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Published in: BMC Cancer 1/2014

Open Access 01-12-2014 | Research article

A comprehensive look at transcription factor gene expression changes in colorectal adenomas

Authors: Janine Vonlanthen, Michal J Okoniewski, Mirco Menigatti, Elisa Cattaneo, Daniela Pellegrini-Ochsner, Ritva Haider, Josef Jiricny, Teresa Staiano, Federico Buffoli, Giancarlo Marra

Published in: BMC Cancer | Issue 1/2014

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Abstract

Background

Biological processes are controlled by transcription networks. Expression changes of transcription factor (TF) genes in precancerous lesions are therefore crucial events in tumorigenesis. Our aim was to obtain a comprehensive picture of these changes in colorectal adenomas.

Methods

Using a 3-pronged selection procedure, we analyzed transcriptomic data on 34 human tissue samples (17 adenomas and paired samples of normal mucosa, all collected with ethics committee approval and written, informed patient consent) to identify TFs with highly significant tumor-associated gene expression changes whose potential roles in colorectal tumorigenesis have been under-researched. Microarray data were subjected to stringent statistical analysis of TF expression in tumor vs. normal tissues, MetaCore-mediated identification of TF networks displaying enrichment for genes that were differentially expressed in tumors, and a novel quantitative analysis of the publications examining the TF genes’ roles in colorectal tumorigenesis.

Results

The 261 TF genes identified with this procedure included DACH1, which plays essential roles in the proper proliferation and differentiation of retinal and leg precursor cell populations in Drosophila melanogaster. Its possible roles in colorectal tumorigenesis are completely unknown, but it was found to be markedly overexpressed (mRNA and protein) in all colorectal adenomas and in most colorectal carcinomas. However, DACH1 expression was absent in some carcinomas, most of which were DNA mismatch-repair deficient. When networks were built using the set of TF genes identified by all three selection procedures, as well as the entire set of transcriptomic changes in adenomas, five hub genes (TGFB1, BIRC5, MYB, NR3C1, and TERT) where identified as putatively crucial components of the adenomatous transformation process.

Conclusion

The transcription-regulating network of colorectal adenomas (compared with that of normal colorectal mucosa) is characterized by significantly altered expression of over 250 TF genes, many of which have never been investigated in relation to colorectal tumorigenesis.
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Metadata
Title
A comprehensive look at transcription factor gene expression changes in colorectal adenomas
Authors
Janine Vonlanthen
Michal J Okoniewski
Mirco Menigatti
Elisa Cattaneo
Daniela Pellegrini-Ochsner
Ritva Haider
Josef Jiricny
Teresa Staiano
Federico Buffoli
Giancarlo Marra
Publication date
01-12-2014
Publisher
BioMed Central
Published in
BMC Cancer / Issue 1/2014
Electronic ISSN: 1471-2407
DOI
https://doi.org/10.1186/1471-2407-14-46

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