Pan-cancer analysis of the prognostic and immunological role of GJB2: a potential target for survival and immunotherapy

Pan-cancer analysis identifies EIPR1 as a potential prognostic and immunological biomarker for lung adenocarcinoma and its functional validation

BACKGROUND

EARP and GARP complex-interacting protein 1 (EIPR1) may be a new oncogene in tumors, influencing the prognosis and invasion of cancer. However, a systematic analysis of the function of EIPR1 in various cancers remains vacant. Thus, we proceeded with a comprehensive analysis to ascertain the role of EIPR1 among various cancers.

METHODS

We explored EIPR1 expression in pan-cancer, and its association with clinical stage, survival, gene mutations and methylation by the TIMER 2.0, GEPIA2, cBioPortal, and UALCAN. The protein-protein interaction (PPI) network, immune infiltration, and immune checkpoint assessments of EIPR1 was performed using the STRING and SangerBox. The role of EIPR1 expression in lung adenocarcinoma (LUAD) was explored by the R software. The impact of EIPR1 expression on LUAD progression was studied through in vitro assays.

RESULTS

EIPR1 was overexpressed in most cancers and revealed as a potential prognostic biomarker in tumors, involving in tumorigenesis by affecting its methylation and gene mutations. The immune infiltration and immune checkpoints of tumors were related to the expression of EIPR1. Additionally, EIPR1 expression affected the survival, diagnosis, clinicopathological features, tumor microenvironment, and drug sensitivity of LUAD patients. Validation studies demonstrated that EIPR1 knockdown suppressed the malignant growth, invasion, and migration of LUAD cells.

CONCLUSIONS

This study delivers an extensive landscape for the oncogenesis and immunological characteristics of EIPR1, which reveals that EIPR1 may serve as a potential biological target for future prognosis and immune treatment in tumors, especially in LUAD.

Multi-Omics Pan-Cancer Profiling of HSD17B10 Unveils Its Prognostic Potential, Metabolic Regulation, and Immune Microenvironment Interactions

This study systematically analyzed the expression and clinical significance of Hydroxysteroid 17-beta dehydrogenase type 10 (HSD17B10) in 33 cancers by integrating TCGA, GTEx, and other multi-omics databases. HSD17B10 was highly expressed in 14 cancers, like GBM and LGG, but low in 5, such as KIRC. Its expression correlated closely with overall survival (OS) and disease-free survival (DFS). In GBM-LGG, LGG, and other cancers, high HSD17B10 expression was linked to lower survival rates, indicating that it could be an independent prognostic marker. HSD17B10 also had a two-way relationship with the tumor's immune microenvironment. In cancers such as GBM-LGG, high expression correlated positively with immune/stromal scores. However, in most cancers like LUAD, it was negatively associated with B- and T-cell infiltration. Epigenetic analysis showed that low methylation in the HSD17B10 promoter region might drive its high expression in tumors such as SARC, and specific methylation sites (e.g., CG26323797) were significantly related to patient survival. Functional enrichment analysis revealed that HSD17B10 participated in tumor progression by regulating oxidative phosphorylation, mitochondrial metabolism, and RNA methylation. Single-cell and spatial transcriptome data further demonstrated that HSD17B10 had a cell-type-specific expression pattern in colorectal cancer. This study provides a theoretical basis for HSD17B10 as a pan-cancer prognostic marker and therapeutic target.

Transcriptomic analysis of ROS1+ non-small cell lung cancer reveals an upregulation of nucleotide synthesis and cell adhesion pathways

Introduction

The transcriptomic characteristics of ROS1+ non-small cell lung cancer (NSCLC) represent a crucial aspect of its tumor biology. These features provide valuable insights into key dysregulated pathways, potentially leading to the discovery of novel targetable alterations or biomarkers.

Methods

From The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases, all available ROS1+ (n = 10), ALK+ (n = 5) and RET+ (n = 5) NSCLC tumor and ROS1+ cell line (n = 7) RNA-sequencing files were collected. In addition, 10 healthy lung RNA-seq samples were included. Differential gene expression with DESeq2 (R package) and gene co-expression (WGCNA, R package) analyses were performed. Functional annotation was performed through Gene Set Enrichment Analysis (GSEA) using Webgestalt and RNAseqChef, Over-Representation Analysis (ORA) through Enrichr. iRegulon was used to identify enriched transcription factors that regulate a gene co-expression module.

