A unique honour and opportunity to give a 1.5 hour lecture to young biomarker scientists to introduce biomarkers and their importance in translational medicine and personalized healthcare.
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2015 10-06 Building Bridges Biomarker symposium FIMM Helsinki, Alain van Gool
1. Biomarkers in personalized health(care):
past, present and future
Professor of Personalized Healthcare
Head Radboud Center for Proteomics, Glycomics
and Metabolomics
Coordinator Radboud Technology Centers
Applied Biomarker Scientist
Prof Alain van Gool
Building Bridges Autumn 2015:
Biomarkers in Clinical and Translational Research
-‐ the ABCs of Biomarkers
Helsinki
6 Oct 2015
2. My mixed perspectives in personalized health(care)
8 years academia (NL, UK)
(molecular mechanisms of disease)
13 years pharma (EU, USA, Asia)
(biomarkers, Omics)
4 years med school (NL)
(personalized healthcare, Omics, biomarkers)
4 years applied research institute (NL, EU)
(biomarkers, personalized health, nutrition)
A person / citizen / family man
(adventures in EU, USA, Asia)
1991-1996
(PhD)
1996-1998
(post-doc)
2009-2012
(visiting prof)
1999-2007 2007-2009 2009-2011
2011-now
2011-now
2 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
3. Biomarkers in personalized health(care)
past, present and future
• From Diagnosis
• To Translational Medicine
• To Personalized/Stratified/Precision Medicine
• To Personalized Health(care)
• Some do’s and don’ts
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 20153
4. Biomarkers in the early days
600 BC:
Sushruta, famous Indian surgeon
Diagnosis of diabetes diabetes, then called “sweet urine disease”, by determining if
ants were attracted to a person’s urine.
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 20154
5. Biomarkers in the early days
{Kumar and van Gool, RSC, 2013}
1506:
The urine wheel
Use color, smell and taste of urine
to diagnose disease and decide
best treatment
Ullrich Pinder
Epiphanie Medicorum
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 20155
6. Biomarker need from pharma industry
• In old days little understanding of cause of disease
• Use of natural compounds from plant and animal
• Limited testing in laboratory + trial and error in clinic
• Frequently not effacious and/or serious side effects in patients
• Unacceptable approach (ethical, financial)
• Start rational and translational drug discovery and development
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 20156
7. Translational medicine in pharma
Basic Research
In Vitro Studies
Target Validation
Animal Models
Phase I and Phase II
-PoC- Studies
Phase III Studies
Clinical Research
Forward TranslationForward Translation
Reverse TranslationReverse Translation
(View drug development
as customer)
(Feed back clinical needs
and samples)
[van Gool et al, Drug Disc. Today 2010]
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 20157
8. Limited view from the outside
Source: Gary Larson
Animal models Patient-related outcomes
Source: National University Hospital Singapore
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 20158
9. Key is to have a good view inside
High need for molecular tools that allow a look into the black box
and improve disease management: biomarkers
Drug exposure ?
Diagnosis ?
Cross-species differences ?
Patient classification ?
Prognosis ?
Target engagement ?
Modulation of mechanism ?
Off-target drug effects ?
Treatment Phenotype
Mechanism ?
Other (latent) diseases ?
Person
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 20159
10. Biomarkers
{Biomarkers definition working group, 2001 }
Definition: ‘a characteristic that is objectively measured and evaluated as
an indicator of normal biological processes, pathogenic processes, or
pharmacologic responses to a therapeutic intervention’
Or ‘Whatever works in adding value’
Molecular biomarkers provide a molecular impression of a biological system
(cell, animal, human)
Biomarkers can be various sorts of data, or combinations thereof
Dutch CC meeting ‘Personalized Health Care”
Ede, 2 October 2013
Alain van Gool
Lecture LKCH, UMC Utrecht
29 October 2013
Alain van Gool
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201510
11. Biomarker-based translational medicine
• Does the compound get to the site of action?
• Does the compound cause its intended
pharmacological/ functional effects?
• Does the compound have beneficial effects on disease
or clinical pathophysiology?
• What is the therapeutic window (how safe is the drug)?
• How do sources of variability in drug response in target
population affect efficacy and safety?
Lead
Optimization
Exploratory
Development PoC
Lead
Discovery
Target
Discovery
Exposure ?
Mechanism ?
Efficacy ?
