidimensions mechanisms in immune cell modulation is important for revealing the mechanisms of immunotherapy failure and developing new therapeutic targets and strategies.

Investigation of GPR143 as a promising novel marker for the progression of skin cutaneous melanoma through bioinformatic analyses and cell experiments

BACKGROUND

Skin cutaneous melanoma (SKCM) is an aggressive and life-threatening skin cancer. G-protein coupled receptor 143 (GPR143) belongs to the superfamily of G protein-coupled receptors.

METHODS

We used the TCGA, GTEx, CCLE, and the Human Protein Atlas databases to examine the mRNA and protein expression of GPR143. In addition, we performed a survival analysis and evaluated the diagnostic efficacy using the Receiver-Operating Characteristic (ROC) curve. Through CIBERSORT, R programming, TIMER, Gene Expression Profiling Interactive Analysis, Sangerbox, and Kaplan-Meier plotter database analyses, we explored the relationships between GPR143, immune infiltration, and gene marker expression of immune infiltrated cells. Furthermore, we investigated the proteins that potentially interact with GPR143 and their functions using R programming and databases including STRING, GeneMANIA, and GSEA. Meanwhile, the cBioPortal, UALCNA, and the MethSurv databases were used to examine the genomic alteration and methylation of GPR143 in SKCM. The Connectivity Map database was used to discover potentially effective therapeutic molecules against SKCM. Finally, we conducted cell experiments to investigate the potential role of GPR143 in SKCM.

RESULTS

We demonstrated a significantly high expression level of GPR143 in SKCM compared with normal tissues. High GPR143 expression and hypomethylation status of GPR143 were associated with a poorer prognosis. ROC analysis showed that the diagnostic efficacy of the GPR143 was 0.900. Furthermore, GPR143 expression was significantly correlated with immune infiltration in SKCM. We identified 20 neighbor genes and the pathways they enriched were anabolic process of pigmentation, immune regulation, and so on. Genomic alteration analysis revealed significantly different copy number variations related to GPR143 expression in SKCM, and shallow deletion could lead to high expression of GPR143. Ten potential therapeutic drugs against SKCM were identified. GPR143 knockdown inhibited melanoma cell proliferation, migration, and colony formation while promoting apoptosis.

CONCLUSIONS

Our findings suggest that GPR143 serves as a novel diagnostic and prognostic biomarker and is associated with the progression of SKCM.

Comprehensive Analysis Reveals the Potential Roles of CDKN3 in Pancancer and Verification in Endometrial Cancer

Background

Cyclin-dependent kinase inhibitor 3 (CDKN3) has been studied in many cancers. However, the comprehensive and systematic pancancer analysis of CDKN3 genes is still lacking.

Methods

Data were downloaded from online databases. R was used for analysis of the differential expression and gene alteration of CDKN3 and of the associations between CDKN3 expression and survival, signaling pathways, and drug sensitivity. Clinical samples and in vitro experiments were selected for verification.

Results

CDKN3 expression was higher in most types of cancers, and this phenotype was significantly correlated with poor survival. CDKN3 showed gene alterations and copy number alterations in many cancers and associated with some immune-related pathways and factors. Drug sensitivity analysis elucidated that CDKN3 could be a useful marker for therapy selection. Clinical samples elucidated CDKN3 expressed high in endometrial cancer tissue. In vitro studies showed that CDKN3 induced pro-tumor effect in immune environment and facilitated endometrial cancer cell proliferation and G1/S phase transition.

Conclusion

CDKN3 has been shown to be highly expressed in most types of cancers and promoted cancer cell progression. CDKN3 may serve as a novel marker in clinical diagnosis, treatment, and prognosis prediction in future.