Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Cancer Care Engineering Colorectal Cancer Gabriela Chiorean, M.D. June 26, 2009 Rationale in colorectal cancer Perform OMICs of healthy, polyps, cancer Compare OMICs between cancer, polyps and healthy: develop new screening and risk assessment tools Analyse changes in OMICs with treatment and correlate with response/toxicity: predictive markers Mathematical modeling and bio-mapping Cancer care delivery Rationale: CCE now GENOMICS METABOLOMICS GLYCOPROTEOMICS BIOMAP C R C LIPIDOMICS Mathematical modeling Schema IUCRO-0221 CCE in CRC active April 2009 N=270 Stratification: -Healthy (n=90) -Polyps (n=90) -Cancer (n=90) stg 1/2 stg 3 S A M P L E S stg 4 metastatic 8-hr fasting Blood (Serum) 7 mL red top Metab, vit D Blood (Plasma) 21 mL purple top Genomics, lipidomics, glycoproteomics Tissue 10 mg polyp or 50 mg cancer / 50 mg normal tissue S H I P D R Y I C E Samples Collection N= 5 Healthy Controls Sign ICS (RN) Screening Colonoscopy – GI Clinic Collect by RN/processing CRS Blood 1x 7 mL glass red top 3 x 7 mL plastic lavender Questionnaires diet/environmental exposures Label specimens Healthy if no polyps/tumor Samples Collection N= 3 Adenomatous Polyps Sign ICS (RN) Polyps identified Screening Colonoscopy – GI Clinic Collect by RN/processing CRS Blood 1x 7 mL glass red top 3 x 7 mL plastic lavender Questionnaires diet/environmental exposures Label specimens Polyp Tissue procurement/Research specialist -Polyp cut in ½ -Place in tube with no preservative -Freeze at -70oC Samples Collection N= 8 Cancer Sign ICS (RN) Call tissue procurement -Tumor tissue ~ 50 mg -Normal mucosa ~ 50 mg -Place in tube with no preservative -Freeze at -70oC Surgery Chemotherapy Follow-up Collect by RN/processing tissue procurement Blood: 1 x 7 mL red top glass tube 3 x 7 mL lavender plastic tubes Questionnaires: diet/environmental exposures Every 3 months Up to 24 months CCE Blood Acquisition Protocols Glass Red Top Tube (1) Volume = 7mL Following blood draw, patients and care givers administered diet and life style questionnaire Glass Purple Top Tubes (EDTA) (3) Volume = 7mL /tube Page: Amber Allen (page #) for transport to laboratory (RT) and processing Maximum time at RT from draw to centrifugation: 45-60 min. Centrifuge: 1500g, RT, 15 min 0.2 mL (2) Whole Blood into freezing tubes containing comet assay solution, mix, place on dry ice, FREEZE (-80oC) Maximum time at RT from draw to Whole Blood Removal: 20 min. Remaining whole blood Serum ( ~ 3mL), place on wet ice Maximum time at RT from draw to centrifuge: 30 min. Centrifuge: 1750g, RT, 15 min REGULAR EPPENDORF TUBES 0.3 mL (2) FREEZE (-80 oC) Metabolomics NMR 0.2 mL (2) FREEZE (-80 oC) Metabolomics MS 0.5 mL (2) FREEZE (-80 oC) Vitamin D Analysis Plasma (~ 6mL), place on wet ice SILICONIZED EPPENDORF TUBES 0.2 mL (2) FREEZE (-80 oC) Lipidomics 0.5 mL (2) LONG TERM STORAGE (LIQUID N2) Pellets (2); resuspend (1), combine with second pellet, re-centrifuge 1750g RT 5 min, decant, place on dry ice: FREEZE (-80 oC) SNP REGULAR EPPENDORF TUBES 1.5 mL (1) FREEZE (-80 oC)Glycoproteomics 0.2 mL (1) FREEZE (-80 oC) Proteomics 1.5 mL (1) LONG TERM STORAGE (LIQUID N2); Regular Eppendorf Tubes 0.2 mL (12) LONG TERM STORAGE (LIQUID N2); Siliconized Eppendorf Tubes Metabolomics Typical 2D GCxGC/MS data from a colon cancer patient serum sample. After derivitization, approximately 800 metabolites are observed (many of the lower intensity peaks are not evident in this figure). Dan Raftery-Purdue Metabolomics Combination of the GC PCA data with NMR PCA data improves the classification to 95%. In the figure, 2 PCs from the GCxGC/TOF dataset are combined with 1 PC from the NMR data. Oblong shapes are used to indicate 95% confidence limits. Schema IUCRO-0198 Metabolomics in CRC N=150 Stratification: -Healthy (n=30) -Polyps (n=30) -Cancer (n=90) stg 1/2 stg 3 S A M P L E S stg 4 metastatic 8-hr fasting Blood (Serum) 7 mL red top Urine 10 mL Tissue 10 mg polyp or 50 mg cancer / 50 mg normal tissue S H I P D R Y I C E Principle Component Analysis of Metabolites in serum in IUCRO-0198 Dan Raftery, Lingyan Liu - Purdue Investigators: Indiana University Gabriela Chiorean - Oncology Pat Loehrer – Oncology Stephen Williams - Oncology Yan Xu - Lipidomics Jim Klaunig - Genomics Bruce Robb - Surgery Eric Wiebke - Surgery Doug Rex - GI Mike Chiorean - GI Charles Kahi - GI Peter Johnstone – Rad Onc Oscar Cummings - Pathology Purdue University Marietta Harrison - Chemistry Daniel Raftery – Metabolomics Fred Regnier – Proteomics - Glycoproteomics Dorothy Teegarden – Vitamin D Min Zhang – Statistical Modeling Jake Chen – Biological Modeling