Innovation in clinical molecular biomarkers: time for quality, not quantity
Prof Alain van Gool
Copenhagen 1 Nov 2016
A short story: Personalized medicine in melanoma
B-RAFV600E mutation Strong growth of cell Growth of tumor
• B-RAFV600E cells always grow and become cancer cells
• RAF inhibitors will block pathway, block cell growth and inhibit cancers that have a B-RAFV600E mutation
• 60% of melanoma patients have B-RAFV600E mutation
• Basis for a personalized medicine !
*
2 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Biomarkers to support clinical development
• Within Schering-Plough 4 Lead Optimisation programs in ERK pathway (2009)
• Need for blood-based biomarker that indicated downstream effects of drugs:
• Inhibition ERK pathway (pharmacodynamic)
• Tumor inhibition (efficacy)
• Extensive transcriptomics profiling: IL-8 as promising candidate biomarker
Data for RAFi #4
RAFi
MEKi
ERKi
RA
Fi #
1
RA
Fi #
2
RA
Fi #
3
RA
Fi #
4
MEK
i #1
MEK
i #2
ERK
i #1
3 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Validation study to confirm IL-8 in melanoma
Literature
{Yurkovetsky, et al. Clin Cancer Res, 2007}
Objectives: • Confirm elevated IL-8 in melanoma
• Develop IL-8 assays for clinical use
4 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Validation study to confirm IL-8 in melanoma
Stage 1 Stage 2 Stage 3 Stage 4
H&E staining; 20x
59 melanoma samples (tumor tissue (ffpe) + matching serum & plasma, stage I-IV, from two independent biobanks) + 40 healthy serum & plasma samples
1. Genetic analysis for BRAFV600E/D mutation in genomic DNA from tissue
2. IL-8 mRNA analysis in tissue samples by in situ hybridisation using bDNA probes (multiplexing with 12 ERK pathway response transcripts)
3. IL-8 protein analysis in tissue samples by immunohistochemistry (in parallel with 4 other ERK pathway response proteins, Ki67, Tunnel)
4. IL-8 protein analysis in matching plasma and serum by IL-8 immunoassay (3 formats: ELISA, Luminex, Mesoscale; singleplex and multiplex)
partial
OK
OK
?
5 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Validation study to confirm IL-8 in melanoma
Literature
{Yurkovetsky, et al. Clin Cancer Res, 2007}
Own data
{Unpublished, 2010}
Cause?
(6 months, 4 fte, USD 1.000.000)
6 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Irreproducibility of data
{Freedman et al, PLOS Biology, 2015}
{2012} {2011} {2013} {2008} {2012}
7 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Categories of errors leading to irreproducibility
{Freedman et al, PLOS Biology, 2015}
8 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Lessons learned?
Particularly for this case: 1. Know sample history
• IL-8 protein appeared sensitive to freeze-thawing
2. Know all relevant information from the source (patient) • Tumor load may be too low for our patients
3. Do these type of expensive validation studies together ! • Share burden, increase power, ensure better data
If we want to innovate clinical molecular biomarkers, we need to increase quality, not quantity of our research.
9 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
10 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Alain’s path 1989-now • Basis in molecular biology
• Academia, pharma, medical center, applied research institutes
• Biomarkers / Omics / technologies
• Mechanisms of disease
• Translational medicine
• Personalized healthcare
Senior Scientist Integrator Biomarkers
Scientific lead DTL-Technologies
Head EATRIS Biomarker Platform
Professor of Personalized Healthcare Head Radboud Center for Proteomics, Glycomics & Metabolomics Coordinator Radboud Technology Centers
11 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Alain’s path 1989-now • Basis in molecular biology
• Academia, pharma, medical center, applied research institutes
• Biomarkers / Omics / technologies
• Mechanisms of disease
• Translational medicine
• Personalized healthcare
Senior Scientist Integrator Biomarkers
Scientific lead DTL-Technologies
Head EATRIS Biomarker Platform
Professor of Personalized Healthcare Head Radboud Center for Proteomics, Glycomics & Metabolomics Coordinator Radboud Technology Centers
Exponential technology developments in laboratories
• Next generation sequencing
• DNA, RNA • Risk analysis and therapy selection
• Mass spectrometry • Proteins, metabolites • Monitoring of disease and treatment effects
• Imaging
• Non invasive images, real time
• Spatial view of intact organs and organisms
500
1000
1500
2000
m/z
5 10 15 20 25 30 35 40 Time [min]
12 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Ongoing: translate laboratory to society
• Point-of-care analysis of few biomarkers
• 1.000.000 signals per proteomics analysis
19 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Biomarker innovation gaps !
