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

© Fraunhofer

Integrated platform for liquid biopsy-basedpersonalized cancer medicine

Dr. Bernhard Polzer

Fraunhofer ITEM-RegensburgPersonalized Tumor Therapy

© Fraunhofer

Personalized cancer therapy

2

Primary tumor Micrometastasissingle tumor cells Metastasis

Molecular Analysis &Therapy Selection

Molecular Analysis &Therapy Selection

© Fraunhofer

Polzer and Klein, Nat Med 2013

Cellular heterogeneity is the basis for therapy resistance

Selection for resistant, aggressive subclones by applied therapies

Cancer is an evolving disease

© Fraunhofer

Personalized cancer therapy

4

Surgery

Primary tumor Micrometastasissingle tumor cells Metastasis

Information on systemic cancer?

metastatic disease

© Fraunhofer

Personalized cancer therapy

5

Surgery

Primary tumor Micrometastasissingle tumor cells Metastasis

Information on systemic cancer? Liquid Biopsy

metastatic disease

© Fraunhofer

Diaz and Bardelli, JCO 2014

Information on systemic cancerin a simple blood test

- Circulating tumor cells (CTCs)

- Circulating tumor DNA (ctDNA)

- miRNA (and other RNAs)

- Extracellular vesicles(e.g. exosomes)

Concept of liquid biopsy

© Fraunhofer

2. Detection of CTC

1. Enrichment for CTC

4. Whole Genome amplification (WGA)

5. Unbiased molecular analysis

Ampli1TM

WGA

e.g.CellSearch®

3. Isolation of single CTC e.g.DepArrayTM

Analysis of circulating tumor cells

© Fraunhofer

T02

T04

T05

T06

T10

T07

CK HER2 CD45 DAPI PIK3CA mutHER2 qPCR

amplified

amplified

amplified

amplified

amplified

amplified

Patient MU09 Primary Her2 negative, CTC count 42 (Veridex)

Molecular heterogeneity in breast cancer

© Fraunhofer

T02

T04

T05

T06

T10

T07

CK HER2 CD45 DAPI PIK3CA mut

wt

wt

H1047R

H1047R

H1047R

H1047R

HER2 qPCR

amplified

amplified

amplified

amplified

amplified

amplified

Patient MU09 Primary Her2 negative, CTC count 42 (Veridex)

Molecular heterogeneity in breast cancer

© Fraunhofer

Liquid biopsy platform at ITEM-R

© Fraunhofer

cfDNA isolationfrom plasma

CTC enrichmentfrom buffy coat

Expertise inpreanalytical workflows andsample logisticsfor liquid biopsy studies

Comprehensive liquid biopsy concept

© Fraunhofer

cfDNA isolationfrom plasma

CTC enrichmentfrom buffy coat

Expertise inpreanalytical workflows andsample logisticsfor liquid biopsy studies

Protocols available for

customized strategies(e.g. epitope based/marker-free)

High blood volumes(50-100 ml, leukapheresis

Other body fluids (e.g. bonemarrow, cerebro-spinal fluid)and organs (e.g. lymph nodes)

Comprehensive liquid biopsy concept

© Fraunhofer

Whole transcriptomeamplification (WTA)

Whole genomeamplification (WGA)

Cell lysis

Quality control forpatient-derived cells

Whole GenomeSequencing (HiSeq)

RNASeq analysis(HiSeq)

CNV analysis(MiSeq)

Whole Exome/PanelSequencing (HiSeq)

Molecular analysis of single cells of patients

lncRNASeq analysis(HiSeq)

Small RNASeq analysis(MiSeq)

Error free single cell Seq(PCTEP2015052436)

Single celltranscriptomicsbioinformatics

(tailored to WTAtechnology)

Single cellgenomics

bioinformatics(tailored to WGA

technology)

Automatedworkflow

© Fraunhofer

liquid biopsy models for:

• testing novel therapies

• personalized therapy

selection

• biomarker/ drug targets

• understanding

metastastic progression

in vivo

in vitro

tumor cells

Preclinical models from liquid biopsy samples

© Fraunhofer

Cell culture 384-wellassay plate

Distribution of patient-derived cellularmodels on assay plates

Compoundadministration (nl)

incubation (37oC)Dispensing of detection reagent on cells

readout(e.g. luminescence)

Compound libraries

MTT, AlamarBlue, protease, ATP

High-throughput screening of compoundsin patient-derived cell models

© Fraunhofer

ITEM-R - your premium partner for liquid biopsysolutions in a clinical context

© Fraunhofer

Poster Z9

Dr. Bernhard [email protected]

Dr. Kamran [email protected]

Fraunhofer Institute for Toxicology and Experimental Medicine - ITEMDivision of Personalized Tumor Therapy, RegensburgAm Biopark 993053 RegensburgGermany