The document discusses the validation of interleukin-8 (IL-8) as a biomarker for melanoma. A study was conducted using 59 melanoma tumor tissue samples and matching serum and plasma to validate that IL-8 is elevated in melanoma. However, the results were inconsistent, as IL-8 protein levels appeared sensitive to freeze-thawing of samples. The author advocates for increasing the quality rather than quantity of biomarker research through improved collaboration to ensure better data and validation.

1. Data for personalized health(care):
time for quality, not quantity
IM Inspiration Point
18 May2017
Prof Alain van Gool

2. 2Sept 2009Update TMRC Singapore
Singapore (2009-2011)

3. 3Sept 2009Update TMRC Singapore
Translational Research Laboratory in the Biopolis

4. 4Update TMRC Singapore
Translational Research Laboratory in the Biopolis

5. 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 !
*
5 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016

6. 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 biomarker identification using pharmaco-’omics (gene/protein
expression): IL-8 as promising candidate biomarker
Data for RAFi #4
RAFi
MEKi
ERKi
RAFi#1
RAFi#2
RAFi#3
RAFi#4
MEKi#1
MEKi#2
ERKi#1
6 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016

7. 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
7 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016

8. 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)
OK
OK
?
8 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016
OK

9. 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)
9 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016

10. Irreproducibility of data
{Freedman et al, PLOS Biology, 2015}
{2012} {2011} {2013} {2008}{2012}
10 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

11. Categories of errors leading to irreproducibility
{Freedman et al,
PLOS Biology, 2015}
11 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

12. 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.
12 Alain van Gool, Biomarker Agora, Copenhagen, 1 Nov 2016

13. 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
Co-initiator of Health-RI
13 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

14. Data for personalized health(care)
time for quality, not quantity
14 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

15. 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]
15 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

16. Advances in mass spectrometry
• Mass spectrometry analysis of glycoproteins in human plasma
• 1/20 microliter analysis: detection of 1.000.000 signals in one scan (1,4 Gb)
• ~40.000 peptides of which >80% contain sugar modification
• Potential to screen patients and identify new biomarkers?
500
1000
1500
2000
m/z
5 10 15 20 25 30 35 40 Time [min]
Proof of principle study:
Biomarkers !?
16 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

17. Serum N-glycopeptide profiling as biomarker discovery
Comprehensive QC analytics

18. 18
New data !
(generators, owners)
18 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

20. … but not all data is useful data !

21. 21 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

22. implementation
innovation
research
22 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

23. Biomarker innovation gaps !
Discovery Clinical
validation/confirmation
Diagnostic
test
Number of
biomarkers
Gap 1
Gap 2
• Too much biomarker discovery
• Too little development to application
23 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

24. 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
Oct 2016: 14,461 biomarkers
Discovery Clinical
validation/confirmation
Diagnostic
test
Number of
biomarkers
Gap 1
Gap 2
24 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

25. Choice for biomarker scientists: discover or confirm?
25 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

26. Need to build biomarker validation pipelines
Standardisation, harmonisation,
knowledge sharing needed in:
1. Assay development
2. Clinical validation
3. Application
26 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

27. Critical component in biomarker R&D: Data
{Wilkinson et al,
Nature Scientific Data, 2016}
• Data capture
• Data stewardship (FAIR)
27 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

28. Introducing 5 infrastructure communities
(local) (European)
(Netherlands)
28 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

29. Genomics
Bioinformatics
Animal
studies
Stem
cells
Translational
neuroscience
Image-guided
treatment
Imaging
Microscopy
Biobank
Health
economics
Mass
Spectrometry
Radboudumc
Technology
Centers
Investigational
products
Clinical
studies
EHR data
analysis
Statistics
Human
performance
Data
stewardship
Molecule
Flow
cytometry
3D lab
29 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

30. Think big, start ‘small’ National Technology Infrastructure
(collective of 40+ partners in DTL)
Ruben Kok
Barend Mons
Alain van Gool
Jaap Heringa
30 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

31. Link to European infrastructures
31 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

32. Joining forces in Netherlands
To drive personalized medicine & health research
32 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

33. https://youtu.be/MpMSkbu9YQg
33 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

34. NWO roadmap large scale infrastructures
34 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

35. NWO roadmap Large Scale Infrastructures
35
Radboudumc involved in 4 cluster proposals for €15-18M projects (2018-2023):
- Elixir (DRE) Arnoud van der Maas (lead = Jaap Heringa)
- X-omics Marcel Nelen, Alain van Gool (= lead)
- MRI & Cognition Mathias Prokop (lead = Peter Hagoort, Peter Luijten)
- NL-Bioimaging-AM Peter Friedl (lead = Dorus Gadella)
- NEMI (Electron-M.) Jack Fransen (lead = Judith Klumpermann)
Deadline 1 June 17:00
35 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017

36. Acknowledgements
Hans Wessels Jolein Gloerich
Roel Tans Esther Willems
Maurice van Dael Jenneke Keizer
Dirk Lefeber Monique van
Leo Kluijtmans Scherpenzeel
Ron Wevers Marcel Verbeek
Marcel Nelen Lucien Engelen
Jan Kremer Bas Bloem
Han Brunner Paul Smits
the Radboudumc Technology Centers
and many others
www.radboudumc.nl/personalizedhealthcare
www.radboudumc.nl/research/technologycenters
www.radboudresearchfacilities.nl
alain.vangool@tno.nl
alain.vangool@radboudumc.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
36 Alain van Gool, IM Inspiration Point, Nijmegen, 18 May 2017