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Regional variation in gene expression in the healthy colon is dysregulated in ulcerative colitis
  1. C L Noble1,2,
  2. A R Abbas3,
  3. J Cornelius2,
  4. C W Lees1,
  5. G-T Ho1,
  6. K Toy4,
  7. Z Modrusan4,
  8. N Pal5,
  9. F Zhong5,
  10. S Chalasani5,
  11. H Clark3,
  12. I D Arnott1,
  13. I D Penman1,
  14. J Satsangi1,
  15. L Diehl2
  1. 1
    Gastrointestinal Unit, University of Edinburgh, Western General Hospital, Edinburgh, UK
  2. 2
    Department of Pathology, Genentech, South San Francisco, USA
  3. 3
    Department of Bioinformatics, Genentech, South San Francisco, USA
  4. 4
    Microarray Department, Genentech, South San Francisco, USA
  5. 5
    Core Labs, Genentech, South San Francisco, USA
  1. Dr C Noble, Gastrointestinal Unit, Molecular Medicine Centre, Western General Hospital, Edinburgh, EH4 2XU, UK; noblecolin{at}


Objective: To investigate differential intestinal gene expression in patients with ulcerative colitis and in controls.

Design: Genome-wide expression study (41 058 expression sequence tags, 215 biopsies).

Setting: Western General Hospital, Edinburgh, UK, and Genentech, San Francisco, USA.

Patients: 67 patients with ulcerative colitis and 31 control subjects (23 normal subjects and 8 patients with inflamed non-inflammatory bowel disease biopsies).

Interventions: Paired endoscopic biopsies were taken from 5 specific anatomical locations for RNA extraction and histology. The Agilent microarray platform was used and confirmation of results was undertaken by real time polymerase chain reaction and immunohistochemistry.

Results: In healthy control biopsies, cluster analysis showed differences in gene expression between the right and left colon. (χ2 = 25.1, p<0.0001). Developmental genes, homeobox protein A13 (HOXA13), (p = 2.3×10−16), HOXB13 (p<1×10−45), glioma-associated oncogene 1 (GLI1) (p = 4.0×10−24), and GLI3 (p = 2.1×10−28) primarily drove this separation. When all ulcerative colitis biopsies and control biopsies were compared, 143 sequences had a fold change of >1.5 in the ulcerative colitis biopsies (0.01>p>10−45) and 54 sequences had a fold change of <−1.5 (0.01>p>10−20). Differentially upregulated genes in ulcerative colitis included serum amyloid A1 (SAA1) (p<10−45) the alpha defensins 5 and 6 (DEFA5 and 6) (p = 0.00003 and p = 6.95×10−7, respectively), matrix metalloproteinase 3 (MMP3) (p = 5.6×10−10) and MMP7 (p = 2.3×10−7). Increased DEFA5 and 6 expression was further characterised to Paneth cell metaplasia by immunohistochemistry and in situ hybridisation. Sub-analysis of the inflammatory bowel disease 2 (IBD2) and IBD5 loci, and the ATP-binding cassette (ABC) transporter genes revealed a number of differentially regulated genes in the ulcerative colitis biopsies.

Conclusions: Key findings are the expression gradient in the healthy adult colon and the involvement of novel gene families, as well as established candidate genes in the pathogenesis of ulcerative colitis.

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  • ▸ Supplementary figures, tables and methods are published online only at

  • JS and LD are joint senior authors.

  • Competing interests: None.

  • Ethics approval: Approval for this study was granted by the Lothian Research Ethics Committee: REC 04/S1103/22.