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Jesse S Siffledeen, Travis Murdoch, Carolyn Slupsky1, Haili Wang, Richard N Fedorak
University of Alberta, Edmonton, Alberta, CanadaCenter of Excellence For Gastrointestinal Inflammation and
Immunity Research
UC Davis, California, USA1
Metabolomics In IBD: Development of Novel Diagnostic Tests for IBD, Polyps and
Cancer
Background
25,00025,000 Genes Genes
7500 Enzymes7500 Enzymes
4000 chemicals
Metabolomics
Proteomics
Genomics
MetabolomicsThe characterization ofsmall molecular weight compounds in biofluids or tissues.
The urinary metablolomic “fingerprint” reflects the somatic (minor) and luminal bacterial (major) constituency
1. Altered luminal microflora play a key pathogenic role in IBD and colonic dysplasia…
2. Changes in microflora have been shown to markedly alter small molecule metabolites…
Analysis of urinary metabolite profile (metabolomics) could differentiate individuals with different luminal bacterial
profiles
Background
Hypothesis
1. Find urinary metabolomic profiles that differentiated patients with IBD from those without IBD and ….
2. …. those with colonic polyps from those without colonic polyps
3. Develop a commercial biomarker for IBD/colonic polyps/cancer and a predictor of response to therapy
Objective
Patients with IBD provided a spot urine sample and completed a demographics questionnaire, HBI (CD; n=30) and modified Mayo Score (UC; n=30)
Patients with IBS (n=30) were controls
Metabolite concentrations were derived from analysis of 600Hz NMR spectra and sorted by partial least squares discriminate analysis
Methods
Metabolomics Workflow
Biofluids or Extracts
NMR or MS Chemical Analysis
1234567ppm
Data Analysis
Urine MetabolomicsNMR spectra analysis defines 69 metabolites (Chenomx®NMRSuite v7.0)
Urine Metabolomics
N= 69 metabolites in order of contribution to separation of group A from group B
Con
cent
ratio
nPartial least square discriminate analysis defines “very important metabolites” and their concentrations
mostcontributingmetabolites
leastcontributingmetabolites
Results – IBD vs Control
Principle componentanalysis uses 69 metabolites to separate IBD vsControl
Sensitivity = 78%Specificity = 89%
Results – Active CD vs Active UC
Separation ofpatients with
active CDvs active UC
Change in Urinary Metabolites
Metabolite Crohn’s Disease
Ulcerative Colits
Levoglucosan*
Sucrose
Hippurate*
Fucose*
Creatine
TMAO*
DMA** of bacterial origin
N=1075 >50 yr
screening
Colonoscopy + biopsy (gold standard)
FOBT (FGT&FIT)Urine metabolomics
Detection of:Polyps
N=116colon cancer
Surgery + biopsyUrine metabolomics
Detection of:Colon cancer
Urine metabolomics from 77 CRC & 236 polyp & 422 normal patients analyzed to develop ColoDxTM
and PolypDxTM = open label diagnostic cohort
Urine metabolomics from 39 CRC & 119 polyp & 211 normal patients blinded for ColoDxTM and PolypDxTM validation = blinded validation cohort
142011 www.metabolomictechnologies.ca
ColoDx ™ & PolypDx ™ Clinical Trial
87 Excluded samples due to:•Incomplete colonoscopy•Other diagnoses•Corrupted urine sample
152011 www.metabolomictechnologies.ca
ColoDx ™ & PolypDx ™ Clinical Trial
Principal component analysis uses 69 metabolites to separate each group
NORMALPOLYP
162011 www.metabolomictechnologies.ca
ColoDx ™ & PolypDx ™ Clinical Trial
After polypectomy the urine metabolomic fingerprint reverts back to a “normal” state
POLYP PostPolypectom
y
DxTM a screening test for colon cancer & polyps
Thresholds Sensitivity Specificity AUC
ColoDx 1 97% 90%
0.99ColoDx 2 87% 96%
ColoDx 3 76% 99%
ColoDxTM detects colon cancer
PolypDxTM detects adenomatous polyps
Finding adenomatous polyps is the real need !172011
ColoDx ™ & PolypDx ™ Clinical Trial
Metabolites Sensitivity Specificity AUC
PolypDx 1 81% 50%
0.73PolypDx 2 71% 61%
PolypDx 3 66% 65%
Test Sensitivity Specificity
PolypDxTM 71 61
Hemoccult II (guaiac) 1 99
Hemoccult ICT (immune) 6 97
Magstrema HemSp/HT(immune)
15 95
Finding adenomatous polyps is the real need !182011
PolypDx ™ Clinical Trial
PolypDxTM sensitivity to detect adenomatous polypscompared to current tests
Test Sensitivity Specificity
PolypDxTM 23 95
Hemoccult II (guaiac) 1 99
Hemoccult ICT (immune) 6 97
Magstrema HemSp/HT(immune)
15 95
PolypDxTM sensitivity to detect adenomatous polypscompared to current tests – specificity held constant
Finding adenomatous polyps is the real need !192011
PolypDx ™ Clinical Trial
Engage subject yearly
PolypDx ® screening test in
commercial development
Colonoscopy
Follow-up/Surveillance
positive
negative
202011 www.metabolomictechnologies.ca
The PolypDx™ Opportunity
