Parkinson’s Disease GWAS and enrichment with MetaCore™

1. Parkinson’s Disease GWAS and enrichment with MetaCore™ Ewan Hunter, PhD January 18, 2010

2. GeneGo Services Customization/ Integration Knowledge base Management Annotation and Curation Wet Lab Services Data Repository Data parsers Maps, interactions, interface skins Project analysis (on/off site) Develop Disease platforms Develop Ontologies Compound Assessment analysis Pathway Analysis Platforms

3. MetaMiner Initiatives Knowledge Management Research and Discovery Toxicology Drug Metabolism/ Positioning Clinical Information Technology TSRI Eli Lilly Astra Zeneca Chicago Children’s Hospital University of Glasgow Sheffield Queensland USC Cystic Fibrosis Dry Eye Oncology Cardiac CNS Metabolic Stem Cells FDA ISB University of Amsterdam Exclusive Project Eli Lilly Tgen Van Andel Harvard Johns Hopkins Exclusive PC contract with top Pharma Vertex IOP TSRI Complete Jackie Immunology Infectious Disease Respiratory Nutrition Skin Pharma TBA TBA GSK Top Pharma 3 cosmetic co’s TBA

4. MetaBase Content Overview • Networkable Objects • Human genes in network 19.910 • Mouse genes in network 18.381 • Rat genes in network 16.228 • Chemical compounds 221.076 • Drugs 2.737 • Endogenous compounds 2.449 • Metabolic Reactions 8.899 • Pubmed journals 2.664 • Pubmed articles (total) 758.139 • Pubmed articles (single citation) 130.058 • Total amount of interactions 941.946 • Protein-Protein 365.129 • Compound – Protein 502.572 • Compound – Compound 9.618 • Protein -Reaction 19.449 • Substrate, Product-Reaction 29.366 • RNA – Protein 15.812 Database • Human genes 45.471 • Human SwissProt proteins 20.328 • Mouse genes 61.311 • Mouse SwissProt proteins 16.209 • Rat genes 36.870 • Rat SwissProt proteins 7.459 • Chemical compounds 691.896 • Compounds withstructures 673.207 • Drugs 5.594 - FDA approveddrugs 1.085 - EU approved drugs 169 - Drugs approved by other committees 692 - US withdrawn drugs 140 - EU withdrawn drugs 54 - Clinical trial drugs 2.258 - Discontinued drugs 1.205 - Preclinical drugs 134 - Biologics 618 • Endogenous compounds 4.776 • Nutritional compounds 93 • Metabolite of xenobiotic 8.199

5. GeneGo Ontologies Ontologies with graphic content Groups and Complexes: 2247 UNIQUE for GeneGo Schemas for human, mouse or rat GeneGo maps: 808 (regulatory processes maps Disease maps Metabolic maps) GeneGo networks 942 UNIQUE for GeneGo (regulatory networks drug target networks toxicity networks metabolic networks disease biomarker networks) ACM2 and ACM4 activation of ERK NF-kB_HUMAN Inflammation_IL-6 signaling

6. GeneGo Pathway Formats GeneGo Networks GeneGo Canonical Maps Signal transduction_Insulin signaling Insulin Receptor Signaling Pathway • Total number to date: 942 • Dynamic • Interactive • Pre-built and build your own • Bigger-global network • Include single or multistep • Include newer findings, more than mainstream signaling • Total number to date: 808 • Subset of a bigger-global network • Static, pre-built • Interactive • Multistep • Well accepted in the field • “Review-article” style- mainstream signaling

7. How to Approach MetaCore Input list Data Mining Functional Representation What do the items on the list collectively represent? Connectivity How do the items on the list connect?

8. GWAS- Pakinson’s Disease Data: SNP identifiers, allelic frequency and odds ratio The odds ratio = as the ratio of the odds of an event occurring in one group (PD siblings) to the odds of it occurring in another group (non-PD siblings). odds ratio =1  condition or event under study is equally likely in both groups. odds ratio > 1  condition or event is more likely in the first group odds ratio <1  condition or event is less likely in the second group.

