Transcript The presentation - Envirogenomarkers

Prospects of genomics technologies
in cancer molecular epidemiology
Soterios A. Kyrtopoulos
National Hellenic Research Foundation, Institute of
Biological Research and Biotechnology, Athens,
Greece
www.ecnis.org
Pros and cons of “1st generation
biomarkers”
Advantages
- highly sensitive and chemical-specific biomarkers of exposure
- information on specific stages of carcinogenesis (e.g. gene or
chromosome mutagenesis)
Disadvantages
- collect information one item at a time
- different assays/technologies for different types of endpoints
- limited mechanistic information
www.ecnis.org
Potential advantages of –omics biomarkers
Genomics
Epigenomics
Transcriptomics
Metabonomics
Proteomics
- can be derived from global, untargeted searches – enormous
dataset in which to look for biomarkers; no prior hypothesis
- use generic technology regardless of disease or exposure of
interest
- provide mechanistic information on multiple endpoints
- combined use of multiple –omics technologies, plus bioinformatics,
can integrate multi-level information and provide a systems biology
approach to biomarker discovery
www.ecnis.org
Current evidence of potential of –omics in
environmental health research
1. Genomics: widespread use in GWAS studies
Massive SNP analysis and search for association with disease risk
Case-control studies, some hundreds to a few thousands of subjects
ORs for individual alleles tend to be rather small (<1.5)
www.ecnis.org
2. Εpigenomics
Bulk hypomethylation, promoter hypermethylation
- Most studies targeted on candidate genes (p16, MGMT, RASSF1A etc)
or on surrogate sequences (alu, LINES)
-Few genome-wide studies, mostly in relation with diseased states
www.ecnis.org
 Perera et al., PLOS One 2009, e4488
Cord blood, children with maternal high/low PAH exposure;
ACSL3 CpG island
 Widschwendter et al., PLoS One 2008, e2656
DNA methylation of peripheral blood cell DNA provides good prediction of
breast cancer risk in a nested case-control study
www.ecnis.org
3. Transcriptomics: Global analysis of gene expression,
search for association with exposure or early effects
Few, rather small studies to date
 Fry et al., PLoS Genetics 3(11) 2007, e207
Gene expression signatures (11 genes) in cord blood of women exposed
to arsenic; could predict exposure of 2nd set of subjects with 79%
accuracy; activation of NFκB inflammation, cell proliferation, stress &
apoptosis pathways
 Forrest et al., Environ Health Perspect. 113 (2005), 801-7
gene expression in PBMC in benzene-exposed workers
6 exposed & 6 controls
Recent unpublished from same group suggest effects at very low
benzene doses
www.ecnis.org
4. Proteomics
- Adsorption on protein chips / SELDI-TOF MS
- Multiplex ELISAs
Luminex LabMAP technology
Few studies, limited to a few tens of subjects
Vermeulen et al., PNAS 102 (2005 ), 17041-6
10 exposed & 10 controls
Decreased levels of CXC-chemokines in serum of benzeneexposed workers identified by array-based proteomics
www.ecnis.org
5. Μetabolomics
full-profile analysis of serum/urine by NMR OR HPLC/MS/MS
Studies so far mostly limited to diseased states
Holmes et al., Nature 453 (2008) 396-400
Human metabolic phenotype diversity and its association with diet and blood
pressure
ΙΝΤΕΡΜΑP project: metabolomic profiles
in relation to blood pressure
& influence of diet & other factors
4,630 subjects, 17 populations
Urine analysis using NMR
www.ecnis.org
Conclusion so far:
Even with small studies, distinct –omics profiles, with
biological meaning, have been identified, implying the
potential to serve as biomarkers of toxic exposure or
disease risk
Questions:
 existing studies based on very small populations
 limited information on exposure
 validation: between study reproducibility / intra-individual variability / ...
 uncertainty regarding technology applicability with samples already stored in
existing biobanks
www.ecnis.org
Genomics biomarkers of environmental health
(EnviroGenomarkers; www.envirogenomarkers.net)
FP7 Collaborative Project; start March 2009, 4 yrs
11 partners incl. 5 ECNIS-associated groups
Main aims:
-Application of wide range of –omics technologies, in combination with
advanced bioinformatics, in the context of molecular epidemiology studies, for
the discovery of
new biomarkers of exposure to toxic environmental agents,
new biomarkers of disease risk, and exploration of their relationships
- Exploration of technical potential and problems in the application of –omics
technologies in large-scale population studies using biosamples in long-term
www.ecnis.org
Epidemiologic design: case-control nested within
prospective cohorts
prospective study
exposure
biomarkers
of exposure
intermediate
–omics
biomarkers of
early effects
relationship of environmental exposures vs
risk biomarkers
disease
risk-predictive biomarkers
1. Biomarkers with risk predictivity: Intermediate biomarkers vs disease
2. Εxposure-disease relastionships: biomarkers of risk vs exposure
3. Early effects of exposure: exposure vs intermediate biomarkers
www.ecnis.org
The EnviroGenomarkers project cohorts
www.ecnis.org
Diseases and exposures
Case-control nested within EPIC Italy and NSHDS
breast cancer vs
PCBs
PAHs
cadmium
B-cell lymphoma vs PCBs
Prospective, Rhea cohort (Crete)
chronic diseases of the nervous and immune system & allergies
establishing themselves in early childhood
vs early life exposure to endocrine disruptors
(PCBs, PAHs, phthalates, polybrominated diphenyl ethers)
www.ecnis.org
Biomarker analyses