Safety ?
Responders ?
{van Gool et al, Drug Disc Today 2010}
{Kumar, van Gool, RSC biomarkers, 2013}
2ND intl Pharma-Nutrition Conference
Singapore, 17 April 2013
Alain van Gool
Lecture LKCH, UMC Utrecht
29 October 2013
Alain van Gool
One strategy
11
12. Biomarker strategy: Data-driven decisions
To be made during testing of drug in preclinical and clinical disease models:
Target engagement? Effect on disease?
yes yes !
no no
• No need to test current
drug in large clinical trial
• Need to identify a more
potent drug
• Concept may still be
correct
• Concept was not correct
• Abandon approach
• Proof-of-Concept
• Proceed to full
clinical
development
“Stop early, stop cheap”
“More shots on goal”
12
13. Rational selection of best targets and drugs works
The 5R’s assessment:
• Right Target
• Right Tissue
• Right Safety
• Right Patients
• Right Commercial Potential
13
14. Adopt rational target selection in pharma research
CarTarDis = Cardiovascular Target Discovery
Public-private partnership, 13 partners, 8 countries, project budget 8.0M Eur
Started 1 Oct 2013 for 4 years
Adopting AstraZeneca’s 5R strategy in drug target selection
(Coordinator)
CarTarDis.eu
14
15. Successes of drug development
Antibiotics Vaccins
Reproductive medicine Oncology
15 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
16. Source: John Arrowsmith: Nature Reviews Drug Discovery 2011
• Success rates of clinical proof-of-concept have dropped from 28% to 18%
• Insufficient efficacy as the most frequent reason
• Targeted therapy through Personalized Medicine may be the solution
• Patient selection using companion diagnostics
A need for Personalized Medicine
(Analysis of 108 failures in phase II)
Reason for failure Therapeutic area
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201516
17. Biomarkers in personalized health(care)
past, present and future
• From Diagnosis
• To Translational Medicine
• To Personalized/Stratified/Precision Medicine
• To Personalized Health(care)
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201517
19. {Source: Chakma. Journal of Young Investigators. 2009}
Principle of Personalized/Precision/Targeted Medicine
19 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
20. Personalised Medicine @Europe
European Science Foundation
30 Nov 2012
Innovative Medicine Initiative 2
8 July 2013
EC Horizon2020
10 Dec 2013
20
20 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
21. Precision medicine @USA
President Obama
State of Union 2015
21 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
22. 22 Alain van Gool, NanoNext.NL, 3 July 2015
Optimal Personalized / Precision / Targeted Medicine
23. Case study: B-RAF mutations and melanoma
{Miller and Mihm,
2006}
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201523
24. Mechanism of pathophysiology in BRAF mutated tumors
V600E
Kinase domain
{Roberts and Der, 2007}
• B-RAFV600E mutation: constitutively active kinase, oncogenic addiction
• Overactivate ERK pathway drives cell proliferation
• RAF inhibitors shown to block growth of tumors with B-RAFV600E mutation
• Prevalence of B-RAFV600E is base for patient selection:
• Melanoma (60%), colon (15%), ovarian (30%), thyroid (30%) cancer
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201524
25. Clinical efficacy of Vemurafenib (PLX-4032, Zelboraf)
Key biomarkers:
Stratification: BRAFV600E mutation
Mechanism: P-ERK
Cyclin-D1
Efficacy: Ki-67
18FDG-PET, CT
Clinical endpoint: progression-free survival (%)
{Source: Flaherty et al, NEJM 2010}{Source: Chapman et al, NEJM 2011}
SelectBio Biomarkers 2014
Cambridge
8 July 2014
Alain van Gool
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201525
26. Development of Vemurafenib (Zelboraf)
{Source: Davis M J , Schlessinger J J Cell Biol 2012}
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201526
27. Clinical efficacy of Vemurafenib
{Wagle et al, 2011, J Clin Oncol 29:3085}
Before Rx Vemurafenib, 15 weeks Vemurafenib, 23 weeks
• Strong initial effects vemurafenib
• Emerging drug resistancy
• Reccurence of aggressive tumors
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201527
28. Tumor tissue heterogeneity
• BRAFV600D/E is considered as
driving mutation in melanoma
• However, also no BRAFV600D/E
mutation found in regions of a
primary melanoma
• Molecular heterogeneity in
diseased tissue
• Biomarker levels in tissue vary
• Biomarker levels in body fluids
will vary
• Major challenge for
(companion) diagnostics in
solid cancers
{Source: Yancovitz, PLoS One 2012}
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201528
29. Exponential technologies
“The only constant is change,
and the rate of change is
increasing”
We are at the knee
of the exponential curve
29 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
30. 30 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
31. Demo room
31 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
32. Exponential developments in biomarker technologies
• 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
Some examples of innovation:
32 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
33. Next Generation Sequencing
{Nature, July 17 2014, 511: 344-}
33 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
34. The epigenome
34 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
35. The microbiome
35 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
36. Emerging protein biomarkers
36
Current diagnostic protein assays:
• Mostly protein abundance
Emerging:
• Post-translational modifications
• Ratio protein isoforms
• Protein complexes
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
51. Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201551
52. • DIY sequence your genome and/or your microbiome
genome
• at a provider, at a pharmacy, at home
• Take your genome to the doctor
• Have a personalized healthcare advice
DIY sequencing
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201552
53. • Measure your brain waves (EEG)
• Recognize conditions for maximal
concentration or relaxation.
