Identification of RNMT as an immunotherapeutic and prognostic biomarker: From pan-cancer analysis to lung squamous cell carcinoma validation.

Dysregulation of RNA guanine-7 methyltransferase (RNMT) plays a crucial role in the tumor progression and immune responses. However, the detailed role of RNMT in pan-cancer is still unknown. Bulk transcriptomic data of pan-cancer were obtained from the Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Cancer Cell Line Encyclopedia (CCLE) databases. Single-cell transcriptomic and proteomics data of lung squamous cell carcinoma (LUSC) were analyzed in the Tumor Immune Single-cell Hub 2 (TISCH2) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) databases, respectively. The correlation between RNMT expression and cancer prognosis was analyzed by Cox proportional hazards regression and Kaplan-Meier analyses. The correlation of RNMT expression with common immunoregulators, tumor mutation burden (TMB), microsatellite instability (MSI), mismatch repair (MMR), and DNA methyltransferase (DNMT) was analyzed. Additionally, the correlation between RNMT expression and immune infiltration level was evaluated. A total of 1287 machine learning combinations were used to construct prognostic models for LUSC. qRT-PCR and Western blot were used to validate the bioinformatics findings of RNMT upregulation in LUSC. RNMT was widely expressed across different cancers, with significant correlation to prognosis in cancers such as kidney chromophobe (KICH) (p = 0.0033, HR = 7.12), liver hepatocellular carcinoma (LIHC) (p = 0.01, HR = 1.41), and others. Notably, RNMT participates in the regulation of the tumor microenvironment. RNMT expression positively correlated with immune cell expression (Spearman's rank correlation, p < 0.05). Moreover, RNMT expression was strongly associated with immunoregulators, TMB, MSI, MMR, and DNMT in most cancer types. Notably, RNMT expression displayed excellent prognostic and immunological performance in LUSC. The expression of RNMT was mainly enriched in B cells of LUSC tissues. qRT-PCR and Western blot verified the high expression of RNMT in LUSC. RNMT expression widely correlated with prognosis and immune infiltration in various tumors, especially LUSC. The RNMT detection may provide a new idea for future tumor immune studies and treatment strategies.

Huang S ，Tan C ，Zheng J ，Huang Z ，Li Z ，Lv Z ，Chen W ，Chen M ，Yuan X ，Chen C ，Yan Q ... -  《-》

Multiomics analysis reveals the involvement of NET1 in tumour immune regulation and malignant progression.

Neuroepithelial cell transforming gene 1 (NET1) is a member of the Ras homologue family member A (RhoA) subfamily of guanine nucleotide exchange factors and a key protein involved in the activation of Rho guanosine triphosphatases, which act as regulators of cell proliferation, cytoskeletal organization, and cell movement and are crucial for cancer spread. Research has shown that NET1 can regulate the malignant biological functions of tumour cells, such as growth, invasion, and metastasis, and it is closely related to the progression of pancreatic cancer, gastric cancer, and liver cancer. However, the comprehensive role and mechanistic function of NET1 in other types of cancer remain largely unexplored. A deeper understanding of the role of NET1 may provide new insights into the molecular mechanisms of cancer progression and metastasis. This study aims to fill this knowledge gap and provide a more comprehensive understanding of the role of NET1 in cancer biology. The Cancer Genome Atlas and Genotype-Tissue Expression databases were utilized to analyse the differential expression of NET1 in normal and cancer tissues. The prognostic value of NET1 in cancer was evaluated through log-rank tests and Cox regression models. Further analysis was conducted to assess the relationships between NET1 expression and clinical features, as well as its diagnostic value. We investigated potential factors contributing to genetic alterations in NET1 to elucidate the role of NET1 in cancer progression. We also explored the relationships between NET1 and genes associated with epigenetic modifications, oncogenes, and tumour characteristics, such as RNA stemness scores (RNAss), DNA stemness scores (DNAss), the tumour mutation burden (TMB), and microsatellite instability (MSI). Additionally, we analysed the associations between NET1 expression and immune cell infiltration, immunoregulatory genes, and sensitivity to therapeutic drugs. We conducted gene set enrichment analysis to further investigate the signalling pathways that might be affected by changes in NET1. The prognostic value of NET1 in triple-negative breast cancer (TNBC) was further validated using real-world and Gene Expression Omnibus (GEO) data. Finally, through both in vivo and in vitro experiments, we confirmed that the overexpression of NET1 contributed to the malignant progression of TNBC cells, and we explored the potential mechanism by which NET1 regulates malignant biological behaviour through cellular experiments. Our study revealed a higher expression level of NET1 in 18 types of tumour tissues than in their corresponding normal tissues. Specifically, we observed high expression of NET1 in LIHC, LUSC, PAAD, and BRCA tumour tissues, which was associated with a poor prognosis. In terms of gene alterations, "amplification", "mutation", and "deep deletion" were identified as the main types of changes occurring in NET1. Among these, "amplification" was predominantly observed in LIHC, LUSC, PAAD, and BRCA. Furthermore, a significant positive correlation was found between copy number variations and the NET1 expression level in various tumours, including LIHC, LUSC, PAAD, and BRCA. We also discovered that NET1 expression was positively correlated with the expression of genes related to epigenetic modification in almost all types of cancer and was related to the expression levels of numerous oncogenes. In certain tumours, a significant positive correlation was noted between the expression of NET1 and TMB, MSI, DNAss, and RNAss. Intriguingly, in most tumours, NET1 expression was strongly negatively correlated with the levels of infiltrating natural killer cells and M1 macrophages. Moreover, NET1 expression was significantly positively correlated with the expression of immune genes in nearly all types of cancer. An analysis of single-cell data revealed that NET1 was expressed primarily in malignant tumour cells in most tumours, with little to no expression in immune cells. Additionally, the expression level of NET1 was associated with sensitivity to various therapeutic drugs. Data from GEO and real-world studies indicated high expression of NET1 in TNBC tissues, which was correlated with a poor prognosis. Cellular experiments indicated that NET1 could regulate the proliferation, invasion, cell cycle, and apoptosis of TNBC cells. Furthermore, NET1 may mediate the malignant proliferation of tumour cells through the AKT signalling pathway. NET1 can serve as a potential prognostic marker for LIHC, LUSC, PAAD, and BRCA tumours. Real-world data further suggest that NET1 can also serve as a prognostic indicator for TNBC. High expression of NET1 may contribute to the malignant proliferation of TNBC cells, potentially through the AKT signalling pathway. Moreover, NET1 may contribute to the formation of an immunosuppressive microenvironment that can promote tumour progression. Therefore, targeting NET1 may represents a promising approach for inhibiting tumour progression.

