Comprehensive Characterization of Common and Cancer-Specific Differently Expressed lncRNAs in Urologic Cancers

Abstract

Urologic cancers, comprising prostate carcinoma (PCa), renal cell carcinoma (RCC), and bladder carcinoma (BCa), were the commonly occurred carcinoma amid males. Long noncoding RNAs (lncRNAs) with the length of more than 200 nt functioned importantly in physiological and pathological advancement. Nevertheless, further investigation regarding lncRNA expression feature and function in urologic cancers should be essential. This study is aimed at uncovering the roles of the differently expressed lncRNAs in urologic cancers. The data of gene expression levels was downloaded from lncRNAtor datasets. The lncRNA expression pattern existing in different urologic cancers was assessed by hierarchical clustering analysis. Gene Ontology (GO) analysis and KEGG pathway analysis were separately applied to evaluate the biological function and process and the biological pathways involving differently expressed lncRNAs. Our results indicated that 18 lncRNA expressions were increased, and 16 lncRNA expressions were reduced in urologic cancers after comparison with that in normal tissues. Moreover, our results demonstrated 61, 422, 137, and 281 lncRNAs were specifically dysregulated in bladder cancer (BLCA), kidney renal clear cell cancer (KIRC), kidney renal papillary cell cancer (KIRP), and prostate adenocarcinoma (PRAD), respectively. Bioinformatics analysis showed that differently expressed lncRNAs displayed crucially in urologic cancers. The prognostic value of common and cancer-specific differently expressed lncRNAs, such as PVT1, in cancer outcomes, was emphasized here. Our research has deeply unearthed the mechanism of differently expressed lncRNAs in urologic cancers development.

Long Non-Coding RNAs as Novel Biomarkers in the Clinical Management of Papillary Renal Cell Carcinoma Patients: A Promise or a Pledge?

“…Through GO analysis, the authors found that pRCC-specific lncRNAs were primarily involved in the morphogenesis of cilium, the process of metabolic, oxidation of fatty acid beta, homeostasis of lipid, and fatty acid beta-oxidation, using acyl-CoA dehydrogenase. KEGG analysis suggested that pRCC-specific lncRNAs principally took part in metabolic pathways, staphylococcus aureus infection, biosynthesis of antibiotics, valine, leucine, and isoleucine degradation, and carbon metabolism [159]. The dysregulation of DLGAP1-AS3, SPON1, ULK4P3, RPL34-AS1, RP11-557H15.3, RP11-368J21.3, ANKRD18DP, LINC00607, and ADORA2A-AS1 were significantly correlated to OS in pRCC and could thus serve as prognostic markers [159].…”

“…KEGG analysis suggested that pRCC-specific lncRNAs principally took part in metabolic pathways, staphylococcus aureus infection, biosynthesis of antibiotics, valine, leucine, and isoleucine degradation, and carbon metabolism [159]. The dysregulation of DLGAP1-AS3, SPON1, ULK4P3, RPL34-AS1, RP11-557H15.3, RP11-368J21.3, ANKRD18DP, LINC00607, and ADORA2A-AS1 were significantly correlated to OS in pRCC and could thus serve as prognostic markers [159].…”

“…They showed that common differently expressed lncRNAs were involved in biological process such as regulating translation, translational initiation, rRNA processing, proteasome-mediated ubiquitin, and DNA replication in pRCC. KEGG analysis showed that common differently expressed lncRNAs were enriched in ribosome, spliceosome, proteasome, Fanconi anemia pathway, and biosynthesis of amino acids in pRCC [159]. The authors also constructed cancer-specific lncRNAs coexpressing networks in the four urologic cancer types under investigation and found that 49 lncRNAs and 794 mRNAs were in pRCC.…”

“…In another study, Yan et al, by using lncRNAtor datasets, demonstrated that 137 lncRNAs were specifically dysregulated (105 lncRNA upregulated and 32 down regulated) in pRCC with respect to normal kidney tissue and different from that dysregulated in other tumors, such as bladder cancer, clear cell RCC, and prostate adenocarcinoma [159]. On the other hand, 34 lncRNAs were differently expressed in all four urologic cancer types [159]. Then, the authors conducted a coexpression network analysis, evaluating the correlation existing in differentially expressed mRNAs and lncR-NAs, to forecast common differently expressed lncRNA functions.…”

“…They found 15 lncR-NAs (RPL32P3, RP11-66N24.3, SNHG1, SNHG11, HERC2P2, AC005154.5, RP5-1180C10.2, RP11-65F13.2, GAS5, AL589743.2, MIR22HG, FDG5-AS1, ZNFX1-AS1, WDFY3-AS2, and RP11-57H14.4) and 498 mRNAs in pRCC. RPL32P3, RP11-66N24.3, RP5-1180C10.2, and SNHG11 were identified to be key regulators in the progression of urologic cancers [159]. Then, the authors used the set of coexpressed mRNAs to determine the role of common differently expressed lncRNAs by using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses.…”