• Use device to train.
DIY EEG imaging
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201553
54. DIY protein biomarker analysis
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201554
58. 58
58 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
59. BUT … Biomarker innovation gaps
Discovery Clinical
validation/confirmation
Diagnostic
test
Number of
biomarkers
Gap 1
Gap 2
Gap 3
59
• Too much biomarker discovery
• Too little development to application
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
60. Biomarker innovation gaps: some numbers
Data from Thomson Reuters Integrity database, February 2015
Alzheimer’s Disease
Chronic Obstructive
Pulmonary Disease
Type II Diabetes Mellitis
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201560
61. Biomarker innovation gaps: some numbers
5 biomarkers/
working day
1 biomarker/
1-3 years
1 biomarker/
3-10 years
?
Eg Biomarkers in time: Prostate cancer
May 2011: n= 2,231 biomarkers
Nov 2012: n= 6,562 biomarkers
Oct 2013: n= 8,358 biomarkers
Nov 2014: n= 10,350 biomarkers
5 Oct 2015: n = 11,856 biomarkers
Discovery Clinical
validation/confirmation
Diagnostic
test
Number of
biomarkers
Gap 1
Gap 2
Gap 3
61 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
62. Reasons for biomarker innovation gap
• Not one integrated pipeline of biomarker R&D
• Publication pressure towards high impact papers
• Lack of interest and funding for confirmatory biomarker studies
• Hard to organize multi-lab studies
• Biology is complex on organism level
• Data cannot be reproduced
• Bias towards extreme results
• Biomarker variability
• …
{Source: John Ioannidis, JAMA 2011}
{Source: Khusru Asadullah, Nat Rev Drug Disc 2011}
Health Valley Event 2014
Nijmegen
13 March 2014
Alain van Gool
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201562
63. “It is simply no longer possible to believe much of the clinical
research that is published, or to rely on the judgment of trusted
physicians or authoritative medical guidelines.
I take no pleasure in this conclusion, which I reached slowly and
reluctantly over my two decades as an editor of The New
England Journal of Medicine.”
Marcia Angell, MD
Former Editor-in-Chief NEJM
Oct 2010
Health Valley Event 2014
Nijmegen
13 March 2014
Alain van Gool
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201563
64. Biomarkers in personalized health(care)
past, present and future
• From Diagnosis
• To Translational Medicine
• To Personalized/Stratified/Precision Medicine
• To Personalized Health(care)
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201564
65. Personalized health(care)
Is more than ‘just’ targeted medicines
It’s personal !
‘I want to stay healthy.’
‘If not, how do I get healthy?’