Discovery Clinical
validation/confirmation
Diagnostic
test
Number of
biomarkers
Gap 1
Gap 2
27 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
• Too much biomarker discovery • Too little development to application
Biomarker innovation gaps: some numbers
~ 5 biomarkers/ working day
1 biomarker/ 1-3 years
1 biomarker/ 2-10 years
Eg Biomarkers in time: Prostate cancer May 2011: 2,231 biomarkers Nov 2012: 6,562 biomarkers Oct 2013: 8,358 biomarkers Nov 2014: 10,350 biomarkers Oct 2015: 11,856 biomarkers 31 Oct 2016: 14,461 biomarkers
Discovery Clinical
validation/confirmation
Diagnostic
test
Number of
biomarkers
Gap 1
Gap 2
28 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Choice for biomarker scientists: discover or confirm?
29 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Good example of multi-laboratory biomarker validation
3 biomarkers: • Aβ42 • T-Tau • P-Tau
30 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Need to build biomarker validation pipelines
Standardisation, harmonisation, knowledge sharing needed in:
1. Assay development
2. Clinical validation
3. Application
33 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Biomarker Development Center (NL)
NL Roadmap Molecular Diagnostics (2012) NL Grant 4.3M Eur (2014)
Biomarker Development Center (NL)
NL Roadmap Molecular Diagnostics (2012) NL Grant 4.3M Eur (2014)
(+ )
Ongoing independent biomarker activities
Europe
USA
{Asadullah et al, Nature Reviews Drug Discovery, Dec 2015}
36 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
European infrastructures
@Radboudumc: Peggy Manders Gerhard Zielhuis
@Radboudumc: Peter Friedl Otto Boerman
@Radboudumc: Otto Boerman (Head Imaging Platform) Alain van Gool (Head Biomarker Platform)
@Radboudumc: Arnoud van der Maas Alain van Gool
@Radboudumc: Saskia de Wildt Paul Smits
37 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
The Good Biomarker Practice initiative
Join forces among Europe’s major academic infrastructures + industry to:
1. Establish “Good Biomarker Practice” guidelines
- on translational research, biomarker technologies, biobanking, data stewardship.
2. Efficiently execute high quality biomarker projects
- work together in clinical validation and development of probable biomarkers.
38 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Critical component in biomarker R&D: Data {Wilkinson et al, Nature Scientific Data, 2016}
• Data capture • Data stewardship (FAIR)
39 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Think big, start ‘small’ National Technology Infrastructure (collective of 40+ partners in DTL)
Ruben Kok
Barend Mons
Alain van Gool
Jaap Heringa
41 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
Rich history of PPP in the Netherlands
(Centre for Translational Molecular Medicine) (Top Institute Pharma)
(BioMolecular Materials)
Public-private collaboration on diagnosis, drugs, devices (2006-2015)
42 Alain van Gool, BBMRI BIOS symposium, Amsterdam. 21 Sept 2016
Joining forces in Netherlands To drive personalized medicine & health research
43 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
44 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
https://youtu.be/MpMSkbu9YQg
Acknowledgements
Hans Wessels Jolein Gloerich
Roel Tans Esther Willems
Maurice van Dael Jenneke Keizer
Dirk Lefeber Monique van
Scherpenzeel
Leo Kluijtmans Ron Wevers
Marcel Verbeek Lucien Engelen
Jan Kremer Bas Bloem
Nathalie Bovy Paul Smits
the Radboudumc Technology Centers
and many others
www.radboudumc.nl/personalizedhealthcare
www.radboudumc.nl/research/technologycenters
www.radboudresearchfacilities.nl
www.linkedIn.com
www.slideshare.net/alainvangool
Many collaborators and funders
Jan van der Greef Ben van Ommen
Ivana Bobeldijk Hans Princen
Lars Verschuren Marjan van Erk
Suzan Wopereis Heleen Wortelboer
Wessel Kraaij Ronald Mooi
Peter van Dijken Cyrille Krul
and many others
CarTarDis
Ruben Kok Barend Mons
Jaap Heringa Merlijn van Rijswijk and
many others
Anton Ussi Florence Bietrix
Laura Bermejo Andreas Scherer
Sulev Koks Marian Hajduch
Giovanni Migliaccio
and many others
48 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016