Results

ROS1+ NSCLC samples were significantly enriched for the nucleotide synthesis and cell adhesion KEGG pathways compared to ALK+ and RET+ samples. Moreover, NOTCH1 was significantly downregulated in ROS1+ NSCLC and PD-L1 was weakly expressed. When comparing ROS1+ tumor versus cell line transcriptomes, an upregulation of MYC and MET was found in cell lines together with a significantly decreased expression of HER3, HER4 and BRAF. Within ROS1-tumors, GJB2 was overexpressed in the CD74- and CLTC-ROS1+ subgroups. The differential expression of IL20RB and GJB2 in cell lines was confirmed through RT-qPCR. Finally, the gene co-expression analysis unveils a gene cluster involving cell cycle-related genes which significantly correlates with the disease stage of patients. In addition, we propose TFDP1 and ISL1 as key ROS1-specific transcription factors.

Conclusion

This study highlights cell adhesion and nucleotide synthesis as crucial signatures in ROS1+ NSCLC. The upregulation of GJB2 may serve as a prognostic biomarker, along with IL20RB, a known mediator of bone metastases. Furthermore, TDFP1 and ISL1 were identified as relevant transcription factors that could potentially regulate the biological processes in ROS1-rearranged NSCLC.

A retrospective analysis of the clinicopathological features and prognostic value of MAPK12 protein expression in diffuse large B-cell lymphoma

PURPOSE

Mitogen-activated protein kinase 12 (MAPK12), also known as p38γ, is a member of the p38 MAPK family and plays a crucial role in tumor occurrence and invasion. However, there is still uncertainty regarding MAPK12 involvement in diffuse large B-cell lymphoma (DLBCL).

METHODS

Our study investigated the expression of MAPK12 mRNA in various types of cancer using bioinformatic analysis. Furthermore, we performed immunohistochemistry (IHC) to detect the expression of MAPK12 in patients with DLBCL and compared clinical indicators and survival rates.

RESULTS

We found that the high expression rate of MAPK12 was 43.1% in DLBCL patients. Several clinical indicators, including IPI scores, Hans classifications, LDH levels, and Ki-67 expression were closely associated with MAPK12 expression. Survival analysis revealed that higher expression of MAPK12 was significantly correlated with shorter progression-free survival (PFS) and overall survival (OS) in DLBCL patients. In addition, both univariate and multivariate analyses revealed IPI score, MAPK12 expression, and rituximab use as the independent OS risk factors (P < 0.05). To explore the functional role of MAPK12 in DLBCL, weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) were used to confirm the involvement of MAPK12 in the regulation of type II interferon production, positive regulation of lymphocyte proliferation, and other related biological processes.

CONCLUSION

DLBCL patients have poor prognoses when MAPK12 levels are high, which is expected to be a therapeutic target and prognostic factor.

Expression, potential biological behaviour and clinical significance of MCM3 in pancreatic adenocarcinoma: a comprehensive study integrating high throughput sequencing, CRISPR screening and in-house immunohistochemistry

BACKGROUND

Minichromosome maintenance complex component 3 (MCM3) plays a key role in various tumours. However, it remains largely unknown what the specific role and clinical significance of MCM3 in pancreatic adenocarcinoma (PAAD) are.

MATERIALS AND METHODS

We integrated high-throughput data from PAAD worldwide to analyse the expression level of MCM3 mRNA. We used immunohistochemistry to analyse MCM3 protein expression levels in 145 cases in the PAAD group and 29 cases in the non-PAAD group. We also mainly analysed the necessity of MCM3 for PAAD growth based on CRISPR screen data. In addition, we used enrichment analysis and protein-protein interaction networks to explore the molecular mechanism of MCM3 in PAAD. We also analysed the correlation between MCM3 expression, components of the immune microenvironment in PAAD tissue and clinical prognosis.

RESULTS

In PAAD, we observed for the first time that MCM3 was significantly highly expressed at both the mRNA (SMD = 0.67, 95% CI: 0.38 ∼ 0.96) and the protein level (p < 0.05). The mRNA (AUC = 0.78, 95% CI: 0.74 ∼ 0.81; sensitivity = 0.66, 95% CI: 0.55 ∼ 0.76; specificity = 0.76, 95% CI: 0.67 ∼ 0.84) and protein (AUC = 0.929) expression levels of MCM3 had a good ability to distinguish between PAAD and non-PAAD tissue. There was heterogeneity reflected by the differential expression of MCM3 protein in PAAD cells. MCM3 played an essential role in PAAD growth, through abnormal DNA replication, p53 signalling and cell cycle checkpoints. PAAD with high MCM3 expression was sensitive to c-75, brivanib, flavopiridol and VNLG/124 drugs, with stable molecular docking models.

