title: Validation of gene expression biomarker analysis for biopsy-based clinical trials in Crohn's disease.
abstract: BACKGROUND
  The ability to measure the expression of proinflammatory cytokines from intestinal biopsies in patients with Crohn's disease in an accurate and reproducible way is critical for proof-of-concept and mechanism-of-action trials; however, the number of biopsies from a segment of the ileum or colon required to yield reproducible results has not been rigorously evaluated. We examined intestinal biopsies from patients with Crohn's disease to validate methods for detecting changes in inflammatory gene expression.
  
  
  METHODS
  To evaluate the reproducibility of gene expression measurements, intestinal biopsies were obtained from designated segments from 6 healthy controls, 6 patients with active Crohn's disease, and 6 patients with inactive Crohn's disease. Disease activity was based on the simple endoscopic score for Crohn's disease. Expression of 7 proinflammatory genes was measured from each biopsy using quantitative polymerase chain reaction. Using a linear mixed effects model, the power to detect transcriptional changes corresponding to active and inactive Crohn's disease was calculated.
  
  
  RESULTS
  Total simple endoscopic score for Crohn's disease score corresponds with expression of most inflammatory biomarkers. For most genes, 2 to 5 biopsies are needed to reduce sampling error to <25% for most genes. To measure changes in mRNA expression corresponding to active versus inactive Crohn's disease, 1 to 2 intestinal biopsies from 3 patients before and after treatment are needed to yield power of at least 80%.
  
  
  CONCLUSIONS
  Measuring proinflammatory gene expression from mucosal biopsies from patients with Crohn's disease is practicable and provides objective biomarkers that can be used in proof-of-concept and mechanism-of-action trials to assess response to therapy.
authors.affiliation: *Inflammatory Bowel Disease Center, Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, California; †San Diego Digestive Disease Research Center, University of California San Diego, La Jolla, California; ‡Department of Medicine, Division of Gastroenterology, University of California San Diego, La Jolla, California; §Clinical and Translational Research Institute, University of California San Diego, La Jolla, California; ‖Department of Medicine, Division of Rheumatology, University of California San Diego, La Jolla, California; ¶Department of Pathology, University of California San Diego, La Jolla, California; **Division of Gastroenterology & Hepatology, Kaiser Permanente, San Diego, California; and ††Department of Epidemiology and Biostatistics, Western University, London, ON, Canada.
authors.forename: Brigid S
authors.initials: BS
authors.lastname: Boland
authors.forename: David L
authors.initials: DL
authors.lastname: Boyle
authors.forename: William J
authors.initials: WJ
authors.lastname: Sandborn
authors.forename: Gary S
authors.initials: GS
authors.lastname: Firestein
authors.forename: Barrett G
authors.initials: BG
authors.lastname: Levesque
authors.forename: Joshua
authors.initials: J
authors.lastname: Hillman
authors.forename: Bing
authors.initials: B
authors.lastname: Zhang
authors.forename: James
authors.initials: J
authors.lastname: Proudfoot
authors.forename: Lars
authors.initials: L
authors.lastname: Eckmann
authors.forename: Peter B
authors.initials: PB
authors.lastname: Ernst
authors.forename: Jesus
authors.initials: J
authors.lastname: Rivera-Nieves
authors.forename: Suresh
authors.initials: S
authors.lastname: Pola
authors.forename: Nedret
authors.initials: N
authors.lastname: Copur-Dahi
authors.forename: Guangyong
authors.initials: G
authors.lastname: Zou
authors.forename: John T
authors.initials: JT
authors.lastname: Chang
mesh_terms: D000328:Adult; D015415:Biomarkers / Q000378:metabolism*; D001706:Biopsy; D016022:Case-Control Studies; D002986:Clinical Trials as Topic; D015331:Cohort Studies; D003424:Crohn Disease / Q000235:genetics* / Q000473:pathology; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D007413:Intestinal Mucosa / Q000378:metabolism*; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D015415:Biomarkers; D012333:RNA, Messenger