Biopsia Líquida: Oncología en Tiempo Real. Federico Rojo Fundación Jiménez Díaz

Transcription

1 Biopsia Líquida: Oncología en Tiempo Real Federico Rojo Fundación Jiménez Díaz

2 Liquid Biopsy in Cancer

3 Liquid Biopsy in Cancer Publication Date: April 5, 2016 Blood Tests replace Surgical Biopsies to create a new multibillion dollar market opportunity...

4 Liquid Biopsy in Cancer Analysis of therapeutic targets and drug resistance conferring gene mutations on peripheral blood samples: Estimation of risk for metastatic relapse or progression Understanding metastatic development Prediction of targeted therapy response Monitoring (minimal residual) disease Tracking secondary ( acquired ) resistance Assessing intratumor heterogeneity Tumor Targets CTCs cfdna cfrna Platelets Exosomes Origins Selected viable tumor cells leaving actively primary and/or metastasis Necrotic and apoptotic tumor cells Necrotic and apoptotic tumor cells Active incorporation of exosomes Active secretion of encapsulated particles by tumor cells Definition Tumor cells Fragmented genomes released from dying tumor cells of primary and/or metastasis Fragmented RNA released from dying tumor cells Circulating platelets Circulating encapsulated particles Analytes DNA, RNA, protein DNA RNA RNA RNA, protein

5 Liquid Biopsy and Cell-Free Tumor DNA Cell free tumor DNA released from a solid tumor cfdna CTCs Origin: Necrotic or apoptotic tumor cells; active secretion Small DNA fragments ( bp) Half life ~2h Clearance by kidney Healthy individual: 3,000 5,000 Genomic Equivalents/ml Cancer: >10,000 Genomic Equivalents/ml Concentration: 0.01% to 60% of total DNA Total DNA elevated for various reasons: inflammation, wound healing, malignant lesions, menstruation, sport

6 First Descriptions of Circulating Tumor DNA

7 Survey of ctdna in Advanced Human Cancer Cases with detectable cdna, Stage IV Cases with detectable cdna, localized vs metastatic Bettegowda et al, Sci Tran Med Feb 2014

8 Analytical Challenge for Plasma DNA Testing Blood Plasma cfdna isolation Analysis Diaz & Bardelli, J Clin Oncol 2014

9 Therascreeen EGFR mutation analysis in plasma 29 mutations in EGFR Sensitivity for activating mutations: 65.7% Specificity: 99.8%

10 Cobas EGFR mutation analysis in plasma 42 mutations in EGFR Semi-quantitative Index (SQI) Sensitivity for activating mutations: 82% Specificity: 98%

11 Principles of BEAMing: BEAMing Beads, Emulsions, Amplification & Magnetics Emulsion Characteristics Droplet size: 3-10 μm diameter fl volume Droplet density: ~ compartments / μl ~ beads / μl Up to 300 million PCR compartments per reaction Vogelstein et al. PNAS 1999; mod. Diehl et al Curr Opin Oncol Beads in Water-in-Oil Emulsions Magnetic beads (1 µm diameter) Light Microscopy of Emulsions (200x)