65 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
66. The route to Personalized Health
66 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
67. Analogy: route planner
GPS to a location
Amsterdam
Traffic jam
Amsterdam
Route 1 Route 2
= Default Traffic jam near Utrecht Alternative route
67 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
68. Personalized Health(care) planner
GPS to health
Health
Route 1 Route 2
= Default
First signs of
disease risk
Alternative route
Now
Health risk
Health
Now
Health
68 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
69. Personalized Health(care) model
Analogies to GPS route planner:
• Technology enabled
• Monitoring should be on the background;
only alert when risk
• Success through participation of user
• Personal choice to actively monitor or not
• Commercial competition of tool builders to
become market leader(s)
• Implementation as standard in society
GPS to health
69 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
70. Know your personal thresholds and intervention options
Personalized
Intervention
of patients-like-me
Risk profiles
of persons-like-me
Big
Biomarker
Data
Molecular
Non-molecular
Environment
…
HomeostasisAllostasisDisease
Time
Disease
Health
Selfmonitoring
Adapted from Jan van der Greef, TNO (2013)
Personal profile
Personalized
Participatory
Pre-emptive
70
Personalized health
Personalized medicine
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
71. Example personal profile-based patient assessment
{Chen et al, Cell 2012, 148: 1293}
Concept:
• Continuous monitoring (n=1)
• Routine biomarkers to alert
• Omics to explain
• Early intervention
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201571
72. Simulate and visualise health interventions {Albert de Graaf}
72 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
73. Biomarkers in personalized health(care)
past, present and future
• From Diagnosis
• To Translational Medicine
• To Personalized/Stratified/Precision Medicine
• To Personalized Health(care)
• Some do’s and don’ts
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201573
74. How to move forward?
1. Focus biomarker research on the end user
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201574
75. Plan biomarker studies based on needs of end user
Discovery Clinical
validation/confirmation
Diagnostic
test
Number of
biomarkers
Gap 1
Gap 2
Gap 3
75
• Don’t do it because you can
• Do it because it is needed
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
76. Connect patient to clinical lab to patient
76
https://www.youtube.com/watch?v=yhLbuX0H7rg
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
77. Case: diagnostic glycoprotein biomarker
• Rare metabolic disease cases
• Combination glycoproteomics and exome sequencing
• Outcome 1: Explanation of disease
• Outcome 2: Dietary intervention as succesful personalized therapy
• Outcome 3: Glycoprofile transferrin developed and applied as diagnostic test
{Tegtmeyer et al, NEJM 370;6: 533 (2014)}
Genomics Glycomics Metabolomics
{Monique van Scherpenzeel, Dirk Lefeber}
77 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
78. Lab values Clinical
outcomes
Pain Mobility Fatigue
INTEGRATE-HTA
Objectives patient and clinican may be different
R van Hoorn, W Kievit, M Tummers, GJ van der Wilt
How to do optimal shared decision making?
Intervention
78
79. Translation is key in Personalized Healthcare !
Personal profile data
Knowledge
Understanding
Decision
Action
79 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
80. Translation is key in Personalized Healthcare !
“I’m afraid you’re
suffering from an
increased IL-1β and
an aberrant miR843
expression”
Adapted from:
?
80 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
81. Translation is key in Personalized Healthcare !
Treatment options
Pro’sCon’s
Select personalized therapy
81 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
82. How to move forward?
1. Focus biomarker research on the end user
2. System biology
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201582
83. System Biology
β-cell Pathology
gluc Risk factor
{Source: Ben van Ommen, TNO}
therapy
Visceral
adiposity
LDL elevated
Glucose toxicity
Fatty liver
Gut
inflammation
endothelial
inflammation
systemic
Insulin resistance
Systemic
inflammation
Hepatic IR
Adipose IR
Muscle metabolic
inflexibility
adipose
inflammation
Microvascular
damage
Myocardial
infactions
Heart
failure
Cardiac
dysfunction
Brain
disorders
Nephropathy
Atherosclerosis
β-cell failure
High cholesterol
High glucose
Hypertension
dyslipidemia
ectopic
lipid overload
Hepatic
inflammation
Stroke
IBD
fibrosis
Retinopathy
Physical inactivity
Caloric excess
Chronic Stress
Disruption
circadian rhythm
Parasympathetic
tone
Sympathetic
arousal
Worrying
Hurrying
Endorphins
Gut
activitySweet &
fat foods
Sleep disturbance
Inflammatory
response
Adrenalin
Fear
Challenge
stress
Heart rate
Heart rate
variability
High cortisol
α-amylase
Lipids, alcohol, fructose
Carnitine, choline
Stannols, fibre
Low glycemic index
Epicathechins
Anthocyanins
Soy
Quercetin, Se, Zn, …
Metformin
Vioxx
Salicylate
LXR agonist
Fenofibrate Rosiglitazone
Pioglitazone
Sitagliptin
Glibenclamide
Atorvastati
n
Omega3-fatty acids
Pharma
Nutrition
Lifestyle
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201583
84. EC DG for Research and Innovation
Alain van Gool
Brussels, 11 Sept 2012
Relating tissue pharmacology – biomarker - therapy
84
85. Translating knowledge to field labs
1. Implementation-plan ‘Personalized diagnosis of
(pre)diabetic and their lifestyle treatment in
Dutch Health care’.
