publication . Preprint . Other literature type . 2018

Identification of a primitive intestinal transcription factor network shared between oesophageal adenocarcinoma and its pre-cancerous precursor state

Connor Rogerson; Edward Britton; Sarah Withey; Neil Hanley; Yeng S. Ang; Andrew D. Sharrocks;
Open Access
  • Published: 28 Jul 2018
  • Publisher: Cold Spring Harbor Laboratory
Abstract
<jats:title>Abstract</jats:title><jats:p>Oesophageal adenocarcinoma (OAC) is one of the most frequent causes of cancer deaths and yet compared to other common cancers, we know relatively little about the molecular composition of this tumour type. To further our understanding of this cancer we have used open chromatin profiling to decipher the transcriptional regulatory networks that are operational in OAC. We have uncovered a transcription factor network that is usually found in primitive intestinal cells during embryonic development, centred on HNF4A and GATA6. These transcription factors work together to control the OAC transcriptome. Importantly, we show that...

data.nci.nih.gov/docs/publications/esca_2017/;  Cancer  Genome  Atlas  Research  Network,  2017).  Baek,  S.,  Goldstein,  I.,  and  Hager,  G.L.  (2017).  Bivariate  Genomic  Footprinting  Detects  Changes  in  Transcription Factor Activity. Cell Rep. 19, 1710-1722.  Langmead,  B.,  Trapnell,  C.,  Pop,  M.,  and  Salzberg,  S.  (2009).  Ultrafast  and  memory‐efficient  alignment of short DNA sequences to the human genome. Genome Biol. 10, R25.  San Roman, A.K., Aronson, B.E., Krasinski, S.D., Shivdasani, R.A., and Verzi, M.P. (2015). Transcription  factors  GATA4  and  HNF4A  control  distinct  aspects  of  intestinal  homeostasis  in  conjunction  with  transcription factor CDX2. J. Biol. Chem. 290, 1850-1860.  Wei,  T.  and  Simko  V.  (2017).  R  package  "corrplot":  Visualization  of  a  Correlation  Matrix  (Version  0.84). Available from https://github.com/taiyun/corrplot 

Abstract
<jats:title>Abstract</jats:title><jats:p>Oesophageal adenocarcinoma (OAC) is one of the most frequent causes of cancer deaths and yet compared to other common cancers, we know relatively little about the molecular composition of this tumour type. To further our understanding of this cancer we have used open chromatin profiling to decipher the transcriptional regulatory networks that are operational in OAC. We have uncovered a transcription factor network that is usually found in primitive intestinal cells during embryonic development, centred on HNF4A and GATA6. These transcription factors work together to control the OAC transcriptome. Importantly, we show that...

data.nci.nih.gov/docs/publications/esca_2017/;  Cancer  Genome  Atlas  Research  Network,  2017).  Baek,  S.,  Goldstein,  I.,  and  Hager,  G.L.  (2017).  Bivariate  Genomic  Footprinting  Detects  Changes  in  Transcription Factor Activity. Cell Rep. 19, 1710-1722.  Langmead,  B.,  Trapnell,  C.,  Pop,  M.,  and  Salzberg,  S.  (2009).  Ultrafast  and  memory‐efficient  alignment of short DNA sequences to the human genome. Genome Biol. 10, R25.  San Roman, A.K., Aronson, B.E., Krasinski, S.D., Shivdasani, R.A., and Verzi, M.P. (2015). Transcription  factors  GATA4  and  HNF4A  control  distinct  aspects  of  intestinal  homeostasis  in  conjunction  with  transcription factor CDX2. J. Biol. Chem. 290, 1850-1860.  Wei,  T.  and  Simko  V.  (2017).  R  package  "corrplot":  Visualization  of  a  Correlation  Matrix  (Version  0.84). Available from https://github.com/taiyun/corrplot 

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