9. Data Format and Data Loading

10. Define Thresholds

11. Single Experiment Workflow: Enrichment Histograms for Canonical Pathway Maps

12. Alzheimer's disease: extracellular Amyloid beta toxicity.

13. Disease Biomarker Map Overlay

14. Alzheimer's disease: extracellular Amyloid beta toxicity Ca++ Channels

15. Interesting SNPs and Associated Genes for Parkinson’s From this table we can also appreciate that another gene of interest from this canonical pathway map is not only the Amyloid beta A4 precursor protein but that 3 subunits of the Ca2 channel have a significant association to Parkinson’s. This is of interest as there are studies that suggest the disruption in Ca2+ homeostasis within the dopamine neurons of the substantia nigra lead to loss of these SN neurons Sulzer and Schmitz (2007) Parkinson’s Disease: Return of an Old Prime Suspect. Neuron, 55, 8-10

16. Recent Review in the Parkinson’s Disease Field A recent review in Trends in Neurosciences, “Calcium homeostasis, selective vulnerability and Parkinson's disease” (TINS, 23 March 2009 doi:10.1016/) Has pointed that a very good theory of neuronal degeration/death of the dopamine neurons in the substantianigra pas compacta (SNc) Is to do with the homeostatic control of Ca2+ within these neurons. The neurons of the SNc are selectively vulnerable to homeostatic Ca2+ stress as particularly Ca2+ ion channels are responsible for maintaining an autonomous pacemaking within these neurons. This Function is unlike other adult neurons in the brain, the pacemaking activity is believed to be important in maintaining dopamine levels in regions that are innervated by these neurons, particularly the striatum. The L-type Ca2+ channels are responsible for this pacemaker activity within the SNc neurons and the combined GWAS and Enrichment analysis within MetaCore, we have indentified 3 subunits of the Ca2+ channel

17. Recent Review in the Parkinson’s Disease Field A recent review in Trends in Neurosciences, “Calcium homeostasis, selective vulnerability and Parkinson's disease” (TINS, 23 March 2009 doi:10.1016/) Has pointed that a very good theory of neuronal degeration/death of the dopamine neurons in the substantia nigra pas compacta (SNc) Is to do with the homeostatic control of Ca2+ within these neurons. The neurons of the SNc are selectively vulnerable to homeostatic Ca2+ stress as particularly Ca2+ ion channels are responsible for maintaining an autonomous pacemaking within these neurons. This Function is unlike other adult neurons in the brain, the pacemaking activity is believed to be important in maintaining dopamine levels in regions that are innervated by these neurons, particularly the striatum. The L-type Ca2+ channels are responsible for this pacemaker activity within the SNc neurons and the combined GWAS and Enrichment analysis within MetaCore, we have indentified 3 subunits of the Ca2+ channel

18. Recent findings in relation to results found with MetaCore™ The L-type Ca2+ channels are responsible for this pacemaker activity within the SNc neurons and the combined GWAS and Enrichment analysis within MetaCore, we indentified 3 subunits of the Ca2+ channel The beta-subunit of the L-type Ca2+ has a large Odds Ratio (1.781) And relatively significant association p-value 0.0094 for association To Parkinson’s Disease

19. Conclusion of GWAS and MetaCore Therefore Is PD simply a reflection of accelerated aging in neurons that rely too heavily upon Ca2+ channels to do theirbusiness? Age is undoubtedly the single strongest risk factor for PD. The ‘wear and tear’ theory of PD does not require a pathogenic agent. Moreover, it argues that there is no disease ‘onset’ other than the one created by the emergence of symptoms when the surviving SNc DA neurons Are incapable of fully compensating for the loss of neighboring neurons (1). It also predicts that we will all develop symptoms if we live long enough. Why then do some people become symptomatic in their 50 s, others in their 60 s or 70 s or not at all? Genetic and environmental factors certainly could account for this variation One of these genetic factors could be mutations within the Ca2+ L-type channel, which through malfunction, the Homeostasis of Ca2+ is not regulated and accelerate the ageing process within these neurons. (1) Zigmond, M.J. et al. (1990) Compensations after lesions of central dopaminergic neurons: some clinical and basic implications. Trends Neurosci. 13, 290–296

20. Can PD be prevented? If PD is a consequence of Ca2+-accelerated aging in SNc DA neurons (and in those neurons with a similar phenotype) then reducing Ca2+ flux should delay the onset of PD symptoms and slow its progression. A recent case-control study of hypertensive patients found a significant reduction in the observed risk of PD with Calcium channel Antagonists( CCA) use, but not with medications that reduce blood pressure in other ways