Lecture describing workflows and case studies from the Translational Metabolic Laboratory @Radboudumc how to translate x-omics biomarker signatures to clinical implementation. I also highlighted new developments to join forces in the Netherlands X-omics Initiative, United for Metabolic Disease and events/book launches in the next months.

1. Clinical X-omics biomarkers to drive
Personalized Healthcare
Prof Alain van Gool
2nd Conference Validation of Biomarkers
COST CliniMARK
Basel, 28 Mar 2019
Professor Personalized Healthcare
Head Translational Metabolic Laboratory
Coordinator Radboudumc Technology Centers
Chair EATRIS Biomarker Platform
Lead PI of Netherlands X-omics Initiative

3. www.radboudumc.nl

4. Personalized healthcare in rare metabolic diseases
Normal Dutch parents
Son Brian, 2002, low birth weight, lactic acidosis, hypoglycaemia
Intellectual diability, movement disorder, epilepsy
† age 3,5 yr (respiratory failure)
Son Joel, 2009, same clinical phenotype
† age 1,5 yr (epilepsy)
Clinical phenotype:
Suspicion of mitochondrial dysfunction
4 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019
{Wortmann et al, Human Biology 2017}
Case study

5. Lab tests • ATP production ↓, Creatine phosphate production ↓
• But OXPHOS enzyme complex I-V normal
• Candidate gene sequencing: no variant
• Mechanism of disease?
• In 2010: Whole Exome Sequencing - WARS2
mutations{medicalxpress.com}
{Rodenburg, Biochim
Biophys Acta, 2016}
Case study

6. New mechanism of disease • WARS2 is mtDNA-coded
tryptophanyl-tRNA synthases
• Novel mutation causes
instability of WARS2 protein
• Less charging of Trp-tRNATrp
• New prenatal genetic test !
Case study
{Wortmann et al, Human Biology 2017}
6 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

7. Meet & greet @ Translational Metabolic Laboratory
Case study
7 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

8. Lessons learned
• Fast translational of biomarker research to implementation
in academic clinical laboratories
• Technology innovation is driving impact in personalized
healthcare
• Crucial to combine different molecular views (X-omics)
Case study
8 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

9. Role of X-omics biomarkers in Personalized Healthcare
Personalized diagnosis
Personalized therapy
= Personalized healthcare
+Patient participation
X-Omics
Therapy monitoring
9 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

10. Genomic impact in Personalized Health(care)
Personalized medicine:
B-RAFV600E drugs for melanoma
Personalized health:
BRCA-driven preventive surgery
10 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

11. The power of omics in diagnostics
Single
biomarker
Omics
panel
Patient 1
Patient 2
• Higher diagnostic yield
• Contextualisation of change
↑ increase
↓ decrease
11 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

12. Diagnostic progress by Whole Exome Sequencing
Human Genetics Nijmegen (Lisenka Vissers, Marcel Nelen, Han Brunner et al)
Retrospective analysis of Intellectual Disability cohort (n=150)
Sanger sequencing
Gene-by-gene
5.4 tests / patient (1-28)
Whole Exome Sequencing
All genes at once
1 test / patient
12 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

13. Next: Whole Genome Sequencing
Circus plots of Whole Genome Sequences of two metastatic cancer patients
Source: Edwin Cuppen, Hartwig Medical Foundation
13 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

14. Interpretation of genetic variants becomes the issue
“Functional studies can be a powerful tool in
support of pathogenicity”
Richards et al., Genet Med. (2015)17:405-24
Variant classification:
1. Benign
2. Likely benign
3. Uncertain significance
4. Likely pathogenic
5. Pathogenic
Guidelines American College of Medical Genetics and Genomics (ACMG)
More sequence data =
more unknown variants
14 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

15. Complexity of biological systems
Text book
DNA
RNA
Protein
Metabolite
Reality
{Karr, Cell 2012}Environment
15 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

16. Complexity in protein biology
21.000 genes
1.000.000 -2.000.000
protein forms
N-Glycosylation
Truncation
Phosphorylation
Acetylation
Ubiquitination
…
16 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

17. ‘DNA’ variants: changes in code
• Benign: 370 mL → 371 mL
• Pathogenic, easy to notice: 370 mL → 970 mL
• Pathogenic, hard to notice: sugar → salt
RNA variants: translation and communication
Protein variants: interpretation and execution

