Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiling of pancreatic epithelial cells in response to tissue contextual changes

ABSTRACT: To understand the molecular process associated with tissue morphogenesis of pancreatic epithelial cells, we profiled the transcriptomes of normal or malignant pancreatic organoids formed in three-dimenstional reconsitututed basement membrance (rBM). Cell monolayers cultured on rBM-coated culture plastics were used as controls. HPDE (immortalized pancreatic epithelial cells) and PANC-1 cells (pancreatic cancer cells) were seeded on reconstituted basement membrane (rBM)-coated culture plastics or cultured on top of three-dimensional (3D) rBM gels. Total RNA samples were collected from cell monolayers or 3D cell clusters (formed at day 2), pancreatic tubules or tumor spheroids (formed at day 6) in the rBM culture, followed by global gene expression profiling.

ORGANISM(S): Homo sapiens

SUBMITTER: Wei-Yu Wang

PROVIDER: E-GEOD-42270 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:MicroRNAs (miRNAs) regulate developmental events such as branching morphogenesis, epithelial to mesenchymal transition (EMT) and its reverse process mesenchymal to epithelial transition (MET). In this study, we performed small RNA sequencing of a breast epithelial progenitor cell line (D492), and its mesenchymal derivative (D492M) cultured in three-dimensional reconstituted basement membrane (3D-rBM) matrix. Large differences in miRNA expression were seen between D492 and D492M. Among the most downregulated miRNAs in D492M was miR-203a, a miRNA that plays an important role in epithelial differentiation. When analyzed over time (21 days) in 3D culture, increased expression of miR-203a was seen in D492, concomitant with increased complexity of the branching structures. When miR-203a was overexpressed in D492M (D492MmiR-203a), a partial reversion towards epithelial phenotype was seen. Gene expression analysis of D492M and D492MmiR-203a revealed that peroxidasin (PXDN), a collagen IV cross-linker was one of the most significantly downregulated genes in D492MmiR-203a. Bioinformatic analysis revealed that PXDN has three putative binding sites for miR-203a in its 3-prime UTR. When a miR-203a mimic was transfected into D492M, reduced PXDN expression was seen. Conversely, inhibition of miR-203a in D492MmiR-203a with a miR-203a inhibitor increased PXDN expression, demonstrating that miR-203a acts as a repressor of PXDN. To verify the binding of miR-203a to the 3’-UTR of PXDN we set up a luciferase reporter assay that confirmed the binding. Collectively, we have demonstrated that miR-203a expression temporally correlates with branching morphogenesis in 3D-rBM and is suppressed in the mesenchymal state. Overexpression of miR-203a in D492M induces a partial MET and reduces the expression of PXDN. Furthermore, we demonstrate that miR-203a is a novel repressor of PXDN. MiR-203-PXDN axis may be an important regulator in branching morphogenesis, EMT and basement membrane remodeling. \

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Gene expression profiling of pancreatic epithelial cells in response to tissue contextual changes

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