2. Use of Oral Glucose Tolerance Test as a
stratification biomarker for (pre)diabetic
patients
3. Advice a tailored treatment (lifestyle and/or
medical)
4. Monitor added value of stratification
5. Communicate results and
lessons learned
Being implemented in
1st line care
(region Hillegom,
Netherlands)
Alliance “Expedition Sustainable Care,
starting with diabetes”
85 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
86. Explore personalized interventions by Pharma-Nutrition
Shared Innovation Programs through public-private consortia
Higher efficacy / less side effects
86
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201586
87. How to move forward?
1. Focus biomarker research on the end user
2. System biology
3. Build biomarker development pipelines based on
“Good Biomarker Practices”
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201587
88. Build biomarker validation pipelines
Standardisation, harmonisation,
knowledge sharing needed in:
1. Assay development
2. Clinical validation
3. Regulatory acceptance
NL Roadmap Molecular Diagnostics (2012) NL Grant 4.3M Eur (2014)
Move towards EU funding (2016)
89. Define, share and act on“Good Biomarker Practices”
Some items in need of standardisation:
• Reproducibility, quality requirements
• Study design & statistical power
• Variability & heterogeneity
• Specimen acquisition & pre-analytics
• Sample preparation
• Patient & associated clinical data
• Analytical standards & quality control
Not reinvent the wheel.
Standardisation, harmonisation, knowledge sharing needed in:
1. Assay development
2. Clinical validation
3. Biomarker qualification
• Assay/platform development
• Quality system manufacturing
• Data analysis & management
• Regulatory requirements
• Ethical, IP & legal aspects
• Early HTA
• Quality in documentation & publication
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201589
90. Good example of multi-center biomarker validation
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201590
91. How to move forward?
1. Focus biomarker research on the end user
2. System biology
3. Build biomarker development pipelines based on
“Good Biomarker Practices”
4. Validate more biomarkers in one go
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201591
92. Validate more biomarkers in one go
1. Determine the context of change in a biomarker.
2. Drive validation of multiple biomarkers at once
Multiple
measures
Patient 1 Patient 2
Technologies are already out there:
• Next generation sequencing
• Microarrays
• Multiplex immunoassays
Single
measure
• Targeted mass spectrometry
• Binding assays
• Mass spec imaging
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201592
93. How to move forward?
1. Focus biomarker research on the end user
2. System biology
3. Build biomarker development pipelines based on
“Good Biomarker Practices”
4. Validate more biomarkers in one go
5. Value negative results
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201593
94. Case: Tissue proteomics profiling project Protein expression
(positive controls)
GO Protein distributions
Cellular compartments
LFQ scatter plot
Biological replicates
y= 0.9834x + 130390
R2=0.9842
Q: downstream effects of transgene?
Hippocampus tissue of Transgenic mice
4 Conditions: WT, TG, WT treated, TG treated with drug
5 Biological replicates; 2D LC-MS/MS analysis (20 fractions, 1 hour gradient)
Label-Free Quantitation (LFQ – MaxQuant)
• LC-MS/MS analyses: 400
• MS spectra: 1.937.394
• MS/MS spectra: 2.323.458
• Detected isotope patterns: 66.602.271
• Isotope patterns sequenced: 1.295.489
• Average absolute mass deviation: 1,38 ppm
• 1,3 Terrabyte data
PCA analysis – loading plot
• Matched MS/MS spectra to peptides: 500.317
• Identified proteins: 3.187
• Quantified proteins: 2.365 (≥2 peptides/protein)
• Differential proteins: 276 (p<0.05)
• Average CV < 21%*
* Combining biological and technical reproducability
Transgene
Downstream
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201594
95. How to move forward?
1. Focus biomarker research on the end user
2. System biology
3. Build biomarker development pipelines based on
“Good Biomarker Practices”
4. Validate more biomarkers in one go
5. Value negative results
6. Interpret data in personalized way
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201595
96. healthy disease disease +
treatment
Interpret data with self-normalisation
Subgroups
100%
Normalisation of responders
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201596
97. How to move forward?
1. Focus biomarker research on the end user
2. System biology
3. Build biomarker development pipelines based on
“Good Biomarker Practices”
4. Validate more biomarkers in one go
5. Value negative results
6. Interpret data in personalized way
7. Use available resources
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201597
98. Research Biomarkers Diagnostics
Department of Laboratory Medicine, Radboudumc
Integrated Translational Research and Diagnostic Laboratory, 220 fte, yearly budget ~ 28M euro.
