Molecular Diagnostics Molecular Diagnostics – –How to How to
Molecular Diagnostics –How to Build Synergy with Imaging? Michael D. Kuo, Kuo, M.D. Department p of Radiology gy UCSD School of Medicine Slides not to be reproduced without permission of author EGFR Signaling: K-Ras Wild K-RAS Jonker Karapetis NEJM 2007 Jonker, 2007, 2008 Mutated K-RAS Slides not to be reproduced without permission of author Disease Management Symptoms Diagnostic Di i Imaging Labs Image-Guided g Tissue Bx Molecular Analysis Treatment Molecular DX Determination (K-Ras, HER2) Tissue Dx Molecular-based Treatment Determination Treatment Response Treatment Response Slides not to be reproduced without permission of author Slides not to be reproduced without permission of author Human Genome Sequencing Nature 409, 934-941 2001 Science 291, 1304-1351 2001 Slides not to be reproduced without permission of author Information Flow in Biological Systems Molecular Phenotype Prognosis p Tx Response TTP Toxicity Information Storage 20,000-25,000 Processing 40,000-65,000 Execution 100,000-450,000 Slides not to be reproduced without permission of author Spotted DNA Microarrays Slides not to be reproduced without permission of author Gene Expression Reflects Cellular States Slides not to be reproduced without permission of author Molecular Portraits of Human Tumors G Genes Tumors/Samples Slides not to be reproduced without permission of author Survival-Associated Survival Associated Programs Van de Vijver NEJM 2002 Slides not to be reproduced without permission of author Canonical biological programs Chang PLOS Biology 2004 PNAS 200 Slides not to be reproduced without permission of author Hepatocellular Carcinoma Survival Gene Expression Signature Slides not to be reproduced without permission of author Hoshida NEJM 2008 Breast Cancer Slides not to be reproduced without permission of author Oncotype DX™ Clinical Validation: B 14 R B-14 Results lt – DRFS DRFS for the three distinct cohorts identified 100% 90% 80% DRF FS 70% 60% P <0.00001 <0 00001 50% 40% 30% Low Risk (RS <18) n = 338 20% Intermediate Risk (RS 18-30) n = 149 10% High Risk (RS ≥31) n = 181 0% 0 2 4 6 Years 8 10 12 14 16 Paik et al. N Engl J Med. 2004;351:2817-2826. Slides not to be reproduced without permission of author Shortcomings of ArrayArray-based Approaches • Expensive p • Tissue handling and storage • Normalization within experiments and across experiments • Invasive • Sample Bias • Limitation for repeated sampling across the course of a disease Slides not to be reproduced without permission of author Conventional Pathology: the Diagnostic Di i G Gold ld S Standard d d Problems • Histopathology – Invasive – Limited predictive value • Clinical outcome • Treatment response • Newer genomic based tests (oncotypeDx, Mammaprint) – Greater predictive value, however, – Still require tissue (invasive) – Still diagnosed by imaging – Time consuming – Expensive 7/23/2009 16 Slides not to be reproduced without permission of author The Current Radiological Paradigm • Imaging • Macroscopic • Histology 7/23/2009 17 Slides not to be reproduced without permission of author Disease Management Symptoms Image-Guided g Tissue Dx Treatment Determination Labs Diagnostic Di i Imaging Tissue Dx Molecular Analysis Treatment Molecular DX Treatment Response Slides not to be reproduced without permission of author Today Slides not to be reproduced without permission of author Patient 529230-139.7 AA B Patient 510601-12.1 C Slides not to be reproduced without permission of author Global Association Maps Internal Arteries Image trait selection Preprocessing 138 traits Data selection (6732 genes) Capsule Image Traits Expression data Clustering Module network procedure Puddle Ann notations Texture Heterogeneity Ima age Tra aits Modules Post-processing Gene partition Gene reassignment to modules Functional modules Annotation analysis G hi presentation Graphic t ti Genes Hypodense Halo Classification program learning Validation in independent cohort of patients Imaging Classes Slides not to be