Lecture at the Biomarkers Europe 2023 conference for an audience of pharma scientists and omics/data solution providers. I outlined several initiatives of potential interest and discussed development of our sensitive personalized clinical biomarker test for minimal residual disease monitoring in multiple myeloma.

1. Multi Omics Data-Based Innovations In
Translational Biomarker Research
Biomarkers and Precision Oncology Europe 2023
14-15 November 2023
Prof. Alain van Gool
Professor Personalized Healthcare
Translational Metabolic Laboratory
Radboudumc Technology Centers
Radboud Healthy Data Programme
Netherlands X-omics Initiative
EATRIS Biomarker Platform

2. to have a significant impact on health(care)
Core tasks: Patient care, research, education
Medical faculty of Radboud University
12.000 employees; 3.500 students

3. 3 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
www.radboudumc.nl/research/ technologycenters

4. 4 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Translational Metabolic Laboratory
Part of dept Human Genetics (750 people)
Specialized in inherited metabolic syndromes
• Diagnostics – patient care (ISO15189)
• Innovation – new biomarker tests, methods
• Research – disease mechanisms, omics technologies
• Education – translational medicine, omics biomarkers
www.radboudumc.nl/tml
“We create personalized diagnostics”

5. The Netherlands X-omics Initiative
National Roadmap Large Scale Research Infrastructure
2018-2029
40M euro, partially funded by NWO
Objectives:
1. Advance X-omics technologies far beyond
state-of-the-art
2. Realize a genuinely integrated X-omics
infrastructure in NL
3. Develop and demonstrate impact of robust X-
omics analysis
Coordinator:
Alain van Gool
X-omics.nl

6. Data Stewardship
& Integration (WP2)
Multi-omics
technologies (WP1)
Genomics
Epigenetics
Transcriptomics
Proteomics
Metabolomics
Quality Assessment
(WP3)
Data
Generation
Data
Curation
Quality
Assessment
Data
Variability
Multi-omics Toolbox
Academia & Industry
Pilot Access
• SOPs
• Guidelines for best practices
• Reference materials
• Quality parameters
• Data analytical tools
• Criteria for reference values
• Troubleshooting guidelines
• Repository of multi-omics data
An open access WEB
resource, containing:
Enable high-quality research in PM, including
accelerating the implementation of accurate
patient stratification and treatment management
Emanuela Oldoni
EATRIS scientific
programme manager
flagship project

7. canSERV in a nutshell
7
Grant agreement No. 101058620 canSERV in a nutshell
+400 servicesin 10 Research Fields 1 application platform
Want to accelerate your research with
free access to scientific services?
www.canserv.eu/calls
CAMS –
Common Access Management System
One-stop shop for cancer research services –
Browse our catalogues and find the right service(s) for your cancer research
13 Research Infrastructures
150+ associated service providers
Emanuela Oldoni
EATRIS scientific
programme manager

8. Radboud Healthy Data program
19 Sept 2023 Radboud AI event
reveal
connect
improve
apply
Research data &
infrastructures
Application in
health & medical
practices
AI model
development
sustainable & scalable
Local strategic initiative
2023-2028; 21M euro
Funded by Reinier Post Foundation,
Radboud University, Radboudumc
Radboud Healthy Data core team
Strengthening
our data & AI infrastructure
@Radboud campus
to boost translational research
in health and healthcare

9. 9 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Clinical multi-omics data to drive personalized healthcare
Personalized analysis
Genomics
Metabolomics
Glycomics
Glycoproteomics
Deep Learning/ AI
Integrated diagnostics
System biology
Diagnosis of (new)
disease mechanisms
Transcriptomics
Proteomics
Epigenetics
Cellomics
…-omics
Development and monitoring
of (new) personalized
therapies

10. 10 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Some of our recent clinical omics innovations
Automated metabolomics-based
screening of Genetic Metabolic
Disorders in ISO15189 diagnostics
Hoegen et al, Metabolites 2021
Intensity
AI-based facial phenotypic recognition of
rare genetic diseases
Dingemans et al, Nature Genetics 2023
Plasma glycoproteomics delivers high-
specificity disease biomarkers
Wessels et al, J Adv Res 2023

