Congenital Muscular Dystrophy
Biomarker Discovery
James Collins MD, PhD
Assistant Professor
Division of Neurology
Cincinnati Children’s Hospital Medical Center
Disclosures
Research Foundation Grant:
Cure Congenital Muscular Dystrophies
partnered with S.A.M.
(www.curecmd.org)
Biomarker
“A characteristic that is objectively
measured and evaluated as an
indicator of normal biological
processes, pathogenic processes, or
pharmacologic responses to a
therapeutic intervention.”
Biomarkers Definition Working Group, NIH Clin Pharmacol Ther 2001;69:89-95
Biomarker
 Clinical practice
• identify risk for or diagnose a disease
• assess disease severity or
progression
• predict prognosis
• or guide treatment
http://www.biomarkersconsortium.org/index.php?option=com_content&task=view&id=132&Itemid=184
Biomarker
http://www.prostateuk.org/psa/psa.htm
CMD Biomarker Discovery
Liotta, et al. Nature, 2003.
Taniguchi, M. et al., Biochem Biophys Res Commun, 2006. 342(2): p. 489-502.
Biomarker
 Drug development
•
•
•
•
•
How does a drug work in the body
Is the drug safe or effective
What dose of the drug is effective
Response to a treatment
Treatment trial - FDA regulatory
approval process
http://www.biomarkersconsortium.org/index.php?option=com_content&task=view&id=132&Itemid=184
Drug development
Therapeutic
Intervention
affects
Measured to/
Substitute for
Biomarker
Clinical
Endpoint
Beneficial or Harmful
Effects Not Measured by a
Biomarker
Effects of therapeutic interventions on
biomarkers and clinical endpoints in clinical
trials.
Biomarkers Definition Working Group, NIH. Clin Pharmacol Ther 2001;69:89-95
Biomarker development
 Discovery phase
• Proximal fluids, cell lines, animal models, tissue of interest
• candidates
 Qualification phase
• Human plasma
• Confirm candidate molecules
 Verification phase
• Population-based (specificity)
 Validation and clinical assay development
• Sensitivity and specificity
Rifai, N., M.A. Gillette, and S.A. Carr, Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol,
2006. 24(8): p. 971-83.
Biomarker discovery
 Genomics
• Relevant disease genes, expression profiles,
signaling pathways
 Proteomics
• Protein expression and post-translational
modifications
 Metabolomics
• small molecule metabolites specific to disease
 Imaging
• Imaging changes reflect disease state
RNA Expression Profiling of Blood from Humans
Apply RNA to
MICROARRAYS
Whole Blood
STORE -700C
GeneSpring, Partek
and NCI public software
to analyze data
Isolate RNA
DAVID, KEGG and
others for pathways
Cluster analysis of genes [with ≥ 2.5-fold change]
blood of DMD compared to healthy age matched
males)
Wong, B., et al., Gene expression in blood of subjects with Duchenne muscular
dystrophy. Neurogenetics, 2009. 10(2): p. 117-25.
DMD Gene expression profile
Steroid treatment effect
Lit L. et al., Pharmacogenomics J, 2009. 9(6): p. 411-8.
Proteomics approach
http://biogratech.com/resources/From+blood+withdrawal+to+RBC+proteomics.PNG
Gene expression profiling CMD
Merosin-deficient mice models (dy/dy) muscle
 contractile proteins
• shift towards embryonic and perinatal
myosin forms
 genes involved in cellular adhesion
 procollagen genes
 genes related to immune response and
complement activation
•van Lunteren, E. et al., Physiol Genomics, 2006. 25(1): p. 85-95.
Gene expression profiling CMD
Fukuyama-type CMD and Merosin - deficient patients
expression profile in muscle
 up-regulation
• extracellular matrix and
• basement membrane component genes
 unique expression pattern
• dystrophin-deficient muscle
• Unique profile of FCMD compared to MDC1A
Taniguchi, M., et al.Biochem Biophys Res Commun, 2006. 342(2): p. 489-502
Proteomics - CMD
 no published proteomic studies
 14th international congress WMS society 2009, Geneva,
Switzerland
 Abstract
• Col6a1-/- mice vs WT using 2D-DGE showed 37 proteins
differentially expressed in diaphragm
Bovelenta et al. NMD 2009 EM.P.5.01; doi:10.1016/j.nmd.2009.06.268
Going Forward: “Bench to Bedside”
 merosin deficient CMD (proteomic and gene
expression profiling)
 CMD subtypes
 Verification: animal models / biobank tissues
 Qualification: therapeutic interventions
 Validation
 Teaming up with multiple academic centers, private
and governmental agencies
• Biomarker correlation with natural history outcome
measures, imaging, and functional mobility scales
• Goal: biomarker profile assay use as surrogate end point
Challenges





Access to patients and samples
Heterogeneity
Progressive disorders
defining functional endpoints
Funding / incentives
Acknowledgements
• CMD families
• Carsten Bonnemann
• Kate Bushby
• Ton DeGrauw
• Prasad Devarajan
• Andrew Hershey
• Anne Rutkwoski
• Brenda Wong
References
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Biomarkers Definition Working Group, NIH Clin Pharmacol Ther 2001;69:89-95
Rodland K. Systems biology and biomarker discovery. Disease Markers 2010;28:195-7
http://www.biomarkersconsortium.org/index.php?option=com_content&task=view&id=132&Itemid
=184
Sorani et al. Clinical and biological data integration for biomarker discovery Drug Discovery
Today 2010, doi:10.1016/j.drudis.2010.06.005
Fuller, H.R., et al., Valproate and Bone Loss: iTRAQ Proteomics Show that Valproate Reduces
Collagens and Osteonectin in SMA Cells. J Proteome Res, 2010.
Hampel, H., et al., Biomarkers for Alzheimer's disease: academic, industry and regulatory
perspectives. Nat Rev Drug Discov, 2010. 9(7): p. 560-74.
Rifai, N., M.A. Gillette, and S.A. Carr, Protein biomarker discovery and validation: the long and
uncertain path to clinical utility. Nat Biotechnol, 2006. 24(8): p. 971-83.
Wong, B., et al., Gene expression in blood of subjects with Duchenne muscular dystrophy.
Neurogenetics, 2009. 10(2): p. 117-25.
Lit, L., et al., Corticosteroid effects on blood gene expression in Duchenne muscular dystrophy.
Pharmacogenomics J, 2009. 9(6): p. 411-8.
van Lunteren, E., M. Moyer, and P. Leahy, Gene expression profiling of diaphragm muscle in
alpha2-laminin (merosin)-deficient dy/dy dystrophic mice. Physiol Genomics, 2006. 25(1): p. 8595
Taniguchi, M., et al., Expression profiling of muscles from Fukuyama-type congenital muscular
dystrophy and laminin-alpha 2 deficient congenital muscular dystrophy; is congenital muscular
dystrophy a primary fibrotic disease? Biochem Biophys Res Commun, 2006. 342(2): p. 489-502.
Bovelenta et al. Gene expression and proteome profiles in Col6a1-/- mice, a model of Ullrich
congenital muscular dystrophy. NMD 2009 EM.P.5.01; doi:10.1016/j.nmd.2009.06.268
Liotta, L.A., M. Ferrari, and E. Petricoin, Clinical proteomics: written in blood. Nature, 2003.
425(6961): p. 905.