Close interaction with Dept of Genetics, Pathology and Medical Microbiology
Specialities:
• Proteomics, glycomics, metabolomics
• Enzymatic assays
• Neurochemistry
• Cellulair immunotherapy
• Immunomonitoring
Areas of disease:
• Metabolic diseases
• Mitochondrial diseases
• Lysosomal /glycosylation disorders
• Neuroscience
• Nefrology
• Iron metabolism
• Autoimmunity
• Immunodeficiency
• Transplantation
In development:
• ~500 Biomarkers
• Early and late stage
• Analytical development
• Clinical validation
Assay formats:
• Immunoassay
• Turbidicity assays
• Flow cytometry
• DNA sequencing
• Mass spectrometry
• Experimental human (-ized)
invitro and invivo models for
inflammation and
immunosuppression
Validated assays*:
• ~ 1000 assays
• 3.000.000 tests/year
Areas of application:
• Personalized healthcare
• Diagnosis
• Prognosis
• Mechanism of disease
• Mechanism of drug action
Biomarker development pipeline @ Radboudumc
*CCKL accreditation/RvA/EFI
www.laboratorymedicine.nl
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 201598
100. How to move forward?
1. Focus biomarker research on the end user
2. System biology
3. Build biomarker development pipelines based on
“Good Biomarker Practices”
4. Validate more biomarkers in one go
5. Value negative results
6. Interpret data in personalized way
7. Use available resources
8. Seek interdisciplinary team work
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015100
102. Alain van Gool, 2nd Precision Medicine Congress, London, 15 Sept 2015102
Try-outs at REshape Innovation Center
Lucien Engelen
103. Multi-partner collaborations in Health Informatics
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015103
104. Speak each other’s language
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015104
105. 105
Teach how to work inter-disciplinary
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
106. How to move forward?
1. Focus biomarker research on the end user
2. System biology
3. Build biomarker development pipelines based on
“Good Biomarker Practices”
4. Validate more biomarkers in one go
5. Value negative results
6. Interpret data in personalized way
7. Use available resources
8. Seek interdisciplinary team work
9. Copy best practice
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015106
107. Copy best practice
•Nation wide coverage
•66 regional networks
•3000 trained experts
•12 disciplines
prof Bas Bloem
dr Marten Munneke
107 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
108. 5. Supportive
technology
1. Network of
experts
2. The patient
as partner
4. Transparant
quality controle
3. Integral reward for outcome, not production
5 key components of ParkinsonNet
108 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
109. Demonstrated added value
Regular care
ParkinsonNet care
% Hip fracture Cost per patient*
*Hospitals, medication, care at home
109 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
110. 110 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
111. Dutch export product …
King Willem
Alexander
Bas
Bloem
Marten
Munneke
Queen
Maxima
111 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
112. How to move forward?
1. Focus biomarker research on the end user
2. System biology
3. Build biomarker development pipelines based on
“Good Biomarker Practices”
4. Validate more biomarkers in one go
5. Value negative results
6. Interpret data in personalized way
7. Use available resources
8. Seek interdisciplinary team work
9. Copy best practice
10. Spread the word
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015112
116. Acknowledgements
Ron Wevers
Jolein Gloerich
Hans Wessels
Monique Scherpenzeel
Dirk Lefeber
Leo Kluijtmans
Lucien Engelen
Paul Smits
Maroeska Rovers
Nathalie Bovy
Bas Bloem
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
Jan van der Greef
Ben van Ommen
Bas Kremer
Lars Verschuren
Ivana Bobeldijk
Marjan van Erk
Carina de Jongh
Peter van Dijken
Peter Wielinga
Robert Kleemann
Suzan Wopereis
and many others And funders
CarTarDis
116 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015