Identification of aberrantly expressed long non-coding RNAs in stomach adenocarcinoma
نویسندگان
چکیده
AIM Stomach adenocarcinoma (STAD) is a common malignancy worldwide. This study aimed to identify the aberrantly expressed long non-coding RNAs (lncRNAs) in STAD. RESULTS Total of 74 DElncRNAs and 449 DEmRNAs were identified in STAD compared with paired non-tumor tissues. The DElncRNA/DEmRNA co-expression network was constructed, which covered 519 nodes and 2993 edges. The qRT-PCR validation results of DElncRNAs were consistent with our bioinformatics analysis based on RNA-sequencing. The DEmRNAs co-expressed with DElncRNAs were significantly enriched in gastric acid secretion, complement and coagulation cascades, pancreatic secretion, cytokine-cytokine receptor interaction and Jak-STAT signaling pathway. The expression levels of the nine candidate DElncRNAs in TCGA database were compatible with our RNA-sequencing. FEZF1-AS1, HOTAIR and LINC01234 had the potential diagnosis value for STAD. MATERIALS AND METHODS The lncRNA and mRNA expression profile of 3 STAD tissues and 3 matched adjacent non-tumor tissues was obtained through high-throughput RNA-sequencing. Differentially expressed lncRNAs/mRNAs (DElncRNAs/DEmRNAs) were identified in STAD. DElncRNA/DEmRNA co-expression network construction, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to predict the biological functions of DElncRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was subjected to validate the expression levels of DEmRNAs and DElncRNAs. Moreover, the expression of DElncRNAs was validated through The Cancer Genome Atlas (TCGA) database. The diagnosis value of candidate DElncRNAs was accessed by receiver operating characteristic (ROC) analysis. CONCLUSIONS Our work might provide useful information for exploring the tumorigenesis mechanism of STAD and pave the road for identification of diagnostic biomarkers in STAD.
منابع مشابه
Identification and Functional Prediction of Long Non-Coding RNAs Responsive to Drought stress in Lens culinaris L.
Drought stress is one of the main environmental factors that affects growth and productivity of crop plants, including lentil. In the course of evolution evolution, crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged in plant in response to drought and other abiotic stresses. In the present study, after identifying lncRNAs within the expression profile of lentil, RNA-s...
متن کاملP87: The Role of the Long Non-Coding RNA Sequences (LncRNAs) in Neurological Disorders
Precise interpretation of the transcriptome sequences in the several species showed that the major part of genome has been transcribed; however, just a few amounts of the transcription sequences have open-reading frames which are conversed during the evolution. So, it is unlikely that many of the transcribed sequences code the proteins. Among the all human non-coding transcripts, at least 10000...
متن کاملComputational Identification of Micro RNAs and Their Transcript Target(s) in Field Mustard (Brassica rapa L.)
Background: Micro RNAs (miRNAs) are a pivotal part of non-protein-coding endogenous small RNA molecules that regulate the genes involved in plant growth and development, and respond to biotic and abiotic environmental stresses posttranscriptionally.Objective: In the present study, we report the results of a systemic search for identifi cation of new miRNAs in B. rapa using homology-based ...
متن کاملLong non-coding RNAs and their significance in human diseases
Protein-coding genes account for only a small fraction of the human genome and most of the genomic sequences are transcriptionally silent, but recent observations indicate significant functional elements, including non-coding protein transcripts in the human genome. Long non-coding RNAs (lncRNAs) have been defined as transcripts of >200 nucleotides without protein-coding capacity that perform t...
متن کاملSNHG6 203 and SNHG6 201 Transcripts Can be Used as Contributory Factors for a Well-Timed Prognosis and Diagnosis of Colorectal Cancer
Background:Long non-coding RNAs, as a big part of non-coding RNAs, are considered functionally more than past. These transcripts could be involved in carcinogenesis. SNHG6, as a long non-coding RNA, has been reported to be expressed more in colorectal cancer tissues than non-cancerous ones. Colorectal cancer as a malignancy needs fast prognostic and diagnostic methods for well...
متن کامل