ABSTRACT
Objective This study aimed to analyze the differences in the molecular characteristics of transcriptome between esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). Methods We obtained transcriptomic data on ESCC and EAC from the TCGA database, screened differentially expressed mRNAs, lncRNAs and miRNAs in cancer and the adjacent tissues, and constructed a network of ESCC- and EAC-related competitive endogenous RNA (ceRNA). We predicted the target genes and performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses on important miRNAs, and compared the molecular features of the transcriptomes between ESCC and EAC. Results The ceRNA network analysis showed that PVT1, LINC00524, miR-204, miR-383, HOXC8 and NTRK2 played important regulatory roles in both ESCC and EAC. Totally, 13 227 regulatory target genes were predicted with miR-204-5p via miRWalk and 232 target genes screened from the miRDB database. GO analysis revealed 38 enrichments, mainly involved in the regulation of cell-matrix adhesion, morphogenesis of cell membrane projection, and β-catenin combination, KEGG analysis showed 4 relevant pathways: the hedgehog, life-regulating, estrogen and relaxin signaling pathways, and survival analysis manifested LINC00261, MLIP-IT1 and LINC00504 as survival-related differentially expressed lncRNAs, hsa-mir-338 as differentially expressed miRNA, but no mRNA in ESCC. Survival-related differentially expressed lncRNAs in EAC included CYP1B1-AS1 and HOTAIR, and differentially expressed mRNAs included IL11, NTRK2, ANGPT2 and PBK. Of the differentially expressed lncRNAs in both ESCC and EAC, 150 (15.4%) were up-regulated and 158 (26.8%) down-regulated; of the miRNAs, 22 (24.2%) up-regulated and 8 (27.6%) down-regulated; and of the mRNAs, 234 (20.5%) up-regulated and 418 (23.7%) down-regulated. Conclusion There are significant molecular differences between ESCC and EAC, and the differentially expressed lncRNA, miRNA and mRNA may provide some new targets and molecular markers for the treatment and prognosis of esophageal carcinoma.
ABSTRACT
Objective Differentially-expressed lncRNAs in hepatocellular carcinoma (HCC) among different races remain unclarified at present time. This study aimed to analyze the shared and specific differential expression profiles of lncRNAs in HCC patients of the yellow, white and black races in the TCGA database and predict their functions and regulatory mechanisms. Methods We screened differentially expressed lncRNAs in the cancer and paracancer tissues of the HCC patients of the yellow, white and black races, compared differential expression profiles of lncRNAs and identified the common differentially expressed lncRNAs among the three races. We performed COX regression survival analysis on the differentially expressed lncRNAs, constructed a ceRNA network, and predicted the target genes and their regulatory mechanisms by GO and KEGG enrichment analyses and prediction of the transcription factors. Results Totally 49 HCC-related lncRNAs were found in all the three races, with 21.5% overlapped in the white and black races, 7.8% in the white and yellow and 5.8% in the black and Asians. GO enrichment analysis showed that the target genes of LINC01224 in the all three races were related to DNA replication and transposition, gene expression regulation, epigenetics, silencing of miRNAs, and gene silencing after RNA transcription, while KEGG analysis revealed a correlation of LINC01224 with the cell cycle and DNA replication. Target genes were not predicted in the 11 survival-related lncRNAs in the patients of the white race. Of the 6 survival-related lncRNAs in the yellow patients, the target gene of AC093609.1 was shown to be involved in the activity of the ionic channel, regulation of cardiomyopathy- and cardiomyocyte adrenalin-related signaling pathways, various metabolic functions, fat degradation, ABC protein transportation, and amino acid metabolism. Conclusion HCC-related expression profiles of lncRNAs have a great similarity between the white and black races, but a high differentiality between the yellow and the white or black. LINC01224 may be involved in the relation of tumor growth in all the three races, while AC093609.1 and AC126118.1 specific of the yellow race play an important role in tumor metabolism.