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

Taniguchi, M. et al., Biochem Biophys Res Commun, 2006. 342(2): p. 489-502.

Liotta, et al. Nature, 2003.

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 Clinical Biomarker 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.

2006.

24

(8): p. 971-83.

Nat Biotechnol,

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 -70 0 C

Isolate RNA GeneSpring, Partek and NCI public software to analyze data 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 14 th 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

1.

2.

3.

4.

5.

6.

7.

8.

9.

10.

11.

12.

13.

References

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. 85 95 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, 425(6961): p. 905.

Clinical proteomics: written in blood.

Nature, 2003.