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, Manuel Salto-Tellez

Research output: Contribution to journalArticlepeer-review

43 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)20863-20874
Number of pages12
Issue number25
Publication statusPublished - 28 Aug 2015
Externally publishedYes


  • CHN2
  • Kazald1
  • p53
  • Pathology Section
  • small intestine cancer
  • Oligonucleotide Array Sequence Analysis
  • Epigenesis, Genetic
  • Humans
  • Middle Aged
  • Gene Expression Regulation, Neoplastic
  • Intestine, Small/pathology
  • Male
  • Gene Expression Profiling
  • Biomarkers, Tumor
  • DNA Methylation
  • Genes, p53
  • DNA Mutational Analysis
  • Aged, 80 and over
  • Adult
  • Female
  • Retrospective Studies
  • Adenocarcinoma/pathology
  • Intestinal Neoplasms/pathology
  • Treatment Outcome
  • Chimerin Proteins/genetics
  • CpG Islands
  • Aged
  • High-Throughput Nucleotide Sequencing
  • Mutation
  • Pathology, Molecular
  • Nucleophosmin


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