Filtering High-Dimensional Methylation Marks With Extremely Small Sample Size: An Application to Gastric Cancer Data

TMTC1 promotes invasiveness of ovarian cancer cells through integrins β1 and β4

Ovarian cancer is the most lethal gynecological malignancy and is characterized by peritoneal disseminated metastasis. Although O-mannosyltransferase TMTC1 is highly expressed by ovarian cancer, its pathophysiological role in ovarian cancer remains unclear. Here, immunohistochemistry showed that TMTC1 was overexpressed in ovarian cancer tissues compared with adjacent normal ovarian tissues, and high TMTC1 expression was associated with poor prognosis in patients with ovarian cancer. Silencing TMTC1 reduced ovarian cancer cell viability, migration, and invasion in vitro, as well as suppressed peritoneal tumor growth and metastasis in vivo. Moreover, TMTC1 knockdown reduced cell-laminin adhesion, which was associated with the decreased phosphorylation of FAK at pY397. Conversely, TMTC1 overexpression promoted these malignant properties in ovarian cancer cells. Glycoproteomic analysis and Concanavalin A (ConA) pull-down assays showed that integrins β1 and β4 were novel O-mannosylated protein substrates of TMTC1. Furthermore, TMTC1-mediated cell migration and invasion were significantly reversed by siRNA-mediated knockdown of integrin β1 or β4. Collectively, these results suggest that TMTC1-mediated invasive behaviors are primarily through integrins β1 and β4 and that TMTC1 is a potential therapeutic target for ovarian cancer.

Identification of New Key Genes and Their Association with Breast Cancer Occurrence and Poor Survival Using In Silico and In Vitro Methods

Breast cancer is one of the most prevalent types of cancer diagnosed globally and continues to have a significant impact on the global number of cancer deaths. Despite all efforts of epidemiological and experimental research, therapeutic concepts in cancer are still unsatisfactory. Gene expression datasets are widely used to discover the new biomarkers and molecular therapeutic targets in diseases. In the present study, we analyzed four datasets using R packages with accession number GSE29044, GSE42568, GSE89116, and GSE109169 retrieved from NCBI-GEO and differential expressed genes (DEGs) were identified. Protein-protein interaction (PPI) network was constructed to screen the key genes. Subsequently, the GO function and KEGG pathways were analyzed to determine the biological function of key genes. Expression profile of key genes was validated in MCF-7 and MDA-MB-231 human breast cancer cell lines using qRT-PCR. Overall expression level and stage wise expression pattern of key genes was determined by GEPIA. The bc-GenExMiner was used to compare expression level of genes among groups of patients with respect to age factor. OncoLnc was used to analyze the effect of expression levels of LAMA2, TIMP4, and TMTC1 on the survival of breast cancer patients. We identified nine key genes, of which COL11A1, MMP11, and COL10A1 were found up-regulated and PCOLCE2, LAMA2, TMTC1, ADAMTS5, TIMP4, and RSPO3 were found down-regulated. Similar expression pattern of seven among nine genes (except ADAMTS5 and RSPO3) was observed in MCF-7 and MDA-MB-231 cells. Further, we found that LAMA2, TMTC1, and TIMP4 were significantly expressed among different age groups of patients. LAMA2 and TIMP4 were found significantly associated and TMTC1 was found less correlated with breast cancer occurrence. We found that the expression level of LAMA2, TIMP4, and TMTC1 was abnormal in all TCGA tumors and significantly associated with poor survival.

Prognostic value of the ferroptosis-related gene SLC2A3 in gastric cancer and related immune mechanisms

SLC2A3 is a ferroptosis marker engaged in transmembrane glucose transport. However, the effect of SLC2A3 on the prognosis of patients with cancer remains unclear. This study aimed to explore the prognostic implications of SLC2A3 and its underlying immune mechanisms in gastric cancer. The mRNA expression profiles and corresponding clinical data of patients with gastric cancer were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus databases. Differentially expressed genes related to SLC2A3 were identified using the R package “limma.” Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, gene set enrichment analysis, and gene set variation analysis were used to explore the underlying mechanisms. The protein–protein and miRNA interaction networks were analyzed using Cytoscape software. Immune cell infiltration was assessed using single-sample gene set enrichment analysis. Univariate and multivariate Cox regression analyses revealed the relationship between SLC2A3 expression and prognosis. SLC2A3 was found to be highly expressed in tumor tissues and was associated with an unfavorable prognosis in patients with gastric cancer. Functional enrichment analysis showed that SLC2A3 is related to cytokine–cytokine receptor interaction, epithelial–mesenchymal transition, T cell receptor signaling pathway, B cell receptor signaling pathway, and immune checkpoints. SLC2A3 is also involved in immune response regulation and is regulated by multiple miRNAs, including miR-195-5p, miR-106a-5p, miR-424-5p, and miR-16-5p. Univariate and multivariate Cox regression analyses indicated that SLC2A3 can be used as an independent prognostic factor for predicting the outcome in patients with gastric cancer. SLC2A3 and related miRNAs are potential prognostic biomarkers and therapeutic targets.