Integrative bioinformatics analysis of prognostic alternative splicing signatures in gastric cancer

DHX34 as a promising biomarker for prognosis, immunotherapy and chemotherapy in Pan-Cancer: A Comprehensive Analysis and Experimental Validation

Background: As a member of the DExD/H-box RNA helicase family, DHX34 has demonstrated a significant correlation with the development of multiple disorders. Nevertheless, a comprehensive investigation between DHX34 and pan-cancer remains unexplored. Methods: We analyzed the value of DHX34 in pan-cancer based on some databases, such as The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and The Human Protein Atlas (HPA) by use the R language as well as some online analysis tools, including STRING, TISIDB, TISCH2. And based on our samples we performed Western blot (WB), qPCR and immunohistochemical staining (IHC) experiments. Results: DHX34 was highly expressed in most tumors, including Liver Hepatocellular Carcinoma (LIHC), compared to corresponding normal tissues. Among cervical cancers, DHX34 mutation frequency was the highest. Intriguingly, a positive correlation was observed between DHX34 expression and Mutational Burden (TMB) across 12 tumor types, and Microsatellite Instability (MSI) across 10 tumor types. Remarkably, DHX34 exhibited a favorable diagnostic value in a multitude of tumors. High expression of DHX34 is associated with poor prognosis in tumors such as adrenocortical carcinoma (ACC), renal papillary cell carcinoma (KIRP), low-grade glioma (LGG), and LIHC. Correlation analysis indicated that DHX34 expression correlated with clinicopathological features in a variety of tumors. The Protein-Protein Interaction (PPI) network and GSCALite database suggested that DHX34 and its ten co-expression genes might promote cancer progression by regulating the cell cycle. Gene Set Enrichment Analysis (GSEA) results further showed that DHX34 was positively correlated with pathways such as cell cycle, mitosis, and gene transcription regulation. The TISIDB database showed that DHX34 expression was closely associated with immune infiltration. Based on the TISCH2 database, we found that DHX34 was expressed in a number of immune cells, with relatively high expression in monocyte macrophages in LIHC. Conclusions: In summary, our study found that DHX34 is highly expressed in pan-cancer and has diagnostic and prognostic value. Targeting DHX34 may improve the therapeutic efficacy of immunotherapy and chemotherapy in a multitude of tumors.

Relationship between DHX15 expression and survival in colorectal cancer

OBJECTIVE

to explore the relationship between the expression of DEAH-box RNA helicase 15 (DHX15) in colorectal cancer (CRC), its clinical pathological features and survival.

METHOD

DHX15 expression data with clinical pathological features from the Cancer Gene Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) were statistically analyzed for the association between DHX15 expression and overall survival in CRC. The expression of DHX15 was performed by immunohistochemical staining (IHC) using tumor and the adjacent normal tissue, mounted in tissue microarrays. The significance of DHX15 expression to predict survival and prognosis of CRC were analyzed using the Kaplan-Meier method, univariate and multivariate Cox regression analysis.

RESULTS

low expression of DHX15 mRNA and DHX15 protein in CRC were both negative factors for survival. Overall survival of patients with low-expression of DHX15 was significantly lower (χ2 = 8.452, p = 0.004) by Kaplan-Meier evaluation. Low expression of DHX15 in CRC tissues correlated with distal lymph node metastasis (χ² = 7.120, p = 0.008), TNM stage (χ² = 3.935, p = 0.047) and disease recurrence (χ² = 9.524, p = 0.002) in CRC. Low expression of DHX15 (HR = 4.012, 95 % CI: 1.462-11.013, p = 0.007), late TNM stage (HR = 0.067, 95 % CI: 0.029-0.156, p < 0.001) and recurrence (HR = 0.008, 95 % CI: 0.002-0.034, p < 0.001) were risk factors related to the prognosis of CRC patients by univariate Cox regression analysis.

CONCLUSION

our findings reveal a key role for DHX15 in the progress of CRC metastasis and recurrence. DHX15 may be a potential biomarker for CRC targeted therapy.

Identification of prognostic alternative splicing signature in gastric cancer

Background

Aberrant alternative splicing (AS) events could be viewed as prognostic indicators in a large number of malignancies. This study aims to identify prognostic AS events, illuminate the function of the splicing variants biomarkers and provide reliable evidence for formulating public health strategies for gastric cancer (GC) surveillance.

Methods

RNA-Seq data, clinical information and percent spliced in (PSI) values were available in The cancer genome atlas (TCGA) and TCGA SpliceSeq data portal. A three-step regression method was conducted to identify prognostic AS events and construct multi-AS-based signatures. The associations between prognostic AS events and splicing factors were also investigated.

Results

We identified a total of 1,318 survival-related AS events in GC, parent genes of which were implicated in numerous oncogenic pathways. The final prognostic signatures stratified by seven types of AS events or not stratified performed well in risk prediction for GC patients. Moreover, five signatures based on AA, AD, AT, ES and RI events function as independent prognostic indicators after multivariate adjustment of other clinical variables. Splicing network also showed marked correlation between the expression of splicing factors and PSI value of AS events in GC patients.

Conclusion

Our findings provide a landscape of AS events and regulatory network in GC, indicating that AS events might serve as prognostic biomarkers and therapeutic targets for GC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13690-022-00894-3.

Comprehensive Analysis of Alternative Splicing in Gastric Cancer Identifies Epithelial-Mesenchymal Transition Subtypes Associated with Survival

Alternatively spliced RNA isoforms are a hallmark of tumors, but their nature, prevalence, and clinical implications in gastric cancer have not been comprehensively characterized. We systematically profiled the splicing landscape of 83 gastric tumors and matched normal mucosa, identifying and experimentally validating eight splicing events that can classify all gastric cancers into three subtypes: epithelial-splicing (EpiS), mesenchymal-splicing (MesS), and hybrid-splicing. These subtypes were associated with distinct molecular signatures and epithelial-mesenchymal transition markers. Subtype-specific splicing events were enriched in motifs for splicing factors RBM24 and ESRP1, which were upregulated in MesS and EpiS tumors, respectively. A simple classifier based only on RNA levels of RBM24 and ESRP1, which can be readily implemented in the clinic, was sufficient to distinguish gastric cancer subtypes and predict patient survival in multiple independent patient cohorts. Overall, this study provides insights into alternative splicing in gastric cancer and the potential clinical utility of splicing-based patient classification.

SIGNIFICANCE

This study presents a comprehensive analysis of alternative splicing in the context of patient classification, molecular mechanisms, and prognosis in gastric cancer.