Pang J ，Huang X ，Gao Y ，Guan X ，Xiong L ，Li L ，Yin N ，Dai M ，Han T ，Yi W ... -  《Scientific Reports》

Pan-cancer analysis shows that BCAP31 is a potential prognostic and immunotherapeutic biomarker for multiple cancer types.

B-cell receptor-associated protein 31 (BCAP31) is a widely expressed transmembrane protein primarily located in the endoplasmic reticulum (ER), including the ER-mitochondria associated membranes. Emerging evidence suggests that BCAP31 may play a role in cancer development and progression, although its specific effects across different cancer types remain incompletely understood. The raw data on BCAP31 expression in tumor and adjacent non-tumor (paracancerous) samples were obtained from the Broad Institute Cancer Cell Line Encyclopedia (CCLE) and UCSC databases. We also examined the association between BCAP31 expression and clinicopathological factors. Using the Cox proportional hazards model, we found that high BCAP31 levels were linked to poor prognosis. To further explore BCAP31's role, we analyzed the relationship between copy number variations (CNV) and BCAP31 mRNA expression using data from The Cancer Genome Atlas (TCGA). Additionally, the association between BCAP31 expression and signature pathway scores from the MsigDB database provided insights into the tumor biology and immunological characteristics of BCAP31.We assessed the relationship between tumor immune infiltration and BCAP31 expression using the TIMER2 and ImmuCellAI databases. The ESTIMATE computational method was employed to estimate the proportion of immune cells infiltrating the tumors, as well as the stromal and immune components, based on TCGA data. To investigate drug sensitivity in relation to BCAP31 expression, we utilized GDSC2 data, which included responses to 198 medications. We explored the relationship between BCAP31 gene expression and response to immunotherapy. Additionally, the study involved culturing KYSE-150 cells under standard conditions and using siRNA-mediated knockdown of BCAP31 to assess its function. Key experiments included Western blotting (WB) to confirm BCAP31 knockdown, MTT assays for cell proliferation, colony formation assays for growth potential, Transwell assays for migration and invasion, and wound healing assays for motility. Additionally, immunohistochemistry (IHC) was performed on tumor and adjacent normal tissue samples to evaluate BCAP31 expression levels. BCAP31 was found to be significantly overexpressed in several prevalent malignancies and was associated with poor prognosis. Cox regression analysis across all cancer types revealed that higher BCAP31 levels were predominantly linked to worse overall survival (OS), disease-free interval (DFI), disease-specific survival (DSS), and progression-free interval (PFI). In most malignancies, increased BCAP31 expression was positively correlated with higher CNV. Additionally, BCAP31 expression was strongly associated with the tumor microenvironment (TME), influencing the levels of infiltrating immune cells, immune-related genes, and immune-related pathways. Drug sensitivity analysis identified six medications that showed a significant positive correlation with BCAP31 expression. Furthermore, BCAP31 expression impacted the outcomes and prognosis of cancer patients undergoing immune therapy. The functional assays demonstrated that BCAP31 knockdown in KYSE-150 cells significantly inhibited cell migration, invasion, and proliferation while enhancing colony formation ability. WB and immunohistochemistry analyses confirmed elevated BCAP31 expression in tumor tissues compared to adjacent normal tissues in esophageal cancer, lung adenocarcinoma, and gastric adenocarcinoma. BCAP31 has the potential to serve as a biomarker for cancer immunology, particularly in relation to immune cell infiltration, and as an indicator of poor prognosis. These findings provide a new perspective that could inform the development of more targeted cancer therapy strategies.

