Dataset Information

Transcriptomic and computational analysis identified LPA metabolism, KLHL14 and KCNE3 as novel regulators of Epithelial-Mesenchymal Transition.

ABSTRACT: Epithelial-mesenchymal transition (EMT) is a complex biological program between physiology and pathology. Here, amniotic epithelial cells (AEC) were used as in vitro model of transiently inducible EMT in order to evaluate the transcriptional insights underlying this process. Therefore, RNA-seq was used to identify the differentially expressed genes and enrichment analyses were carried out to assess the intracellular pathways involved. As a result, molecules exclusively expressed in AEC that experienced EMT (GSTA1-1 and GSTM3) or when this process is inhibited (KLHL14 and KCNE3) were identified. Lastly, the network theory was used to obtain a computational model able to recognize putative controller genes involved in the induction and in the prevention of EMT. The results suggested an opposite role of lysophosphatidic acid (LPA) synthesis and degradation enzymes in the regulation of EMT process. In conclusion, these molecules may represent novel EMT regulators and also targets for developing new therapeutic strategies.

SUBMITTER: Di Lollo V

PROVIDER: S-EPMC7060278 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Transcriptomic and computational analysis identified LPA metabolism, KLHL14 and KCNE3 as novel regulators of Epithelial-Mesenchymal Transition.

Di Lollo V V Canciello A A Orsini M M Bernabò N N Ancora M M Di Federico M M Curini V V Mattioli M M Russo V V Mauro A A Cammà C C Barboni B B

Scientific reports 20200306 1

Epithelial-mesenchymal transition (EMT) is a complex biological program between physiology and pathology. Here, amniotic epithelial cells (AEC) were used as in vitro model of transiently inducible EMT in order to evaluate the transcriptional insights underlying this process. Therefore, RNA-seq was used to identify the differentially expressed genes and enrichment analyses were carried out to assess the intracellular pathways involved. As a result, molecules exclusively expressed in AEC that expe ...[more]

PMID: 32144311

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Project description:Epithelial-mesenchymal transition (EMT) involving down-regulation of E-cadherin is thought to play a fundamental role during early steps of invasion and metastasis of carcinoma cells. The aim of our study was to elucidate the role of EMT regulators Snail, SIP1 (both are direct repressors of E-cadherin), and Twist (an activator of N-cadherin during Drosophila embryogenesis), in primary human gastric cancers. Expression of Snail, SIP1, and Twist was analyzed in 48 gastric carcinomas by real-time quantitative RT-PCR in paraffin-embedded and formalin-fixed tissues. The changes of expression levels of these genes in malignant tissues compared to matched non-tumorous tissues were correlated with the expression of E- and N-cadherin. From 28 diffuse-type gastric carcinomas analyzed reduced E-cadherin expression was detected in 11 (39%) cases compared to non-tumorous tissues. Up-regulated Snail could be found in 6 cases with reduced or negative E-cadherin expression. However, there was no correlation to increased SIP1 expression. Interestingly, we could detect abnormal expression of N-cadherin mRNA in 6 cases, which was correlated with Twist overexpression in 4 cases. From 20 intestinal-type gastric cancer samples reduced E-cadherin expression was found in 12 (60%) cases, which was correlated to up-regulation of SIP1, since 10 of these 12 cases showed elevated mRNA levels, whereas Snail, Twist, and N-cadherin were not up-regulated. We present the first study investigating the role of EMT regulators in human gastric cancer and provide evidence that an increase in Snail mRNA expression is associated with down-regulation of E-cadherin in diffuse-type gastric cancer. We detected abnormally positive or increased N-cadherin mRNA levels in the same tumors, probably due to overexpression of Twist. SIP1 overexpression could not be linked to down-regulated E-cadherin in diffuse-type tumors, but was found to be involved in the pathogenesis of intestinal-type gastric carcinoma. We conclude that EMT regulators play different roles in gastric carcinogenesis depending on the histological subtype.

Project description:Epithelial to mesenchymal transition (EMT) is the process by which stationary epithelial cells transdifferentiate to mesenchymal cells with increased motility. EMT is integral in early stages of development and wound healing. Studies have shown that EMT could be a critical early event in tumor metastasis that is involved in acquisition of migratory and invasive properties in multiple carcinomas.In this study, we used 15 published gene expression microarray datasets from Gene Expression Omnibus (GEO) that represent 12 cell lines from 6 cancer types across 95 observations (45 unique samples and 50 replicates) with different modes of induction of EMT or the reverse transition, mesenchymal to epithelial transition (MET). We integrated multiple gene expression datasets while considering study differences, batch effects, and noise in gene expression measurements. A universal differential EMT gene list was obtained by normalizing and correcting the data using four approaches, computing differential expression from each, and identifying a consensus ranking. We confirmed our discovery of novel EMT genes at mRNA and protein levels in an in vitro EMT model of prostate cancer - PC3 epi, EMT and Taxol resistant cell lines. We validate our discovery of C1orf116 as a novel EMT regulator by siRNA knockdown of C1orf116 in PC3 epithelial cells.Among differentially expressed genes, we found known epithelial and mesenchymal marker genes such as CDH1 and ZEB1. Additionally, we discovered genes known in a subset of carcinomas that were unknown in prostate cancer. This included epithelial specific LSR and S100A14 and mesenchymal specific DPYSL3. Furthermore, we also discovered novel EMT genes including a poorly-characterized gene C1orf116. We show that decreased expression of C1orf116 is associated with poor prognosis in lung and prostate cancer patients. We demonstrate that knockdown of C1orf116 expression induced expression of mesenchymal genes in epithelial prostate cancer cell line PC3-epi cells, suggesting it as a candidate driver of the epithelial phenotype.This comprehensive approach of statistical analysis and functional validation identified global expression patterns in EMT and candidate regulatory genes, thereby both extending current knowledge and identifying novel drivers of EMT.

Dataset Information

Transcriptomic and computational analysis identified LPA metabolism, KLHL14 and KCNE3 as novel regulators of Epithelial-Mesenchymal Transition.

Publications

Transcriptomic and computational analysis identified LPA metabolism, KLHL14 and KCNE3 as novel regulators of Epithelial-Mesenchymal Transition.

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