Patients with inflammatory bowel disease exhibit dysregulated responses to microbial DNA.
BACKGROUND
A critical role for the gut epithelium lies in its ability to discriminate between pathogens and commensals and respond appropriately. Dysfunctional interactions between microbes and epithelia are believed to have a role in inflammatory bowel disease (IBD). In this study, we analyzed microbiota and gene expression in IBD patients and examined responses of mucosal biopsies to bacterial DNA.


METHODS
Biopsies were taken from non-inflamed areas of the colon in healthy controls (HC) and Crohn's disease (CD) and ulcerative colitis (UC) patients in remission. Biopsies were snap-frozen or cultured with DNA from Lactobacillus plantarum (LP) or Salmonella dublin (SD). Gene expression was analyzed under basal conditions and in response to DNA. Gene networks were analyzed using Ingenuity Pathways software. Mucosal-associated microbiota was analyzed using terminal restriction fragment length polymorphism. Frequency of single nucleotide polymorphisms in NOD2 and TLR9 was assessed.


RESULTS
Patients with IBD had altered microbiota, enhanced expression of inflammatory genes, and increased correlations between specific gene expression and microbes. Principle component analysis showed CD and UC patients to cluster independently from healthy controls in both gene expression and microbial analysis. DNA from LP stimulated anti-inflammatory pathways in controls and UC patients, but induced an upregulation of IL17A in CD patients. There were no differences in SNP frequencies of TLR9 or NOD2 in the groups.


CONCLUSIONS
Patients with Crohn's disease exhibit altered responses to bacterial DNA. These findings suggest that the gut response to bacterial DNA may depend not only on the specific type of bacterial DNA, but also on the host.
Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
Naomi S C
NS
Hotte
Saad Y
SY
Salim
Robert H
RH
Tso
Eric J
EJ
Albert
Phil
P
Bach
John
J
Walker
Levinus A
LA
Dieleman
Richard N
RN
Fedorak
Karen L
KL
Madsen
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001706:Biopsy; D016000:Cluster Analysis; D015331:Cohort Studies; D003106:Colon / Q000378:metabolism* / Q000382:microbiology* / Q000473:pathology; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000008:administration & dosage / Q000494:pharmacology; D005260:Female; D005786:Gene Expression Regulation / Q000187:drug effects*; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000382:microbiology*; D048191:Lactiplantibacillus plantarum / Q000235:genetics; D008297:Male; D054892:Metagenome / Q000235:genetics*; D008875:Middle Aged; D053473:Nod2 Signaling Adaptor Protein / Q000235:genetics; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D025341:Principal Component Analysis; D012475:Salmonella / Q000235:genetics; D018709:Statistics, Nonparametric; D051217:Toll-Like Receptor 9 / Q000235:genetics
D017931:DNA Primers; D004269:DNA, Bacterial; C429018:NOD2 protein, human; D053473:Nod2 Signaling Adaptor Protein; C495371:TLR9 protein, human; D051217:Toll-Like Receptor 9