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Metabolomics In IBD: Development of Novel Diagnostic Tests for IBD, Polyps and Cancer Jesse S Siffledeen, Travis Murdoch, Carolyn Slupsky1, Haili Wang, Richard N Fedorak University of Alberta, Edmonton, Alberta, Canada Center of Excellence For Gastrointestinal Inflammation and Immunity Research UC Davis, California, USA1 Background Metabolomics The characterization of small molecular weight compounds in biofluids or tissues. Metabolomics 4000 chemicals Proteomics 7500 Enzymes Genomics 25,000 Genes The urinary metablolomic “fingerprint” reflects the somatic (minor) and luminal bacterial (major) constituency Background 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… Hypothesis Analysis of urinary metabolite profile (metabolomics) could differentiate individuals with different luminal bacterial profiles Objective 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 Methods 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 Metabolomics Workflow Biofluids or Extracts pp m 7 6 5 4 3 2 1 Data Analysis NMR or MS Chemical Analysis Urine Metabolomics NMR spectra analysis defines 69 metabolites (Chenomx®NMRSuite v7.0) Partial least square discriminate analysis defines “very important metabolites” and their concentrations Concentration Urine Metabolomics most contributing metabolites least contributing metabolites N= 69 metabolites in order of contribution to separation of group A from group B Results – IBD vs Control Principle component analysis uses 69 metabolites to separate IBD vs Control Sensitivity = 78% Specificity = 89% Results – Active CD vs Active UC Separation of patients with active CD vs active UC Change in Urinary Metabolites Metabolite Crohn’s Disease Levoglucosan* Sucrose Hippurate* Fucose* Creatine TMAO* DMA* * of bacterial origin Ulcerative Colits www.metabolomictechnologies.ca ColoDx ™ & PolypDx ™ Clinical Trial N=116 colon cancer N=1075 >50 yr screening Surgery + biopsy Urine metabolomics Detection of: Colon cancer Colonoscopy + biopsy (gold standard) FOBT (FGT&FIT) Urine metabolomics Detection of: Polyps 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 87 Excluded samples due to: •Incomplete colonoscopy •Other diagnoses •Corrupted urine sample 14 2011 www.metabolomictechnologies.ca ColoDx ™ & PolypDx ™ Clinical Trial Principal component analysis uses 69 metabolites to separate each group POLYP 2011 NORMAL www.metabolomictechnologies.ca 15 ColoDx ™ & PolypDx ™ Clinical Trial After polypectomy the urine metabolomic fingerprint reverts back to a “normal” state POLYP 2011 Post Polypectomy www.metabolomictechnologies.ca 16 ColoDx ™ & PolypDx ™ Clinical Trial DxTM a screening test for colon cancer & polyps ColoDxTM detects colon cancer Thresholds Sensitivity Specificity ColoDx 1 97% 90% ColoDx 2 87% 96% ColoDx 3 76% 99% AUC 0.99 PolypDxTM detects adenomatous polyps Metabolites Sensitivity Specificity PolypDx 1 81% 50% PolypDx 2 71% 61% PolypDx 3 66% 65% AUC 0.73 Finding adenomatous polyps is the real need ! 2011 17 PolypDx ™ Clinical Trial PolypDxTM sensitivity to detect adenomatous polyps compared to current tests Test Sensitivity Specificity PolypDxTM 71 61 Hemoccult II (guaiac) 1 99 Hemoccult ICT (immune) 6 97 Magstrema HemSp/HT 15 95 (immune) Finding adenomatous polyps is the real need ! 2011 18 PolypDx ™ Clinical Trial PolypDxTM sensitivity to detect adenomatous polyps compared to current tests – specificity held constant Test Sensitivity Specificity PolypDxTM 23 95 Hemoccult II (guaiac) 1 99 Hemoccult ICT (immune) 6 97 Magstrema HemSp/HT 15 95 (immune) Finding adenomatous polyps is the real need ! 2011 19 The PolypDx™ Opportunity Engage subject yearly negative PolypDx ® screening positive test in commercial Colonoscopy development Follow-up/Surveillance 2011 www.metabolomictechnologies.ca 20