11. 11 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Personalized healthcare in Multiple Myeloma
• 2nd most common
hematological malignancy
• Monoclonal plasma cells in
bone marrow that secrete a
monoclonal (M) protein
• Treatment by chemotherapy,
steroids and specific drugs
• ~50% of patients achieve
Minimal Residual Disease
(MRD)
• Need to restart therapy as
soon as disease relapses!
{Cancer Facts & Figures 2021, ACS
Kumar et al. Lancet Oncology 2016}
The story of today:

12. 12 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Lack of sensitive and easy detection of Minimal Residual Disease
Sampling error caused
by tumor
heterogeneity
Cumbersome and invasive
procedure
for repetitive monitoring
• Diagnostic test
blood M-protein by
gel electrophoresis
• Current tests for MRD:
• Isolate bone marrow
• Analysis stromal cells by Flow Cytometry
or Genomics (PCR, NGS)
Healthy
Multiple
myeloma

13. 13 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Insufficient sensitivity of current M-protein diagnostics
0,001
0,01
0,1
1
10
100
0 200 400 600 800 1000 1200 1400
[M
protein]
(g/L)
Sampling day
Maintenance
therapy
Earlier relapse detection: A more sensitive, easy, longitudinal method is needed
Limit of Detection gel-based method
? ?
?
?
?

14. 14 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Variable region:
patient- & MM specific
(VDJ-rearrangements)
Constant region:
non-specific
Can we use plasma proteomics to monitor MRD in Multiple Myeloma ?
Parallel Reaction Monitoring (PRM):
Approach:
Direct measurement of rearranged region of the M-
protein by targeted proteomics in plasma samples
(= MS MRD methode)
• Higher specificity?
• Higher sensitivity?

15. 15 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Unique M-protein clonotypic peptides per patient
{Langerhorst et al, Clin Chem 2021}
Can we identify myeloma-specific
clonotypic peptides?
Large scale analysis of tumor specific
RNA-seq data (n=609 MM patients)
Conclusion:
• 100% of the 609 included patients have
patient-specific clonotypic peptides
• Personalized diagnosis possible

16. 16 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
{Noori, Zajec et al, HemaSphere, 2022}
Conclusions:
• MS MRD method is feasible for
monitoring and early detection relapses
• Re-analysis of archived gels possible
Mass spectrometry strongly increases sensitivity detection M-protein
• Archived gels
• Punch out M protein bands
• Mass spec analysis
• De novo sequencing
• Semi-quantitation
• Monitor patients in time
Gel-based
method
Mass spec
method
Treatment period

17. 17 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
NGS-MRD MS-MRD
VERSUS
{Langerhorst, Noori et al, Clin Chem, 2021}
(selected as Top Story by Clin Chem)
Conclusions:
• Similar sensitivity
• Perform equally well as prognostic biomarker
Plasma proteomic MS-MRD assay performance
IFM2009 trial
Next generation sequencing – bone marrow
Current practice
Mass spectrometry - plasma
Innovation

18. 18 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
MS-MRD allows for dynamic monitoring of MM patients
{Langerhorst, Noori et al, Clin Chem, 2021}
Red lines: (early) relapse detected by MS-MRD methode
during maintenance therapy
Conclusions:
• Dynamic MS-MRD allow early detection of relapse
• Relapse during maintenance-treatment is strongly
correlated with poor prognosis
Limit of Detection gel-based method
Limit of Detection mass spec-based MS-MRD method
IFM2009 trial

19. 19 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
MS-MRD Longitudinal follow-up
Limit of Detection gel-based method
Limit of Detection mass spec-based method
0,001
0,01
0,1
1
10
100
0 200 400 600 800 1000 1200 1400
[M
protein]
(g/L)
Sampling day
Maintenance
therapy
1000x !
Conclusions:
• Early relapse detection: >1 year earlier
compared to gel-based method (M-spike)
{Noori, Wijnands et al. Blood Cancer J 2023}