CONCLUSION

MCM3 is likely to be a critical element in promoting the initiation and growth of PAAD. Flavopiridol may exert its anti-PAAD effect through the interaction between MCM3, classic CDK1 targets in the cell cycle checkpoint and p53 pathway as well as related molecules in other pathways.

Identification and validation of ion channels-related mRNA prognostic signature for glioblastomas

Glioblastomas (GBM) is a kind of malignant brain tumor with poor prognosis. Identifying new biomarkers is promising for the treatment of GBM. The mRNA-seq and clinical data were obtained from The Cancer Genome Atlas and the Chinese Glioma Genome Atlas databases. The differentially expressed genes were identified using limma R package. The prognosis-related genes were screened out and a risk model was constructed using univariate, least absolute shrinkage and selection operator, and multivariate Cox analysis. Receiver operating characteristic curve was used to assess the efficiency of model. Kaplan-Meier survival curve was applied for the survival analysis. Mutation analysis was conducted using maftools package. The effect of immunotherapy was analyzed according to TIDE score, and the drug sensitivity analysis was performed. The Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment Analysis enrichment analyses were performed for the functional analysis. The regulatory network was constructed by STRING and Cytoscape software. RT-qPCR was performed to validate the expression of 3 hub genes in vitro. A risk model was constructed based on 3 ion channels related genes (gap junction protein beta 2 [GJB2], potassium voltage-gated channel subfamily h member 6 [KCNH6], and potassium calcium-activated channel subfamily n member 4 [KCNN4]). The risk score and hub genes were positively correlated with the calcium signaling pathway. Patients were divided into 2 groups based on the risk score calculated by 3 signatures. The infiltration levels of T cell, B lineage, monocytic lineage, and neutrophils were increased in high risk group, while TIDE score was decreased. IC50 of potential drugs for GBM treatment was elevated in the high risk group. Furthermore, GJB2, KCNH6, and KCNN4 were oncogenic, and GJB2 and KCNN4 were upregulated, while KCNH6 was downregulated in high risk group and GBM cells. The regulatory network showed that KCNH6 was targeted by more miRNA and transcription factors and KCNN4 interacted with more drugs. We constructed a three-signature risk model, which could effectively predict the prognosis of GBM development. Besides, KCNH6 and KCNN4 were respectively considered as the targets of molecular targeted treatment and chemotherapy.

GJB2 Promotes HCC Progression by Activating Glycolysis Through Cytoplasmic Translocation and Generating a Suppressive Tumor Microenvironment Based on Single Cell RNA Sequencing

Despite substantial breakthroughs in the treatment of hepatocellular carcinoma (HCC) in recent years, many patients are diagnosed in the middle or late stages, denying them the option for surgical excision. Therefore, it is of great importance to find effective therapeutic targets of HCC. In this study, it is found that Gap junction protein beta-2 (GJB2) is highly enriched in malignant cells based on single-cell RNA sequencing and higher expression of GJB2 indicates a worse prognosis. The localization of GJB2 in HCC cancer cells is changed compared with normal liver tissue. In cancer cells, GJB2 tends to be located in the cytoplasm and nucleus, while in normal tissues, GJB2 is mainly located on the cell membrane. GJB2 is related to glycolysis, promoting NF-κB pathway via inducing the ubiquitination degradation of IκBa, and activating HIF-1α/GLUT-1/PD-L1 pathway. In addition, GJB2 knockdown reshapes tumor immune microenvironment and Salvianolic acid B inhibits the activity of GJB2. In conclusion, GJB2 promotes HCC progression by activating glycolysis through cytoplasmic translocation and generating a suppressive tumor microenvironment. Salvianolic acid B inhibits the expression of GJB2 and enhances the sensitivity of anti-PD1 therapy, which may provide insights into the development of novel combination therapeutic strategies for HCC.

