title: Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn's disease and discriminative value of FOXP3 mRNA expression.
abstract: OBJECTIVE
  Crohn's disease (CD) and intestinal tuberculosis (ITB) are both chronic granulomatous conditions with similar phenotypic presentations. Hence, there is need for a biomarker to differentiate between both these two diseases. This study aimed at genome-wide gene expression analysis of colonic biopsies from confirmed cases of ITB and CD in comparison with controls. To evaluate the role of T regulatory cells, forkhead box P3 (FOXP3) mRNA expression was quantified in serum as well as in colonic biopsies from patients with ITB and with the controls.
  
  
  METHODS
  Paired samples, including serum and colonic biopsies, were taken from 33 study subjects (CD, ITB and controls), and total RNA was extracted. Human whole genome gene expression microarray analysis was performed using the Illumina HumanWG-6 BeadChip Kit with six total RNA samples of the three groups in duplicates. Real-time PCR for FOXP3 mRNA expression was analyzed in serum samples and colonic biopsy samples (4-CD, 5-ITB, 4-controls).
  
  
  RESULTS
  In CD and ITB there was 1.5-fold upregulation of 92 and 382 genes and 1.5-fold downregulation of 91 and 256 genes, respectively. Peroxisome proliferators via the PPARγ pathway were most significantly downregulated (P < 0.005) in CD. Additionally, the IL4/5/6 signaling pathways and Toll-like receptor signaling pathway were identified as significantly differentially regulated (P < 0.005) at > 2-fold change. In ITB, the complement activation pathway, specifically the classical pathway, was the most significantly upregulated. FOXP3 mRNA expression was significantly elevated in colonic biopsies obtained from ITB patients as compared with CD cases (4.70 ± 2.21 vs 1.48 ± 0.31, P = 0.016).
  
  
  CONCLUSIONS
  FOXP3 mRNA expression in colonic mucosa could be a discriminatory marker between ITB and CD. Upregulation of the complement activation pathway in ITB suggests that pathogenetic mechanisms for ITB are similar to those of pulmonary tuberculosis. In CD, downregulation of PPARγ was seen in colonic tissue, suggesting that restoration of PPARγ-dependent anti-microbial barrier function may be a therapeutic target.
authors.affiliation: Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India, and vins_ahuja@hotmail.com.
authors.forename: Vineet
authors.initials: V
authors.lastname: Ahuja
authors.affiliation: The Centre for Genomic Application (An IGIB-IMM collaboration), New Delhi, India.
authors.forename: Swati
authors.initials: S
authors.lastname: Subodh
authors.affiliation: The Centre for Genomic Application (An IGIB-IMM collaboration), New Delhi, India.
authors.forename: Amit
authors.initials: A
authors.lastname: Tuteja
authors.affiliation: Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India, and.
authors.forename: Veena
authors.initials: V
authors.lastname: Mishra
authors.affiliation: Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India, and.
authors.forename: Sushil Kumar
authors.initials: SK
authors.lastname: Garg
authors.affiliation: The Centre for Genomic Application (An IGIB-IMM collaboration), New Delhi, India.
authors.forename: Neha
authors.initials: N
authors.lastname: Gupta
authors.affiliation: Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India, and.
authors.forename: Govind
authors.initials: G
authors.lastname: Makharia
authors.affiliation: Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India, and.
authors.forename: S K
authors.initials: SK
authors.lastname: Acharya
keywords: Crohn’s disease; FOXP3 mRNA; intestinal tuberculosis; microarray gene expression profiling; signaling pathway