Characterization of mRNA Expression and Endogenous RNA Profiles in Bladder Cancer Based on The Cancer Genome Atlas (TCGA) Database

Abstract

Background Bladder cancer is a multifactorial disease with increasing incidence and mortality. Genetic alterations and altered expressions of mRNAs, long non-coding RNAs (lncRNAs), and miRNAs have been shown to play important roles in the tumorigenesis of bladder cancer. However, the functions of key RNAs and their regulatory network in bladder cancer are still to be elucidated. Material/Methods RNA profiles were downloaded from The Cancer Genome Atlas (TCGA) database. The differentially expressed mRNAs, lncRNAs, and miRNAs in bladder cancer were acquired through analyses of data from 414 bladder cancer tissues and 19 normal bladder tissues. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis was performed by using “DAVID6.8” and the R package “ClusterProfile”. Protein–protein interaction and competing endogenous RNA (ceRNA) networks were constructed by using “STRING” database and Cytoscape 3.6.2. Based on the clinical data and Cox regression, a prognosis model was established, and survival analysis was performed. Results A total of 1819 mRNAs, 659 lncRNAs, and 160 miRNAs were identified as significantly differentially expressed in bladder cancer of which 52 mRNAs, 58 lncRNAs, and 22 miRNAs were incorporated in the ceRNA network. CFL2 and TPM2 were found to be downregulated and showed significant correlation to each other in bladder cancer. HOXB5 and 6 lncRNAs ( ADAMTS9-AS1, AC112721.1, LINC00460, AC110491.1, LINC00163, and HCG22 ) were strongly associated with high-grade, disease stages, and overall survival. Conclusions In this study, we have identified differentially expressed mRNAs, lncRNAs, and miRNAs in bladder cancer which were strongly associated with oncogenesis and prognosis. Further experimental studies are necessary to validate these results.

A co-expression network for differentially expressed genes in bladder cancer and a risk score model for predicting survival

“…Chu et al (2018)[40]30.615/ n = 407NA/ NA7ZNF230; BCL2L14; AHNAK; TMEM109; APOL2; AGER; AOC2Z. Xu et al (2019)[41]NA0.735/ n = 412NA/ NA11MXRA7; EMP1; TNFA1P8L3; SERPINB12; SAPCD1; GABRG1; PLEKHG4B; ABCA4; PTPRR; XAGE2; PEX5LNote: NA represents “not available”, Ref. represents References…”

LncRNA LINC00460 promotes EMT in head and neck squamous cell carcinoma by facilitating peroxiredoxin-1 into the nucleus

“…Analyses of the expression profiles of lncRNAs in HNSCC cells from the Cancer RNA-Seq Nexus (CRN) database have shown that the expression of LINC00460 is upregulated [14, 15]. Located on chromosome 13q33.2 and transcribed as a 913-nt transcript, LINC00460 has been reported to play important roles in tumorigenesis and progression in various tumors and is significantly correlated with survival in the context of several cancer types, including lung cancer [16–19], esophageal cancer [20–22], colorectal cancer [23, 24], nasopharyngeal carcinoma [25], papillary thyroid carcinoma [26], ovarian cancer [27], gastric cancer [28, 29], renal carcinoma [30], meningioma [31], and bladder and urothelial carcinoma [32, 33] . According to previous studies, LINC00460 exhibits aberrant expression in and may directly participate in the pathogenesis of HNSCC [13, 34, 35].…”

Molecular subtyping of glioblastoma based on immune-related genes for prognosis

“…Finally, 14 genes were screened and the corresponding gene families were annotated in accordance with the human gene classification in the HGNC database 43 . Moreover, GO enrichment analyses were carried out using these 14 prognosis-specific immune-related genes and clusterProfile 44 of R package.…”