Sun Y ，Li Z ，Liu J ，Xiao Y ，Pan Y ，Lv B ，Wang X ，Lin Z ... -  《Frontiers in Immunology》

Pyroptosis-related long-noncoding RNA signature predicting survival and immunotherapy efficacy in patients with lung squamous cell carcinoma.

Pyroptosis-related long-noncoding RNAs (PRlncRNAs) play an important role in cancer progression. However, their role in lung squamous cell carcinoma (LUSC) is unclear. A risk model was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression analysis based on RNA sequencing data from The Cancer Genome Atlas database. The LUSC cohort was divided into high- and low-risk groups based on the median risk score. For the prognostic value of the model, the Kaplan-Meier analysis, log-rank test, and Cox regression analysis were performed. A nomogram was constructed to predict the prognosis of patients, using a risk score and clinical parameters such as age, sex, clinical stage, and tumor node metastasis classification (TNM) stage. Afterwards, six common algorithms were employed to assess the invasion of immune cells. The Gene Set Enrichment Analysis (GSEA) was conducted to identify differences between patients at high and low risk. Furthermore, the pRRophetic package was employed to forecast the half-maximal inhibitory doses of prevalent chemotherapeutic drugs, while the tumor immune dysfunction and exclusion score was computed to anticipate the response to immunotherapy. The expression levels of the seven PRlncRNAs were examined in both LUSC and normal lung epithelial cell lines using RT-qPCR. Proliferation, migration, and invasion assays were also carried out to investigate the role of MIR193BHG in LUSC cells. Patients in the low-risk group showed prolonged survival in the total cohort or subgroup analysis. The Cox regression analysis showed that the risk model could act as an independent prognostic factor for patients with LUSC. The results of GSEA analysis revealed that the high-risk group showed enrichment of cytokine pathways, Janus tyrosine kinase/signal transducer and activator of the transcription signalling pathway, and Toll-like receptor pathway. Conversely, the low-risk group showed enrichment of several gene repair pathways. Furthermore, the risk score was positively correlated with immune cell infiltration. Moreover, patients in the high-risk category showed reduced responsiveness to conventional chemotherapeutic medications and immunotherapy. The majority of the long noncoding RNAs in the risk model were confirmed to be overexpressed in LUSC cell lines compared to normal lung epithelial cell lines by in vitro tests. Further studies have shown that downregulating the expression of MIR193BHG may inhibit the growth, movement, and infiltration capabilities of LUSC cells, whereas increasing the expression of MIR193BHG could enhance these malignant tendencies. This study found that PRlncRNAs were linked to the prognosis of LUSC patients. The risk model, evaluated across various clinical parameters and treatment modalities, shows potential as a future reference for clinical applications.

Zhan X ，Li J ，Ding Y ，Zhou F ，Zeng R ，Lei L ，Zhang Y ，Feng A ，Qu Y ，Yang Z ... -  《-》

Clinical and Immunological Significance of ANKRD52 in Pan-Cancer.

Ankyrin repeat domain 52 (ANKRD52) is a regulatory component of the protein phosphatase 6 (PP6) holoenzyme. Evidence has emerged to suggest involvement of ANKRD52 in tumor metastases and cancer cell escape from T cell-mediated elimination and immunotherapy but there has been no research across different cancer types. The current study explored the biological functions of ANKRD52 by combining data from many databases. The aim was to expose new diagnostic or treatment biomarkers for malignant tumors. The roles of ANKRD52 with respect to immunotherapy in 33 human cancer types were analyzed by combining data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Cancer Cell Line Encyclopedia (CCLE), UCSC Xena, the Tumor Immune Estimation Resource (TIMER), TISIDB and Cellminer. Bioinformatics methods were used to analyze the association between ANKRD52 expression and prognosis, immunological indicators (immune cell infiltration, ESTIMATE scores and tumor microenvironment (TME) signatures), tumor mutational burden (TMB), microsatellite instability (MSI) and drug sensitivity. ANKRD52 expression was generally higher in 24 tumor tissues than in normal tissues and was associated with poor prognosis, especially in kidney chromophobe (KICH). Lower expression was observed in advanced cancer. ANKRD52 expression was strongly linked to major immunological indicators, such as immune cell infiltration, ESTIMATE scores, TME signatures, as well as expression of immune and tumor-related genes. Expression was also associated with indicators of immunotherapy efficacy and outcome, such as TMB in 7 cancer types and MSI in 12. In addition, ANKRD52 expression was linked to sensitivity to a number of anticancer drugs. ANKRD52 had a distinct immune function in breast invasive carcinoma (BRCA) that correlated negatively with most immune indicators. Expression was enriched in proliferation-, differentiation- and metabolism-related pathways and linked to other immune cells and TME signatures. A nomogram to predict 3- or 5-year overall survival (OS) of patients with BRCA was constructed. ANKRD52 may have utility as an oncological and immunological biomarker. New insights into oncogenesis are presented and the development of ANKRD52-targeting to increase the therapeutic efficacy of immunotherapy combined with chemotherapy explored.

Yin HZ ，Zhang MC ，Wu H 《-》