Post on 16-Feb-2017
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
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
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 2015 3
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 2015 4
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 2015 5
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 2015 6
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 Translation Forward Translation
Reverse Translation Reverse 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 2015 7
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 2015 8
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 2015 9
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 2015 10
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
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
Rational selection of best targets and drugs works
The 5R’s assessment:
• Right Target
• Right Tissue
• Right Safety
• Right Patients
• Right Commercial Potential
13
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
Successes of drug development
Antibiotics Vaccins
Reproductive medicine Oncology
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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 2015 16
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 2015 17
Consider individual differences in life science research
18
18 Alain van Gool, Pharma-Nutrition 2015, 13 March 2015
{Source: Chakma. Journal of Young Investigators. 2009}
Principle of Personalized/Precision/Targeted Medicine
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Personalised Medicine @Europe
European Science Foundation 30 Nov 2012
Innovative Medicine Initiative 2 8 July 2013
EC Horizon2020 10 Dec 2013
20
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Precision medicine @USA
President Obama State of Union 2015
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22 Alain van Gool, NanoNext.NL, 3 July 2015
Optimal Personalized / Precision / Targeted Medicine
Case study: B-RAF mutations and melanoma
{Miller and Mihm,
2006}
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015 23
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 2015 24
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 2015 25
Development of Vemurafenib (Zelboraf)
{Source: Davis M J , Schlessinger J J Cell Biol 2012}
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015 26
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 2015 27
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}
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Exponential technologies
“The only constant is change, and the rate of change is
increasing”
We are at the knee of the exponential curve
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Demo room
31 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
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
Next Generation Sequencing
{Nature, July 17 2014, 511: 344-}
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The epigenome
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The microbiome
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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
Glycomics
Intact glycoproteins
Free glycans
Glycopeptides 500
750
1000
1250
1500
1750
m/z
10 15 20 25 30 35 40 Time [min]
PGM1 profile
CID fragmentation spectrum
37 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
Discovering new glycoprotein biomarkers
• 1D LC-MS/MS glycoproteomics in plasma • Detection of ~12.000 unique deconvoluted monoisotopic masses per
single analysis (> 50% are glycopeptides)
500
1000
1500
2000
m/z
5 10 15 20 25 30 35 40 Time [min]
Proof of principle study:
38 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
Intact protein analysis
39
Bottum-up proteomics
Top-down proteomics
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
Intact complexome analysis as new biomarker?
• Native tissue biopsies
• Isolate intact membrane complexes
• Separate and isolate complexes using native gels
• LC-MS/MS analysis of intact proteins
• Data analysis
Tissue 1 (n=3)
Tissue 2 (n=3)
Subunit
Subunit – tissue 1
Subunit – tissue 2
• Identified protein sequence of subunit • Deduce simulated sequences from database • Determine fit with experimental data
40
© ImaBiotech 2014
m/z Int.
X1, Y1
m/z Int.
X2, Y1
m/z Int.
X3, Y1
m/z Int.
X4, Y1
m/z Int.
X4, Y2
m/z Int.
X3, Y2
m/z Int.
X2, Y2
‘Nb of pixels’ = ‘nb of mass spectra’
Mass Spectrometry Imaging (MSI)? {Source: Gregory Hamm}
© ImaBiotech 2014
m/z
Int.
Each m/z signal = One specific MS image
Mass Spectrometry Imaging (MSI)?
© ImaBiotech 2014
Mass Spectrometry Imaging (MSI)?
‘Nice images’ & Reliable information
H.E. Staining
Molecular images overlay
©2014 ImaBiotech
PD
P
K
Toxico
logy
MSI - Q
MSI
400 µm resolution
40 µm resolution
20 µm resolution
Mass Spectrometry Imaging (MSI): Spatial Resolution
Spatial resolution = difference between two pixels of the image
© ImaBiotech 2014
Lipid markers distribution:
m/z 538.98
CE = Cholesteryl ester PC = Phosphatidylcholine TG= Triacylglycerol Heme b= Hemoglobine b
MALDI-MSI reveals regionally distinct lipid profiles in atherosclerotic plaque
Biomarker Discovery: CVD Disease
CarTarDis
© ImaBiotech 2014
Discovery of CVD biomarkers using MSI?
Lipids relative quantification in histological regions
Shoulder region
Fibrous cap
Calcified region
Necrotic core
LPC (18:1)
…lysophosphatidylcholine (LPC)
CarTarDis
Biomarker Discovery: CVD Disease
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48
New data !
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
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www.scanadu.com
Personalized advice
Action
Selfmonitor Cloud
Lifestyle Nutrition Pharma
DIY monitoring of vital signs
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Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015 51
• 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 2015 52
• 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 2015 53
DIY protein biomarker analysis
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015 54
‘insideables’
‘wearables’
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015 55
58
58 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
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
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 2015 60
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
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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 2015 62
“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 2015 63
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 2015 64
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
The route to Personalized Health
66 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
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
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
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
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 …
Ho
meo
sta
sis
A
llo
sta
sis
D
isease
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
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 2015 71
Simulate and visualise health interventions {Albert de Graaf}
72 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
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 2015 73
How to move forward?
1. Focus biomarker research on the end user
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015 74
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
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
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}
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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
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
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
Translation is key in Personalized Healthcare !
Treatment options
Pro’s
Con’s
Select personalized therapy
81 Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
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 2015 82
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
activity Sweet & 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
Atorvastatin
Omega3-fatty acids
Pharma
Nutrition Lifestyle
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015 83
EC DG for Research and Innovation
Alain van Gool
Brussels, 11 Sept 2012
Relating tissue pharmacology – biomarker - therapy
84
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”
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Explore personalized interventions by Pharma-Nutrition
Shared Innovation Programs through public-private consortia
Higher efficacy / less side effects
86
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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”
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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)
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 2015 89
Good example of multi-center biomarker validation
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015 90
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 2015 91
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 2015 92
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 2015 93
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
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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 2015 95
healthy disease disease + treatment
Interpret data with self-normalisation
Subgroups
100%
Normalisation of responders
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015 96
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
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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
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www.radboudumc.nl/research/technologycenters
Radboudumc Technology Centers
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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
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Interdisciplinary team work
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Try-outs at REshape Innovation Center
Lucien Engelen
Multi-partner collaborations in Health Informatics
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Speak each other’s language
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Teach how to work inter-disciplinary
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
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
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Copy best practice
• Nation wide coverage
• 66 regional networks
• 3000 trained experts
• 12 disciplines
prof Bas Bloem dr Marten Munneke
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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
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Demonstrated added value
Regular care
ParkinsonNet care
% Hip fracture Cost per patient*
*Hospitals, medication, care at home
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Dutch export product …
King Willem Alexander
Bas Bloem
Marten Munneke
Queen Maxima
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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
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Spread the word
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Spread the word
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Spread the word
Alain van Gool, Building Bridges Biomarker Symposium, Helsinki, 6 October 2015
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
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