title: Validated gene expression biomarker analysis for biopsy-based clinical trials in ulcerative colitis.
abstract: BACKGROUND
  Accurate and reproducible measurement of expression of pro-inflammatory cytokines in colonic biopsies from patients with ulcerative colitis (UC) is essential for proof-of-concept and mechanism-of-action studies. Few studies have rigorously established the number of biopsies required for accurate and reproducible biomarker measurements.
  
  
  OBJECTIVE
  To validate methods for measuring changes in gene expression in colonic biopsy samples.
  
  
  METHODS
  Twelve colonic biopsies were obtained from each of six healthy controls, six patients with inactive UC and seven patients with active UC. Mayo endoscopic scores were used as a clinical reference standard. Quantitative PCR was used to assess mRNA expression of eight known inflammatory genes. The power to detect a reduction in gene expression in active vs. inactive UC was calculated using a linear mixed effect model.
  
  
  RESULTS
  mRNA analysis of colonic biopsies is a sensitive and feasible approach for measuring inflammatory gene expression in colonic biopsies. Inflammatory biomarkers correlate with Mayo endoscopic subscores for each colonic region. For most genes, three rectal biopsies from two to four patients are required to detect changes in gene expression corresponding to active vs. inactive UC to achieve a power of 80% with an alpha of 0.05.
  
  
  CONCLUSIONS
  Our data suggest that systematic measurement of inflammatory biomarkers at the mRNA level can be a valuable tool for hypothesis testing, and assessment of clinical activity and response to therapy in ulcerative colitis.
authors.affiliation: Division of Gastroenterology, Department of Medicine, Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA; UCSD Digestive Diseases Research Development Center, University of California San Diego, La Jolla, CA, USA.
authors.forename: B S
authors.initials: BS
authors.lastname: Boland
authors.forename: D L
authors.initials: DL
authors.lastname: Boyle
authors.forename: W J
authors.initials: WJ
authors.lastname: Sandborn
authors.forename: G S
authors.initials: GS
authors.lastname: Firestein
authors.forename: B G
authors.initials: BG
authors.lastname: Levesque
authors.forename: J
authors.initials: J
authors.lastname: Hillman
authors.forename: B
authors.initials: B
authors.lastname: Zhang
authors.forename: J
authors.initials: J
authors.lastname: Proudfoot
authors.forename: L
authors.initials: L
authors.lastname: Eckmann
authors.forename: P B
authors.initials: PB
authors.lastname: Ernst
authors.forename: J
authors.initials: J
authors.lastname: Rivera-Nieves
authors.forename: S
authors.initials: S
authors.lastname: Pola
authors.forename: N
authors.initials: N
authors.lastname: Copur-Dahi
authors.forename: J T
authors.initials: JT
authors.lastname: Chang
mesh_terms: D000328:Adult; D000368:Aged; D015415:Biomarkers / Q000032:analysis; D001706:Biopsy; D002986:Clinical Trials as Topic; D003093:Colitis, Ulcerative / Q000235:genetics* / Q000473:pathology; D003106:Colon / Q000378:metabolism / Q000473:pathology; D016207:Cytokines / Q000235:genetics*; D005260:Female; D005786:Gene Expression Regulation; D006801:Humans; D008297:Male; D008875:Middle Aged; D012333:RNA, Messenger / Q000378:metabolism
chemical_list: D015415:Biomarkers; D016207:Cytokines; D012333:RNA, Messenger