Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer

Abstract

BackgroundPancreatic ductal adenocarcinoma (PDAC) is known by its aggressiveness and lack of effective therapeutic options. Thus, improvement in current knowledge of molecular changes associated with pancreatic cancer is urgently needed to explore novel venues of diagnostics and treatment of this dismal disease. While there is mounting evidence that long noncoding RNAs (lncRNAs) transcribed from intronic and intergenic regions of the human genome may play different roles in the regulation of gene expression in normal and cancer cells, their expression pattern and biological relevance in pancreatic cancer is currently unknown. In the present work we investigated the relative abundance of a collection of lncRNAs in patients' pancreatic tissue samples aiming at identifying gene expression profiles correlated to pancreatic cancer and metastasis.MethodsCustom 3,355-element spotted cDNA microarray interrogating protein-coding genes and putative lncRNA were used to obtain expression profiles from 38 clinical samples of tumor and non-tumor pancreatic tissues. Bioinformatics analyses were performed to characterize structure and conservation of lncRNAs expressed in pancreatic tissues, as well as to identify expression signatures correlated to tissue histology. Strand-specific reverse transcription followed by PCR and qRT-PCR were employed to determine strandedness of lncRNAs and to validate microarray results, respectively.ResultsWe show that subsets of intronic/intergenic lncRNAs are expressed across tumor and non-tumor pancreatic tissue samples. Enrichment of promoter-associated chromatin marks and over-representation of conserved DNA elements and stable secondary structure predictions suggest that these transcripts are generated from independent transcriptional units and that at least a fraction is under evolutionary selection, and thus potentially functional.Statistically significant expression signatures comprising protein-coding mRNAs and lncRNAs that correlate to PDAC or to pancreatic cancer metastasis were identified. Interestingly, loci harboring intronic lncRNAs differentially expressed in PDAC metastases were enriched in genes associated to the MAPK pathway. Orientation-specific RT-PCR documented that intronic transcripts are expressed in sense, antisense or both orientations relative to protein-coding mRNAs. Differential expression of a subset of intronic lncRNAs (PPP3CB, MAP3K14 and DAPK1 loci) in metastatic samples was confirmed by Real-Time PCR.ConclusionOur findings reveal sets of intronic lncRNAs expressed in pancreatic tissues whose abundance is correlated to PDAC or metastasis, thus pointing to the potential relevance of this class of transcripts in biological processes related to malignant transformation and metastasis in pancreatic cancer.

Long non-coding RNAs in cancer invasion and metastasis

“…[61][62][63] A subset of intronic lncRNAs (PPP3CB, MAP3K14, and DAPK1 loci) expressed in pancreatic tissues was identified; the abundance of these lncRNAs was correlated with PDAC metastasis and were enriched in genes associated with the MAPK pathway. 64,65 Nevertheless, further studies will be necessary to reveal the possible biological functions and molecular mechanisms of these lncRNAs in PDAC tumorigenesis and/or progression, and these intronic lncRNAs might be novel candidate biomarkers of pancreatic tumors.…”

LincRNA-p21 enhances the sensitivity of radiotherapy for human colorectal cancer by targeting the Wnt/β-catenin signaling pathway

“…At present, lincRNAs are emerging as either oncogenes or tumor suppressor genes (11)(12)(13)(14)(15). Previous evidence demonstrated the aberrant expression of lincRNAs in digestive system carcinomas (16)(17)(18)(19)(20)(21). However, the biological function of lincRNAs in the vast majority of digestive system carcinomas remains unclear.…”

Microarray expression profile analysis of long non-coding RNAs in pancreatic ductal adenocarcinoma

“…H19 also promoted PDAC cell invasion and migration at least partially by increasing HMGA2-mediated epithelial-mesenchymal transition (EMT) through antagonizing let-7 (53). The previous studies also reported several other lncRNAs related to PDAC, such as HULC, PVTI, MAP3K14, PPP3Cb, DAPKI and LOC285194 (54)(55)(56)(57). In the present study, we also examined the expression of some most studied lncRNAs in PDAC, such as MALAT1, HOTTIP, H19, HULC, PVTI, MAP3K14, PPP3Cb, DAPKI and LOC285194 in the combination data set of 3 pairs of microarrays, showing that MALAT1 and HOTTIP were significantly upregulated 16.22-and 23.48-fold in PDAC tissues compared with paired non-tumor tissues respectively; however, other lncRNAs were not significantly differentially expressed between PDAC tissues and paired non-tumor tissues.…”