reproduced without permission of authorSegal Nat Biotech 2007 Imaging g g Global Gene Expression p 0.9 0.8 Fraction of Transscriptome Reconsstructed 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 1 5 10 15 20 25 Number of Imaging Traits Used Slides not to be reproduced without permission of author 28 A B Module 700: Cell Proliferation Module 595: Liver Synthetic Function C Module 536: ECM Remodeling Tumor - Liver Difference, Minimum Internal Arteries, Density Tumor Margin Score, Minimum Attenuation Heterogeneity, Maximum Attenuation Heterogeneity, Maximum Tumor - Liver Difference, Maximum Tumor Margin Score, Maximum Necrosis, Density Enhancement Pattern Corrected Image Area g geminin cyclin A2 CHK1 ESPL1 CDC7 VEGF CDC6 PCNA H2AFX MCM5 MCM6 Image trait score: low mRNA: 0.25 high 4 APOB thrombin albumin PHYH GSTO1 ASGR2 factor V factor X CYP27A1 pyruvate kinase transferrin receptor 2 epoxide hydroxylase PCK2 LRP1 Slides not to be reproduced without permission of author thrombospondin 1,2 LTBP2 COL6A3 FGF12 COL6A2 MYL9 COL1A2 IGFBP3 MGP Fibulin 2 MMP7 CTGF MMP2 CYR61 PDFGRA L i Lumican COL3A1 ladinin Prognosis: Venous Invasion • Venous invasion signature Slides not to be reproduced without permission of author Question: Given the role of imaging and doxorubicin in the management of HCC, can specific imaging phenotypes of HCC obtained on standard contrast enhanced CT be associated with drug response gene expression programs defined by gene expression profiling? D Doxorubicin bi i Response R Slides not to be reproduced without permission of author Group 1 (more sensitive) Group 2 (more resistant)) Doxorubicin Association Tumor T mor Margin Score Resistance Score TIMP2 P<0.006, FDR=0.076 P=0.002 P=0.001 RAPTOR CYDL High Tumor Margin Score CASP1 FAAH ADAMTS1 ABCB1 MAP4K4 SNTB1 IL6R CYP4V2 Low Tumor Margin Score CYP27A1 BACE1 Slides not to be reproduced without permission of author Kuo JVIR 2007 Integrative Radiogenomic Analysis Tumor Margin Score Venous Invasion, Gene Expression Venous Invasion, Pathology TMN Stage Doxorubicin Resistance Liver-specific, Gene Expression Slides not to be reproduced without permission of author Imaging Internal Arteries Imaging Gene Expression Patterns Predicting Prognosis Or treatment response Module 595: Liver Synthetic Function Internal Arteries Internal Arteries, Density Absent Present Attenuation Heterogeneity, Maximum Hypodense Halos Necrosis, Density Corrected Image Area Hypodense Halo APOB thrombin albumin PHYH GSTO1 ASGR2 factor V factor X CYP27A1 pyruvate kinase transferrin receptor 2 epoxide hydroxylase Texture Heterogeneity P 1 A 2 Venous invasion Venous invasion genes low genes high Training g Set Group 1 Group 2 Test Set Group1 Group 2 - venous invasion Puddle PCK2 LRP1 Image trait score: low mRNA: 0.25 high 4 + venous invasion n = 30 patients p = 0.004 Sensitivity= y 66% Specificity= 86% Slides not to be reproduced without permission of author n = 32 patients p = 0.03 Sensitivity= y 33% Specificity= 100% Imaging Gene Expression Programs Slides not to be reproduced without permission of author Diehn PNAS 2008 Angiogenesis Intratumoral Spatial Diversity Slides not to be reproduced without permission of author Predicting EGFR Protein O Overexpression i •Assessed EGFR protein i expression i iin 48 independent GBMs •Contrast/Necrosis Contrast/Necrosis ratio was strongly associated with EGFR overexpression (p < 0.005) Slides not to be reproduced without permission of author Imaging Phenotype reflects SurvivalSurvivalAssociated Signature g Slides not to be reproduced without permission of author Patient 529230-139.7 Patient 510601-12.1 Conclusion • Global gene expression profiling represents a rich source of biomarkers that can be associated with different imaging phenotypes • Integrating genome-wide information with imaging can be a powerful means of developing and delivering molecular diagnostics in a practical and clinically relevant way Pu ddl e Slides not to be reproduced without permission of author
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