12

13 Analytical validation: EGFR mutation in NSCLC Reference Assay Sensitivity Specificity Wang S 2013 ARMS 0,22 0,67 Jing CW 2013 HRM 0,64 0,97 Zhang H 2013 MEL 0,67 0,99 Kim HR 2013 PNA-LNA 0,67 0,92 Liu X 2013 ARMS 0,67 0,99 Lv C 2013 DHPLC 0,13 0,88 Kim ST 2013 PNA-LNA 0,18 0,93 Xu F 2012 ARMS 0,25 0,96 Hu C 2012 HRM 0,98 0,17 Zhao X 2012 ME-PCR 0,36 0,95 Yam I 2012 AS-APEX 0,98 0,75 Goto K 2012 ARMS 0,43 0,99 Jiang B 2011 ME-Sequencing 0,76 0,99 He C 2009 ME-PCR 0,94 0,86 Bai H 2009 DHPLC 0,82 0,9 Kuang Y 2009 ARMS 0,7 0,85 Yung TK 2009 ddpcr 0,96 0,92 Kimura H 2007 ARMS 0,75 0,97 Kimura H 2006 ARMS 0,75 0,67 Huang Z 2012 DHPLC 0,64 0,85 Lee JY 2016 ddpcr 0,76 0,88 Reference Assay Sensitivity Specificity Mok t 2015 ME-PCR 0,75 0,96 Karlovich CA 2016 ddpcr 0,73 0,82 Karachaliou N 2015 PNA-LNA 0,81 0,95 Wang Z 2014 ddpcr 0,82 0,97 Zheng D ddpcr 0,84 0,91 Thress KS 2015 ARMS, ME-PCR, ddpcr 0,78-1 0,93-1 Que D 2016 ddpcr 0,89 0,85 Paquale R 2015 ARMS 0,65 0,99 Uchida J 2015 NGS 0,51 0,98 Sriram KB 2011 ME-PCR 0,62 0,97 Taniguchi K 2011 ddpcr 0,64 0,97 Nakamura T 2012 ME-PCR 0,67 0,99 Kim ST 2013 PNA-LNA 0,67 0,92 Brevet M 2011 Sequenom 0,67 0,99 Douillard JY 2014 ARMS 0,63 0,88 Weber B 2014 ME-PCR 0,68 0,93

14 Analytical validation: EGFR mutation in NSCLC Phase I trial with AZD9291 in NSCLC (AURA): 38 pre-dose plasma samples and matched tumor biopsies, after first development of resistance and 2 nd look biopsy have been evaluated cfdna was tested for 3 EGFR mutations (T790M, L858R, Exon 19 del) by 3 methods and compared with tissue Roche cobas PCR Qiagen Therascreen ARMS Sysmex Inostics BEAMing Exon 19 Deletion Assays Sensitivity 86% 82% 90% Specificity 100% 100% 100% Concordance 89% 87% 93% L858R (Exon 21) Assays Sensitivity 90% 78% 100% Specificity 100% 100% 91% Concordance 97% 95% 93% T790M (Exon 20) Assay Sensitivity 41% 29% 69% Specificity 100% 100% 67% Concordance 57% 48% 68% Thress, KS et al. Lung Cancer 2015

15 Clinical validation: 1. Prognosis after neoadjuvant treatment in early breast cancer ChemoNEAR study design Garcia-Murillas, I et al. Science Trans Med 2015

16 Clinical validation: 1. Prognosis after neoadjuvant treatment in early breast cancer Pre-therapy ctdna was not associated to prognosis Post-therapy ctdna was linked to poor prognosis Dynamic mutation tracking is highly accurate in predicting relapse Garcia-Murillas, I et al. Science Trans Med 2015

17 Clinical validation: 1. Prognosis after neoadjuvant treatment in early breast cancer Garcia-Murillas, I et al. Science Trans Med 2015

18 Normal signal Clinical validation: 2. Minimal residual disease in colorectal cancer N= 162 plasma samples (18 patients) Cell-Free Tumor DNA Levels Before and After Surgery Before surgery Day of Surgery After surgery Day 3 After surgery Day 244 Residual Mutant cfdna Diehl et al. Nature Medicine 2008 Mutant signal

19 Clinical validation: 3. Predictive value of plasma EGFR in NSCLC Plasma EGFR mut+ Plasma EGFR mut- Mok, T et al. Clin Cancer Res 2015

20 Clinical validation: 4. Emergence of secondary mutations in colorectal cancer TISSUE PLASMA Bettegowda et al, Sci Tran Med Feb 2014 Misale et al. Nature 2012 Diaz et al. Nature 2012

21 Mensajes finales El estudio de mutaciones en ctdna en algunos escenarios, como NSCLC, está ya analíticamente validado para su uso en la práctica asistencial El estudio de ctdna puede tener utilidad pronóstica, de predicción de respuesta, en el seguimiento y la monitorización de la enfermedad y en la detección de segundas mutaciones asociadas a resistencia Qué método de laboratorio y circuito se debe de crear en cada centro?