Integrated platform for liquid biopsy-based personalized cancer medicine

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1 Integrated platform for liquid biopsy-based personalized cancer medicine Dr. Bernhard Polzer Fraunhofer ITEM-Regensburg Personalized Tumor Therapy

2 Personalized cancer therapy Primary tumor single tumor cells Micrometastasis Metastasis Molecular Analysis & Therapy Selection Molecular Analysis & Therapy Selection 2

3 Cancer is an evolving disease Cellular heterogeneity is the basis for therapy resistance Selection for resistant, aggressive subclones by applied therapies Polzer and Klein, Nat Med 2013

4 Personalized cancer therapy Primary tumor single tumor cells Micrometastasis Metastasis Surgery metastatic disease Information on systemic cancer? 4

5 Personalized cancer therapy Primary tumor single tumor cells Micrometastasis Metastasis Surgery metastatic disease Information on systemic cancer? Liquid Biopsy 5

6 Concept of liquid biopsy Information on systemic cancer in a simple blood test - Circulating tumor cells (CTCs) - Circulating tumor DNA (ctdna) - mirna (and other RNAs) - Extracellular vesicles (e.g. exosomes) Diaz and Bardelli, JCO 2014

7 Analysis of circulating tumor cells 1. Enrichment for CTC 2. Detection of CTC e.g. CellSearch 3. Isolation of single CTC e.g. DepArray TM 4. Whole Genome amplification (WGA) 5. Unbiased molecular analysis Ampli1 TM WGA

8 Molecular heterogeneity in breast cancer Patient MU09 Primary Her2 negative, CTC count 42 (Veridex) CK HER2 CD45 DAPI HER2 qpcr PIK3CA mut T02 T04 T05 T06 T10 T07

9 Molecular heterogeneity in breast cancer Patient MU09 Primary Her2 negative, CTC count 42 (Veridex) CK HER2 CD45 DAPI HER2 qpcr PIK3CA mut T02 T04 T05 T06 T10 T07 wt wt H1047R H1047R H1047R H1047R

10 Liquid biopsy platform at ITEM-R

11 Comprehensive liquid biopsy concept cfdna isolation from plasma Expertise in preanalytical workflows and sample logistics for liquid biopsy studies CTC enrichment from buffy coat

12 Comprehensive liquid biopsy concept Expertise in preanalytical workflows and sample logistics for liquid biopsy studies cfdna isolation from plasma Protocols available for customized strategies (e.g. epitope based/marker-free) CTC enrichment from buffy coat High blood volumes ( ml, leukapheresis Other body fluids (e.g. bone marrow, cerebro-spinal fluid) and organs (e.g. lymph nodes)

13 Molecular analysis of single cells of patients Whole transcriptome amplification (WTA) RNASeq analysis (HiSeq) lncrnaseq analysis (HiSeq) Small RNASeq analysis (MiSeq) Single cell transcriptomics bioinformatics (tailored to WTA technology) Cell lysis Whole genome amplification (WGA) Quality control for patient-derived cells CNV analysis (MiSeq) Whole Genome Sequencing (HiSeq) Whole Exome/Panel Sequencing (HiSeq) Error free single cell Seq (PCTEP ) Single cell genomics bioinformatics (tailored to WGA technology) Automated workflow

14 Preclinical models from liquid biopsy samples in vivo liquid biopsy models for: testing novel therapies tumor cells personalized therapy selection in vitro biomarker/ drug targets understanding metastastic progression

15 High-throughput screening of compounds in patient-derived cell models Cell culture 384-well assay plate Compound administration (nl) Distribution of patient-derived cellular models on assay plates Compound libraries readout (e.g. luminescence) Dispensing of detection reagent on cells incubation (37 o C) MTT, AlamarBlue, protease, ATP

16 ITEM-R - your premium partner for liquid biopsy solutions in a clinical context

17 Poster Z9 Dr. Bernhard Polzer Dr. Kamran Honarnejad Fraunhofer Institute for Toxicology and Experimental Medicine - ITEM Division of Personalized Tumor Therapy, Regensburg Am Biopark Regensburg Germany