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Congenital Muscular Dystrophy
Biomarker Discovery
James Collins MD, PhDAssistant Professor
Division of NeurologyCincinnati Children’s Hospital Medical Center
Disclosures
Research Foundation Grant: Cure Congenital Muscular Dystrophies
partnered with S.A.M. (www.curecmd.org)
“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
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
Liotta, et al. Nature, 2003.
CMD Biomarker Discovery
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
Therapeutic
Intervention BiomarkerClinical
Endpoint
Beneficial or Harmful Effects Not Measured by a
Biomarker
Measured to/ Substitute for
Effects of therapeutic interventions on biomarkers and clinical endpoints in clinical
trials.
Biomarkers Definition Working Group, NIH. Clin Pharmacol Ther 2001;69:89-95
affects
Drug development
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
GeneSpring, Partek and NCI public software to analyze data
DAVID, KEGG and others for pathways
Apply RNA to MICROARRAYS
Whole Blood
Isolate RNA
STORE -700C
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.
http://biogratech.com/resources/From+blood+withdrawal+to+RBC+proteomics.PNG
Proteomics approach
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
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
Fukuyama-type CMD and Merosin - deficient patients expression profile in muscle
Gene expression profiling CMD
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• Carsten Bonnemann
• Kate Bushby
• Ton DeGrauw
• Prasad Devarajan
• Andrew Hershey
• Anne Rutkwoski
• Brenda Wong
• CMD families
References1. Biomarkers Definition Working Group, NIH Clin Pharmacol Ther 2001;69:89-952. Rodland K. Systems biology and biomarker discovery. Disease Markers 2010;28:195-73. http://www.biomarkersconsortium.org/index.php?
option=com_content&task=view&id=132&Itemid=1844. Sorani et al. Clinical and biological data integration for biomarker discovery Drug Discovery
Today 2010, doi:10.1016/j.drudis.2010.06.0055. Fuller, H.R., et al., Valproate and Bone Loss: iTRAQ Proteomics Show that Valproate Reduces
Collagens and Osteonectin in SMA Cells. J Proteome Res, 2010.6. Hampel, H., et al., Biomarkers for Alzheimer's disease: academic, industry and regulatory
perspectives. Nat Rev Drug Discov, 2010. 9(7): p. 560-74.7. 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. 971-83.8. Wong, B., et al., Gene expression in blood of subjects with Duchenne muscular dystrophy.
Neurogenetics, 2009. 10(2): p. 117-25.9. Lit, L., et al., Corticosteroid effects on blood gene expression in Duchenne muscular dystrophy.
Pharmacogenomics J, 2009. 9(6): p. 411-8.10. 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. 85-95
11. 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.
12. 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
13. Liotta, L.A., M. Ferrari, and E. Petricoin, Clinical proteomics: written in blood. Nature, 2003. 425(6961): p. 905.