The detection and analysis of differential regulatory communities in lung cancer

Fatty acid metabolism-related signature suggests an oncogenic role of TEKT1 in endometrial cancer

OBJECTIVE

The study aims to construct a prognostic signature to detect the molecular interaction between the fatty acid metabolism and the progression of endometrial cancer.

MATERIALS AND METHODS

A total of 309 fatty acid metabolism relative genes were analyzed in the endometrial cancer cohort from The Cancer Genome Atlas. Dataset GSE216872 was applied for external validation. The R program was chosen to detect the expression of FAMRGs and execute GO/KEGG analysis. Considering the clinical information and pathological features, a prognostic gene signature was constructed using LASSO Cox regression analysis. According to FAM risk score, endometrial cancer patients were divided into high and low FAM-risk score groups. By differential expression analysis and cytoscape, TEKT1 was identified as the hub gene. Functional enrichments explored the biological process TEKT1 participated. Cellular proliferation, clone formation, migration, invasion, cycle, and apoptosis were assessed to detect the effect of TEKT1 in endometrial cancer. Co-immunoprecipitation and Western blot were performed to determine the mechanism of TEKT1.

RESULTS

A prognostic signature based on 10 FAMRGs (ACACB, PTGIS, BMPR1B, DHCR24, FAAH, GPX1, GPX4, INMT, PON3, PPT2) was generated using Lasso Cox hazards regression analysis in TCGA. TEKT1 was identified as the gene related to fatty acid metabolism. Next, we demonstrated that TEKT1 was highly expressed in endometrial cancer tissues in CPTAC and was mainly involved in the cell cycle and biosynthesis of unsaturated fatty acids. Ex-vivo experiments revealed that TEKT1 promoted proliferation, migration, and invasiveness while inhibiting apoptosis. Further experiments demonstrated that TEKT1 might promote fatty acid synthesis by binding to AMPK-γ for ACC and FASN downregulation.

CONCLUSION

A reliable predictive signature based on genes related to fatty acid metabolism in endometrial cancer was conducted, wherein TEKT1 was mainly implicated as the primary gene of interest. TEKT1 showed affinity to AMPK-γ and probably promoted FA synthesis in endometrial cancer.

TRIM29 facilitates gemcitabine resistance via MEK/ERK pathway and is modulated by circRPS29/miR-770-5p axis in PDAC

AIMS

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease. Chemotherapy based on gemcitabine (GEM) remains the first-line drug for patients with advanced PDAC. However, GEM resistance impairs its therapeutic effectiveness. Therefore, identifying effective therapeutic targets are urgently needed to overcome GEM resistance.

METHODS

The clinical significance of Tripartite Motif Containing 29 (TRIM29) was identified by exploring GEO datasets and TCGA database and its potential biological functions were predicted by GSEA analysis. The regulatory axis was established by bioinformatics analysis and validated by mechanical experiments. Then, in vitro and in vivo assays were performed to validate the roles of TRIM29 in PDAC GEM resistance.

RESULTS

High TRIM29 expression was associated with poor prognosis of PDAC and functional experiments demonstrated that TRIM29 promoted GEM resistance in PDAC GEM-resistant (GR) cells. Furthermore, we revealed that circRPS29 promoted TRIM29 expression via competitive interaction with miR-770-5p and then activated MEK/ERK signaling pathway. Additionally, both in vitro and in vivo functional experiments demonstrated that circRPS29/miR-770-5p/TRIM29 axis promoted PDAC GEM resistance via activating MEK/ERK signaling pathway.

CONCLUSION

Our results identify the significance of the signaling axis, circRPS29/miR-770-5p/TRIM29-MEK/ERK, in PDAC GEM resistance, which will provide novel therapeutic targets for PDAC treatment.

Integrated Bioinformatical Analysis Identifies GIMAP4 as an Immune-Related Prognostic Biomarker Associated With Remodeling in Cervical Cancer Tumor Microenvironment

Tumor microenvironment (TME) is emerging as an essential part of cervical cancer (CC) tumorigenesis and development, becoming a hotspot of research these years. However, comprehending the specific composition of TME is still facing enormous challenges, especially the immune and stromal components. In this study, we downloaded the RNA-seq profiles and somatic mutation data of 309 CC cases from The Cancer Genome Atlas (TCGA) database, which were analyzed by integrative bioinformatical methods. Initially, ESTIMATE computational method was employed to calculate the amount of immune and stromal components. Then, based on the high- and low-immunity cohorts, we recognized the differentially expressed genes (DEGs) as well as the differentially mutated genes (DMGs). Additionally, we conducted an intersection analysis of DEGs and DMGs, ultimately determining an immune-related prognostic signature, GTPase, IMAP Family Member 4 (GIMAP4). Moreover, sequential analyses demonstrated that GIMAP4 was a protective factor in CC, positively correlated with the overall survival (OS) and negatively with distant metastasis. Besides, we utilized the Gene Set Enrichment Analysis (GSEA) to explore the enrichment-pathways in high and low-expression cohorts of GIMAP4. The results indicated that the genes of the high-expression cohort had a high enrichment in immune-related biological processes and metabolic activities in the low one. Furthermore, CIBERSORT analysis was applied to evaluate the proportion of tumor-infiltrating immune cells (TICs), illustrating that several activated TICs were strongly associated with GIMAP4 expression, which suggested that GIMAP4 had the potential to be an indicator for the immune state in TME of CC. Hence, GIMAP4 contributed to predicting the CC patients’ clinical outcomes, such as survival rate, distant metastasis and immunotherapy response. Moreover, GIMAP4 could serve as a promising biomarker for TME remodeling, suggesting the possible underlying mechanisms of tumorigenesis and CC progression, which may provide different therapeutic perceptions of CC, and therefore improve treatment.