Long non-coding RNA expression profiles in gallbladder carcinoma identified using microarray analysis

Abstract

Gallbladder carcinoma (GBC) is the most common biliary tract cancer and exhibits poor patient prognosis. Previous studies have identified that long non-coding RNAs (lncRNAs) serve important regulatory roles in cancer biology. Alterations in lncRNAs are associated with several types of cancer. However, the contribution of lncRNAs to GBC remains unclear. To investigate the lncRNAs that are potentially involved in GBC, lncRNA profiles were identified in three pairs of human GBC and corresponding peri-carcinomatous tissue samples using microarray analysis. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to validate the microarray data. In order to elucidate potential functions, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes analysis, and network analysis were used to determine relevant signaling pathways. Abundant RNA probes were used, and 1,758 lncRNAs and 1,254 mRNAs were detected to be differentially expressed by the microarray. Compared with para-carcinoma tissue, numerous lncRNAs were markedly upregulated or downregulated in GBC. The results demonstrated that the lncRNAs that were downregulated in GBC were more numerous compared with the lncRNAs that were upregulated. Among them, RP11-152P17.2-006 was the most upregulated, whereas CTA-941F9.9 was the most downregulated. The RT-qPCR results were consistent with the microarray data. Pathway analysis indicated that five pathways corresponded to the differentially expressed transcripts. It was demonstrated that lncRNA expression in GBC was markedly altered, and a series of novel lncRNAs associated with GBC were identified. The results of the present study suggest that the functions of lncRNAs are important in GBC development and progression.

Orchestrating a biomarker panel with lncRNAs and mRNAs for predicting survival in pancreatic ductal adenocarcinoma

“…For example, CTA-941F9.9 is downregulated in gallbladder carcinoma and might be important in chondrogenic differentiation. 32,33 LINC00636 is enriched in human epidermal growth factor receptor-2 (HER-2) highly-expressed breast cancer subtype. 34 For mRNAs, MMP9 is well established in carcinogenesis through extracellular matrix remodeling and angiogenesis.…”

“…However, several studies have indicated that several of them might be functionally important. For example, CTA‐941F9.9 is downregulated in gallbladder carcinoma and might be important in chondrogenic differentiation . LINC00636 is enriched in human epidermal growth factor receptor‐2 (HER‐2) highly‐expressed breast cancer subtype .…”

Identification of UBE2T as an independent prognostic biomarker for gallbladder cancer

“…With the rapid development of microarray and RNA sequencing technology, a high amount of differentially expressed genes (DEGs) have been identified in cancer tissues compared with non-tumor tissues ( 9 , 10 ). A previous study identified 758 long non-coding RNAs (lncRNAs) and 1,254 mRNAs in gallbladder cancer tissues compared with adjacent normal tissues ( 11 ). However, clinical trials still lack precise biomarkers for gallbladder cancer ( 12 ).…”

In silico analysis to identify novel ceRNA regulatory axes associated with gallbladder cancer

“…Various groups have analyzed the differential expression of miRNAs (DEMs) in tissue ( Letelier et al, 2014 ; Zhou et al, 2014 ; Goeppert et al, 2019 ), serum/plasma extracellular vesicles ( Ueta et al, 2021 ; Yang et al, 2022 ) using high-throughput studies in GBC. Similarly, other researchers have analyzed differentially expressed lncRNA (DELs) using high-throughput studies ( Ma et al, 2016 ; Wang et al, 2017a ; Wu et al, 2017 ), however, the majority of the studies on lncRNA in GBC are targeted studies. Few of these studies revealed the “lncRNA-miRNA-mRNA network” in GBC in a targeted manner ( Wang et al, 2016a ; Hu et al, 2019 ; Yang et al, 2020 ; Zhang et al, 2020 ).…”