Spatial resolution of the head and neck cancer tumor microenvironment to identify tumor and stromal features associated with therapy response

Head and neck cancer (HNC) is the seventh most common cancer globally, resulting in 440 000 deaths per year. While there have been advancements in chemoradiotherapy and surgery, relapse occurs in more than half of HNCs, and these patients have a median survival of 10 months and a 2-year survival of < 20%. Only a subset of patients displays durable benefits from immunotherapies in metastatic and recurrent HNC, making it critical to understand the tumor microenvironment (TME) underpinning therapy responses in HNC. To recognize biological differences within the TME that may be predictive of immunotherapy response, we applied cutting-edge geospatial whole-transcriptome profiling (NanoString GeoMx Digital Spatial Profiler) and spatial proteomics profiling (Akoya PhenoCycler-Fusion) on a tumor microarray consisting of 25 cores from 12 patients that included 4 immunotherapy-unresponsive (8 cores) and 2 immunotherapy-responsive patients (5 cores), as well as 6 immunotherapy naïve patients (12 cores). Through high-plex, regional-based transcriptomic mapping of the tumor and TME, pathways involved with the complement system and hypoxia were identified to be differentially expressed in patients who went on to experience a poor immunotherapy response. Single-cell, targeted proteomic analysis found that immune cell infiltration of the cancer cell mass and interactions of CD8 T cells with tumor and other immune cells were associated with positive immunotherapy response. The relative abundance of specific tumor phenotypes and their interactions with various immune cells was identified to be different between response groups. This study demonstrates how spatial transcriptomics and proteomics can resolve novel alterations in the TME of HNC that may contribute to therapy sensitivity and resistance.

First report of an Ivorian family with nonsyndromic hearing loss caused by GJB2 compound heterozygous variants

The primary etiology of congenital hearing loss is attributed to genetic factors, with GJB2 identified as a pivotal gene across diverse ethnic groups. Additionally, nonsyndromic hearing loss is predominantly inherited in an autosomal recessive manner. We used Sanger sequencing to analyze GJB2 in 17 deaf children from 13 unrelated Ivory Coast families. One family had two children born with severe congenital deafness and exhibited pathogenic compound heterozygous variants. These variants included a nonsense substitution (c.132G > A or p.Trp44Ter) and a newly discovered duplication of 7 base pairs (c.205_211dupTTCCCCA or p.Ser72ProfsTer32). Segregation testing confirmed these variants, marking the first identification of GJB2 in an Ivorian family with congenital hearing loss.

Expression of the checkpoint kinase BUB1 is a predictor of response to cancer therapies

The identification of clinically-relevant biomarkers is of upmost importance for the management of cancer, from diagnosis to treatment choices. We performed a pan-cancer analysis of the mitotic checkpoint budding uninhibited by benzimidazole 1 gene BUB1, in the attempt to ascertain its diagnostic and prognostic values, specifically in the context of drug response. BUB1 was found to be overexpressed in the majority of cancers, and particularly elevated in clinically aggressive molecular subtypes. Its expression was correlated with clinico-phenotypic features, notably tumour staging, size, invasion, hypoxia, and stemness. In terms of prognostic value, the expression of BUB1 bore differential clinical outcomes depending on the treatment administered in TCGA cancer cohorts, suggesting sensitivity or resistance, depending on the expression levels. We also integrated in vitro drug sensitivity data from public projects based on correlation between drug efficacy and BUB1 expression to produce a list of candidate compounds with differential responses according to BUB1 levels. Gene Ontology enrichment analyses revealed that BUB1 overexpression in cancer is associated with biological processes related to mitosis and chromosome segregation machinery, reflecting the mechanisms of action of drugs with a differential effect based on BUB1 expression.

Intercellular cross-talk through lineage-specific gap junction of cancer-associated fibroblasts related to stromal fibrosis and prognosis

Stromal fibrosis in cancer is usually associated with poor prognosis and chemotherapy resistance. It is thought to be caused by fibroblasts; however, the exact mechanism is not yet well understood. The study aimed to identify lineage-specific cancer-associated fibroblast (CAF) subgroup and their associations with extracellular matrix remodeling and clinical significances in various tumor types using single-cell and bulk RNA sequencing data. Through unsupervised clustering, six subclusters of CAFs were identified, including a cluster with exclusively high gap junction protein beta-2 (GJB2) expression. This cluster was named GJB2-positive CAF. It was found to be a unique subgroup of terminally differentiated CAFs associated with collagen gene expression and extracellular matrix remodeling. GJB2-positive CAFs showed higher communication frequency with vascular endothelial cells and cancer cells than GJB2-negative CAFs. Moreover, GJB2 was poorly expressed in normal tissues, indicating that its expression is dependent on interaction with other cells, including vascular endothelial cells and cancer cells. Finally, the study investigated the clinical significance of GJB2 signature score for GJB2-positive CAFs in cancer and found a correlation with poor prognosis. These results suggest that GJB2-positive CAF is a unique fibroblast subtype involved in extracellular matrix remodeling, with significant clinical implications in cancer.