Network‑based identification of signature genes KLF6 and SPOCK1 associated with oral submucous fibrosis

Abstract

The molecular mechanism of oral submucous fibrosis (OSF) is yet to be fully elucidated. The identification of reliable signature genes to screen patients with a high risk of OSF and to provide oral cancer surveillance is therefore required. The present study produced a filtering criterion based on network characteristics and principal component analysis, and identified the genes that were involved in OSF prognosis. Two gene expression datasets were analyzed using meta-analysis, the results of which revealed 1,176 biologically significant genes. A co-expression network was subsequently constructed and weighted gene modules were detected. The pathway and functional enrichment analyses of the present study allowed for the identification of modules 1 and 2, and their respective genes, SPARC (osteonectin), cwcv and kazal like domain proteoglycan 1 (SPOCK1) and kruppel like factor 6 (KLF6), which were involved in the occurrence of OSF. The results revealed that both genes had a prominent role in epithelial to mesenchymal transition during OSF progression. The genes identified in the present study require further exploration and validation within clinical settings to determine their roles in OSF.

Circulating miRNA-181b-5p, miRNA-223-3p, miRNA-210-3p, let 7i-5p, miRNA-21-5p and miRNA-29a-3p in patients with localized scleroderma as potential biomarkers

“…Starkel et al reported that oxidative stress, KLF6 and TGF-β1 upregulation discriminate non-alcoholic steatohepatitis advancing to fibrosis from uncomplicated steatosis in rats 46 . www.nature.com/scientificreports/ Furthermore, accumulating evidence demonstrates that KLF6 is involved in the occurrence of oral submucous fibrosis 47 . BCL2L11, also known as BIM, is a pro-apoptotic member of the B cell CLL/lymphoma 2 protein family and is an essential modulator of apoptosis 48 .…”

Unravelling host-pathogen interactions: ceRNA network in SARS-CoV-2 infection (COVID-19)

“…The 18 infected samples were studied at different time points of Day1, Day2, Day3, Day5, Day14, and Day28, respectively. The relative expression levels of a gene symbol mapping to multiple probeset IDs were averaged and the probeset IDs with no corresponding gene symbol were eliminated ( Ahmad et al, 2019 , Shriwash et al, 2019 , Singh et al, 2020 ). A three-stage screening protocol was employed to screen the significant differentially expressed genes (DEGs) between two infection status groups, i.e., uninfected vs infected.…”

Unravelling the Role of miR-20b-5p, CCNB1, HMGA2 and E2F7 in Development and Progression of Non-Small Cell Lung Cancer (NSCLC)

“…Probe IDs were mapped to their corresponding HUGO Gene Nomenclature Committee (HGNC) gene symbol(s) using the GPL570 annotation file and hgu133plus2.db package available in R v4.0.2. Expression values of duplicate gene symbols mapping to multiple probe IDs were averaged across the samples [20,21] in both the datasets followed by p-value computation of all unique genes using two-sample paired t-test function. Common genes from both the datasets were identified using the intersect function.…”