18. Functional Omics platforms
Research Biomarkers Diagnostics
Translational Metabolic Laboratory (www.youtube.com/watch?v=yhLbuX0H7rg)
Glycoproteomics
500
1000
1500
2000
m/z
5 10 15 20 25 30 35 40 Time [min]
Metabolomics
400
600
800
1000
1200
1400
m/z
10 20 30 40 50 60 Time [min]
Bottom-up proteomics
Glycomics
Top-down proteomics Functional genomics
18 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

19. 19 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019
Uric acid
Human
samples
Plasma, CSF (urine)
Controls vs. patient
QTOF Mass Spectrometry
- Reverse phase liquid chromatography
- Positive and negative mode
- Features
XCMS
Alignment
Peak comparison
> 10,000 Features
Xanthine
Whole Exome Sequencing
Karlien Coene
Leo Kluijtmans
Ron Wevers
Genomics & Metabolomics
Translational Metabolic Laboratory

20. 20 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019
Uric acid
Human
samples
Plasma, CSF (urine)
Controls vs. patient
QTOF Mass Spectrometry
- Reverse phase liquid chromatography
- Positive and negative mode
- Features
XCMS
Alignment
Peak comparison
> 10,000 Features
Xanthine
Whole Exome Sequencing
Karlien Coene
Leo Kluijtmans
Ron Wevers
Genomics & Metabolomics
Translational Metabolic Laboratory

21. Genomics & Glycomics
SLC8A6
GlycoModelControl(n=40)
SLC10A7-CDG
(n=4)
O
therCDG
-II(n=21)
-150
-100
-50
0
50
100
P33
P32
P17
P39
Modelvalues
99 patients; 47 without known gene defect
- Glycomics profiling on 99
- Intact transferrin glycoprofiling on 99
- Whole Exome Sequencing for 32 cases
PGM1: New Eng J Med 2014
Man1B1: Brain 2014
More subtle changes: here
(manuscript in prep)
Dirk Lefeber
Monique van
Scherpenzeel
Translational Metabolic Laboratory
21 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

22. Genomics & Glycomics
SLC8A6
GlycoModelControl(n=40)
SLC10A7-CDG
(n=4)
O
therCDG
-II(n=21)
-150
-100
-50
0
50
100
P33
P32
P17
P39
Modelvalues
99 patients; 47 without known gene defect
- Glycomics profiling on 99
- Intact transferrin glycoprofiling on 99
- Whole Exome Sequencing for 32 cases
PGM1: New Eng J Med 2014
Man1B1: Brain 2014
More subtle changes: here
(manuscript in prep)
Dirk Lefeber
Monique van
Scherpenzeel
Translational Metabolic Laboratory
22 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

23. Genomics & Glycoproteomics
• 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 !?
Hans Wessels, Alain van Gool, Dirk Lefeber
Translational Metabolic Laboratory
23 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

24. Functional genomics
functional validation
of variants with unknown
significance
CRISPR/Cas9
rescue
biomarkers
animal model
iPSC
+nGFP +nGFP +TAZ
contr BTH BTH
PTPS deficiency PTPS deficiency-Corr#1
TH/βIII-tubulin/DAPI
complementation
Control clpb MO
mdh1Δ
mdh1-P128L
mdh1-P202L
mdh1-G30R
hMDH2
MDH1
-
YPD
fermentation
YPD
respiration
α-actinin
α-ManNAc
CH3
β-ManNAc
CH3
2.10 2.05 2.00
{Rodenburg,
J Inherit Metab Dis, 2018}
micro-organism model
Richard Rodenburg
Omar Tutakhel
Translational Metabolic Laboratory
24 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

25. 25 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019
Precision medicine in genetic-metabolic disease – current
Personalized diagnosis
Genomics
(WES)
Metabolomics
New disease
mechanisms
Personalized therapies
Nature Genetics 2018
NEJM 2014
Nature 2016
NEJM 2014
Genet Med 2017
Translational Metabolic Laboratory
Glycomics

26. Diagnostic glycoproteomics pipeline
Comprehensive QC analytics

27. Diagnostic glycoproteomics pipeline
Comprehensive QC analytics

28. Precision medicine in genetic-metabolic disease - future
Personalized diagnosis
Genomics
(WGS)
Metabolomics
New personalized
therapies
Glycomics
Glycoproteomics
Deep Learning
Artificial Intelligence
System biology
Nature Genetics 2016 Pilot 2017
New disease
mechanisms
Translational Metabolic Laboratory
28 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