20. 20 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
0,001
0,01
0,1
1
10
100
0 200 400 600 800 1000 1200 1400 1600 1800 2000
[M-protein]
(g/L)
Sampling day
Maintenance
therapy 0,001
0,01
0,1
1
10
100
0 200 400 600 800 1000
[M-protein]
(mg/L)
Sampling day
Maintenance
therapy
0,0001
0,001
0,01
0,1
1
10
100
0 200 400 600 800 1000 1200 1400 1600
[M-protein]
(g/L)
Sampling day
Maintenance
therapy
• 41 Patients tested
• Different profiles found
MS-MRD Longitudinal follow-up

21. 21 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Reproducibility
y = 1.0199x - 0.2117
R² = 0.9389
Inter-institute variation
Intra-assay variation Inter-assay variation
(DIA using SILuMAB as off-the-shelf calibrator) {Wijnands, Langerhorst et al. CCLM 2023, in press.}
(instrumental variation)
20x same sample →
all CVs below 15%
(sample prep variation)
3 individual measurements (5 replicates) →
In line with FDA guidelines
all longitudinal samples of 15 patients
measured by 2 institutes →
R² = 0.9389
21 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool

22. 22 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Serious up-scaling
Latest workflow
= per year in NL

23. 23 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Recognition
• Clinical Chemistry Science and Innovation Award 2022
• College of Medical Immunologists Joos Kerckhaert
Award 2022
‘pioneering MS-work on personalized cancer diagnostics’

24. 24 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Multidisciplinary collaboration
Hans Jacobs
Charissa Wijnands
Pieter Langerhorst
Dennis Trede
Gary Kruppa
Lennard Pfennig
Markus Lubeck
Niels Goedecke
Oliver Raether
Pierre-Olivier Schmit
Sven Brehmer
Tharan Srikumar
Pierre Sonigo
Vincent Bonifay
Caroline Rouge
Somayya Noori
Martijn van Duijn
Theo Luider Aurore Perrot
Cyrille Touzeau
Helene Caillon
Jill Corre
Philippe Moreau
Thomas Dejoie
Gad Armony
Hans Wessels
Jolein Gloerich
Alain van Gool
Bruker-Radboudumc
Joint Center for
Translational Omics

25. 25 Biomarkers and Precision Oncology Europe, Berlin, 14 Nov 2023. Alain van Gool
Lessons learned
• Analysis of dynamic biomarkers is key in monitoring Minimal Residual Disease to:
• Restart therapy in time
• Adapt dosing of therapy
• Change to other therapy
• Be more efficient in personalized oncology care
• Mass spectrometry analysis of proteins has added value and good potential in MRD monitoring
• Collaboration between clinic, lab specialists, proteomics labs + between academics and industry is
needed and works!
• Analytical development
• Clinical validation
• Status: MS-MRD test is ready to scale up !

26. Acknowledgements
Charissa Wijnands
Anastasia Tzasta
Pieter Langerhorst
Hans Wessels
Jolein Gloerich
Dirk Lefeber
Purva Kulkarni
Gadi Armony
Richard Rodenburg
Bert van den Heuvel
and others
Marcel Nelen
Albert Heck
Thomas Hankemeier
Peter Bram ‘t Hoen
Daniella Kasteel
Jessie Smits
and others
Collaborators/funders
Helger Ijntema
Alexander Hoischen
Lisenka Vissers
Christian Gillisen
Janneke Weiss
Han Brunner
alain.vangool@radboudumc.nl
www.radboudumc.nl/en/people/alain-van-gool
www.slideshare.net/alainvangool
Dapha Habets
Irene Keularts
Marek Noga
and others
Gary Kruppa
Pierre-Olivier Schmit
Dennis Trede
and others
Emanuela Oldoni
Laura Garcia Bermejo
Andreas Scherer
Florence Bietrix
Eliis Keidong
Toni Andreu
and others
Hans Jacobs
Peter-Bram ‘t Hoen
Anna Niehues
Xiaofeng Liao
Casper de Visser
Junda Huang
Translational Metabolic Laboratory
Human Genetics Nijmegen
Center for Molecular and Biomolecular Informatics