Abstract 4792: Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with clinical utility
Authors: Muhammad A. Alvi, Darragh G. McArt, Paul Kelly, Marc-Aurel Fuchs, Matthew Alderdice, Clare M. McCabe, Victoria Bingham, Claire McGready, Stephen McQuaid, Perry Maxwell, Peter Hamilton, Jacqueline A. James, Richard Wilson, Manuel Salto-Tellez
Journal: Cancer Research (2015)

Abstract Small bowel accounts for only 0.5% of cancer cases in the US; a third of which are adenocarcinomas. But incidence rates have been rising at a rate of 2.4% per year over the last decade. Because of the rarity of this cancer, little is known about its molecular pathology and there are no molecular markers for diagnosis, predicting prognosis or therapeutic intervention. The aim of this study was therefore to look into this disease at a molecular level to better understand its biology and identify biomarkers and potential points of therapeutic intervention. Using a retrospective 28 patient matched normal-tumor cohort next generation sequencing (NGS) was performed using a 50 gene cancer hotspot panel, gene expression arrays were used to profile ∼29,000 RNA transcripts and 450k CpG methylation arrays were used to carry out DNA methylation analysis. We also looked at microsatellite instability (MSI), HER2 and p53 expression. NGS identified novel mutations in IDH1, CDH1, KIT, NRAS, FGFR2, FLT3, NPM1, PTEN, MET, AKT1, RET, NOTCH1 and ERBB4. Previously known mutations such as high-frequency KRAS and TP53 and low-frequency HER2 were also confirmed in our cohort. The average patient had 2.6 mutations with eight patients having only a single mutation to one having seven. Array data revealed 17% of CpGs and 5% of RNA transcripts assayed to be differentially methylated and expressed respectively (p&amp;lt;0.01). Gene expression and DNA methylation data was merged to reveal 266 transcripts where DNA methylation was inversely correlated with gene expression (Spearman &amp;lt; -0.5). Almost 90% of these CpGs were found to be located inside gene bodies, the first exons and 5′ and 3′ UTRs. Almost 60% of the overall genome-wide changes in methylation (hyper and hypo) also occurred inside the gene bodies, the first exons and 5′ and 3′ UTRs. CHN2 was identified as one of the genes consistently hypermethylated and downregulated in tumor compared to normal (Spearman -0.71, p&amp;lt;0.001). This trend was validated using immunohistochemistry and pyrosequencing. Finally 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 = 0.0345, HR = 3.2 and p = 0.0079, HR = 4.9 respectively). Sanger sequencing was used to confirm TP53 mutations and immunohistochemistry analysis confirmed protein overexpression in all mutant cases. Six cases were positive for MSI and three for HER2 overexpression. This study has for the first time highlighted the extent of molecular changes taking place in SBA. The clinical potential of TP53 mutations and Kazald1 hypomethylation as prognostic biomarkers and CHN2 as a diagnostic biomarker are focus areas for further research by our group. Citation Format: Muhammad A. Alvi, Darragh G. McArt, Paul Kelly, Marc-Aurel Fuchs, Matthew Alderdice, Clare M. McCabe, Victoria Bingham, Claire McGready, Stephen McQuaid, Perry Maxwell, Peter Hamilton, Jacqueline A. James, Richard Wilson, Manuel Salto-Tellez. Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with clinical utility. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4792. doi:10.1158/1538-7445.AM2015-4792