Oncotarget

Research Papers: Pathology:

Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility

Muhammad A Alvi, Darragh G McArt, Paul Kelly, Marc-Aurel Fuchs, Matthew Alderdice, Clare M McCabe, Victoria Bingham, Claire McGready, Shailesh Tripathi, Frank Emmert-Streib, Maurice B Loughrey, Stephen McQuaid, Perry Maxwell, Peter W Hamilton, Richard Turkington, Jacqueline A James, Richard H Wilson and Manuel Salto-Tellez _

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Oncotarget. 2015; 6:20863-20874. https://doi.org/10.18632/oncotarget.4576

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Abstract

Muhammad A. Alvi1,*, Darragh G. McArt1,*, Paul Kelly2, Marc-Aurel Fuchs1, Matthew Alderdice1, Clare M. McCabe1, Victoria Bingham1, Claire McGready1, Shailesh Tripathi3, Frank Emmert-Streib3, Maurice B. Loughrey2, Stephen McQuaid1,2, Perry Maxwell1,2, Peter W. Hamilton1, Richard Turkington4, Jacqueline A. James1,2, Richard H. Wilson4, Manuel Salto-Tellez1,2

1Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK

2Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK

3Computational Biology and Machine Learning Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK

4Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK

*These authors have contributed equally to this work

Correspondence to:

Manuel Salto-Tellez, e-mail: m.salto-tellez@qub.ac.uk

Keywords: small intestine cancer, p53, Kazald1, CHN2, Pathology Section

Received: June 09, 2015     Accepted: July 20, 2015     Published: July 30, 2015

ABSTRACT

Small bowel accounts for only 0.5% of cancer cases in the US but incidence rates have been rising at 2.4% per year over the past decade. One-third of these are adenocarcinomas but little is known about their molecular pathology and no molecular markers are available for clinical use.

Using a retrospective 28 patient matched normal-tumor cohort, next-generation sequencing, gene expression arrays and CpG methylation arrays were used for molecular profiling.

Next-generation sequencing identified novel mutations in IDH1, CDH1, KIT, FGFR2, FLT3, NPM1, PTEN, MET, AKT1, RET, NOTCH1 and ERBB4. Array data revealed 17% of CpGs and 5% of RNA transcripts assayed to be differentially methylated and expressed respectively (p < 0.01). Merging gene expression and DNA methylation data revealed CHN2 as consistently hypermethylated and downregulated in this disease (Spearman −0.71, p < 0.001). Mutations in TP53 which were found in more than half of the cohort (15/28) and Kazald1 hypomethylation were both were indicative of poor survival (p = 0.03, HR = 3.2 and p = 0.01, HR = 4.9 respectively).

By integrating high-throughput mutational, gene expression and DNA methylation data, this study reveals for the first time the distinct molecular profile of small bowel adenocarcinoma and highlights potential clinically exploitable markers.


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