Transcriptomics

Dataset Information

296

A combined genomic approach unveils the transcriptional basis of heterogeneity of human pancreatic ductal adenocarcinoma [RNA-seq]


ABSTRACT: The histological grade of carcinomas describes the ability of tumor cells to organize differentiated epithelial structures and has prognostic impact. Molecular control of differentiation in normal and cancer cells relies on lineage-determining transcription factors (TFs) that activate the repertoire of cis-regulatory elements controlling cell type-specific transcriptional outputs. TF recruitment to cognate genomic DNA binding sites results in the deposition of histone marks characteristic of enhancers and other cis-regulatory elements. Here we integrated transcriptomics and genome-wide analysis of chromatin marks in human pancreatic ductal adenocarcinoma (PDAC) cells of different grade to identify first, and then experimentally validate the sequence-specific TFs controlling grade-specific gene expression. We identified a core set of TFs with a pervasive binding to the enhancer repertoire characteristic of differentiated PDACs and controlling different modules of the epithelial gene expression program. Defining the regulatory networks that control the maintenance of epithelial differentiation of PDAC cells will help determine the molecular basis of PDAC heterogeneity and progression. Poly(A) fraction of the total RNA from human pancreatic ductal adenocarcinoma cell lines was extracted and subjected to by multiparallel sequencing. Experiments were carried out in unmodified cells in duplicate, genome edited clonal CFPAC1 cells (2 KLF5-deleted CRISPR-Cas9 clones, 3 ELF3-deleted CRISPR-Cas9 clones and 2 wt clones) and CFPAC1 cells ectopically expressing ZEB1 or empty vector control (in duplicate).

ORGANISM(S): Homo sapiens  

SUBMITTER: Chiara Balestrieri   Giuseppe Diaferia  Gioacchino Natoli 

PROVIDER: E-GEOD-64558 | ArrayExpress | 2016-01-18

SECONDARY ACCESSION(S): GSE64558SRP051606PRJNA271301

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer.

Diaferia Giuseppe R GR   Balestrieri Chiara C   Prosperini Elena E   Nicoli Paola P   Spaggiari Paola P   Zerbi Alessandro A   Natoli Gioacchino G  

The EMBO journal 20160114 6


The histological grade of carcinomas describes the ability of tumor cells to organize in differentiated epithelial structures and has prognostic and therapeutic impact. Here, we show that differential usage of the genomic repertoire of transcriptional enhancers leads to grade-specific gene expression programs in human pancreatic ductal adenocarcinoma (PDAC). By integrating gene expression profiling, epigenomic footprinting, and loss-of-function experiments in PDAC cell lines of different grade,  ...[more]

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