Start off with pilot study to technically validate applicability of
–omics technologies to existing biobank samples

Mimic treatment of biobank samples at the time of their collection
www.ecnis.org
Biomarker analyses
In total, approx. 2,700 blood samples will be analysed
Intermediate biomarkers
Transcriptomics
Epigenomics
Metabonomics
Targeted proteomics (Luminex platform)
[Genome-wide SNP data already available for many subjects]
2-phase approach will mostly be employed:
a) discovery phase (genome-wide); 10-20% of samples
b) validation phase (targeted on limited number of candidates):
all samples
Full cell metabolomics (HPLC/MS) on all samples
www.ecnis.org
Biomarkers of exposure
PCBs: plasma concentrations of selected congeners, using GC/MS
cadmium: erythrocyte levels, using inductively-coupled plasma mass
spectrometry
phthalates: urine metabolites, using HPLC/MS
BDPEs: plasma concentrations of selected congeners, using HPLC/MS
PAHs: DNA adducts (ELISA)
Additional data on biomarkers of carcinogen exposure available from
other projects
Exposure assessment
Other exposure information
FFQs and environmental exposure questionnaires
Data on exposure to air, water and food toxicants available from other
projects
GIS
www.ecnis.org
1 2 3 4 5 6 7 8 9 10
genomics
(SNPs)
diseased
controls
transcriptomics
individual
genomic profile
diseased
controls
epigenomics
diseased
controls
proteomics
metabolomics
diseased
controls
combined
risk
biomarker
diseased
controls
www.ecnis.org
adapted from Butcher & Beck, 2008)
Prospects and challenges
1. Omics technologies have high sensitivity, high throughput and allow
untargeted searches for genomic profiles which can serve as biomarkers
of exposure or early effect
2. Information obtained has mechanistic value
3. Combine with traditional biomarkers for phenotypic anchoring
4. Acculate exposure assessment of utmost importance; good exposure
biomarkers needed
5. Prospect of combined analysis of data from multiple levels of cellular
function
6. Systems-level bioinformatics analysis
7. Suitability of old biobank samples for certain –omics analysis (e.g.
transcriptomics)
8. Detection of risk biomarkers in surrogate tissues (PBLs)
9. Validation, validation, validation
www.ecnis.org
Funded by the European Union FP7,
Theme: Environment (including climate change)
(Grant no. 226756)
Nature, Vol. 458 (9 April 2009), p. 458
www.ecnis.org