29. High need to bring clinical X-omics to higher level
• Technologies: Quality, harmonised, standardised, cheaper, higher throughput
• Translation: Clinical and regulatory acceptance
• Genomics is quite advanced
• Proteomics, metabolomics (and other omics) much less so
29 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

30. Progress further through collaboration
European networks
national
local
30 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

31. www.radboudumc.nl/research/technologycenters
31
X-omics
Data
Clinical
Preclinical
Imaging

32. Collaboration towards Good Biomarker Practices
{van Gool et al, Nature Reviews Drug Discovery, Apr 2017}
COST action CA16113
http://clinimark.eu
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33. New: Handbook of Biomarkers and Precision Medicine
70 manuscripts from experts in pharma,
diagnostics, clinic, technology
1. What is a biomarker and their role in drug
development?
2. Biomarkers in preclinical sciences
3. Biomarkers in translational sciences
4. Biomarker-informed clinical trials
5. The road ahead in precision medicine
6. Lessons from the past and pioneers of the
future
7. Emerging technologies
8. The next frontiers in therapeutic target areas
9. Lessons learned and what’s next?
Publication data April 29th 2019
Draft pricing (Amazon): hardback USD 285,
e-book USD 60
33 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

34. Collaboration in Netherlands X-omics Initiative
www.x-omics.nl
• Access
• Helpdesk / training
• Collaboration
34 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

35. Focus of Netherlands X-omics Initiative
Push omics
technologies
• Resolution
• Sensitivity
• Coverage
Genomics
Proteomics
Metabolomics
• Quality
• Standards
• Data FAIR
at source
X-omics
• Study design
• Sample handling
• Data cataloging
• Quality
• Expertise
• Best practice
• Data integration
• Data analysis
• Best practice
35 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019
• Access
• Helpdesk / training
• Collaboration
“Crossy”
www.x-omics.nl/contact/helpdesk

36. X-omics demonstrators
1. Cell/organoid
• Understanding cancer drug response and resistance
• Drug-induced dynamic pathway analysis
2. Individual
• Understanding personalized differences in rare diseases
• Systemic changes to biological challenges
3. Population
• Understanding genetic variants in Dutch population
• Statistical correlations
To showcase and field test new X-omics capabilities
36 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

37. www.x-omics.nl
37 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

38. X-omics summer school July 2019
1. Biomarkers
2. Next gen sequencing
3. Mass spectrometry
4. Data integration & analysis
5. Case studies
5 days @Radboud University Nijmegen
1-5 July 2019
Theory + Hands-on
38 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019
www.x-omics.nl
www Radboud University.
Quick link: goo.gl/pyrvS6

39. Collaboration in United for Metabolic Disease
• Netherlands multidisciplinary
collaboration
• Clinicians + laboratory
specialists + patients
• Step-wise focus:
1. Awareness
2. Diagnosis
3. Understanding
4. Therapies
5. Care and prevention
• Link to technology in
Netherlands X-omics Initiative
39 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

40. Afterthought: there is no single one reflection of health
• Funhouse mirror effect
• Multiple sources of your
data
• Multiple Omics
• Clinical chemistry
• Electronic Patient Dossier
• Wearables
• Digital biomarkers
• Commercial health tests
• Social media
• Surrounding
• Each give an (incomplete)
image of you
• How to deal with all of this
for your personal health?
{Mira Vegter, Hub Zwart, Alain van Gool, in prep}
40 Alain van Gool, 2nd Conference Validation of Biomarkers, Basel, 28 Mar 2019

41. Acknowledgements
Translational Metabolic Laboratory
Hans Wessels
Dirk Lefeber
Karlien Coene
Leo Kluijtmans
Richard Rodenburg
Jolein Gloerich
Roel Tans
Esther Willems
Omar Tutakhel
Marek Noga
Albert Gerritsen
Purva Kulkarni
and others
Edwin Cuppen
Albert Heck
Thomas Hankemeier
Peter Bram ‘t Hoen
Daniella Kasteel
and others
Collaborators/funders
Human Genetics Nijmegen
Helger Ijntema
Marcel Nelen
Alexander Hoischen
Lisenka Vissers
Christian Gillisen
Han Brunner
and others
alain.vangool@radboudumc.nl
www.radboudumc.nl/en/people/alain-van-gool
www.slideshare.net/alainvangool
CarTarDis
Dapha Habets
Irene Keularts
and others
Rainer Bischoff
Theo Luider
and others