Identification of Differentially Expressed Genes and miRNAs Associated with Esophageal Squamous Cell Carcinoma by Integrated Analysis of Microarray Data

Abstract

<jats:p>To identify candidate key genes and miRNAs associated with esophageal squamous cell carcinoma (ESCC) development and prognosis, the gene expression profiles and miRNA microarray data including GSE20347, GSE38129, GSE23400, and GSE55856 were downloaded from the Gene Expression Omnibus (GEO) database. Clinical and survival data were retrieved from The Cancer Genome Atlas (TCGA). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes (DEGs) was analyzed via DAVID, while the DEG-associated protein-protein interaction network (PPI) was constructed using the STRING database. Additionally, the miRNA target gene regulatory network and miRNA coregulatory network were constructed, using the Cytoscape software. Survival analysis and prognostic model construction were performed via the survival (version 2.42-6) and rbsurv R packages, respectively. The results showed a total of 2575, 2111, and 1205 DEGs, and 226 differentially expressed miRNAs (DEMs) were identified. Pathway enrichment analyses revealed that DEGs were mainly enriched in 36 pathways, such as the proteasome, p53, and beta-alanine metabolism pathways. Furthermore, 448 nodes and 1144 interactions were identified in the PPI network, with <jats:italic>MYC</jats:italic> having the highest random walk score. In addition, 7 DEMs in the microarray data, including miR-196a, miR-21, miR-205, miR-194, miR-103, miR-223, and miR-375, were found in the regulatory network. Moreover, several reported disease-related miRNAs, including miR-198a, miR-103, miR-223, miR-21, miR-194, and miR-375, were found to have common target genes with other DEMs. Survival analysis revealed that 85 DEMs were related to prognosis, among which hsa-miR-1248, hsa-miR-1291, hsa-miR-421, and hsa-miR-7-5p were used for a prognostic survival model. Taken together, this study revealed the important roles of DEGs and DEMs in ESCC development, as well as DEMs in the prognosis of ESCC. This will provide potential therapeutic targets and prognostic predictors for ESCC.</jats:p>

miRNA Profile Based on ART Delay in Vertically Infected HIV-1 Youths Is Associated With Inflammatory Biomarkers and Activation and Maturation Immune Levels

“…In addition to everything described so far related to miRNA-155-5p, that miRNA and miRNA-1248, which is associated with good survival prognoses in cancer (38), both upregulated on EARLY treated HIV-1 patients, strongly correlated with the activation marker HLA-DR, the natural cytotoxicity family activation receptor NKp30 and the inhibiting receptor NKG2A expressed on NK cells and more specifically on the main cytotoxic NK subset, CD16 high and the activated and mature CD56 neg CD16+ NK cells, described as a subset with impaired effector functions in HIV-1 infection (39). Despite the limitation that miRNA profile was determined in the pool of PBMCs without isolated different cell subsets, our results are in agreement with recent insights that have highlighted the role of miRNAs in maintaining killing effect of NK cells in cancer scenario via activation markers modulation (40)(41)(42), in promoting antiviral immunity in the scenario of viral infection (43) and altogether suggests the possible role of both, miRNA-155-5p and miRNA-1248 in regulating inflammatory cytokine production in NK cells, potentially balancing disease progression during chronic HIV infection.…”

MiR-1248: a new prognostic biomarker able to identify supratentorial hemispheric pediatric low-grade gliomas patients associated with progression

“…Finally, miR-1248 has also been suggested as a prognostic biomarker in patients with Wilms tumour and ESCC [59,60], conversely its role as prognostic biomarkers for progressive supratentorial hemispheric pLGGs emerges for the first time in this study.…”

“…Additionally, a wider study of the literature showed that miR-1248 has already been described as an oncomiR correlated with cancer progression in tumours of different tissue-origin [53][54][55][56][57][58][59][60].…”

Identification of therapeutic miRNAs from the arsenic induced gene expression profile of hepatocellular carcinoma

“…The “Search Tool for the Retrieval of Interacting Genes” (STRING) database (version: 11.5) was used to construct a PPI network to comprehend interactions between the DEGs with medium confidence of 0.400 and 5% FDR stringency based on text mining, experiments, databases, and co‐expression which were limited to “Homo sapiens” (Karimizadeh et al, 2019; Zhang et al, 2020). The following network was exported to Cytoscape to find important nodes using the Molecular Complex Detection (MCODE) clustering algorithm and cytoHubba plugin to identify hub genes based on the topological algorithms.…”

“…Micro RNAs (miRNAs) are short read, non-coding RNAs (19-25 nucleotides) associated in several pathways via regulatory network control and subsequently involved in gene expression by forming miRNA-mRNA duplex leading to mRNA degradation (O'Brien et al, 2018;Zhang et al, 2019). miRNA can regulate cellular processes involved in the development of tissue and organs, namely cell differentiation, proliferation, and death (Yao, 2016). Due to this level of involvement, any dysregulation of miRNA-mRNA networks can lead to the onset and progression of human diseases (Dong et al, 2020).…”