Genomics Research Center Research Direction: Assumptions

1. Genomics Research CenterResearch Direction: Assumptions • Limited resources • Focused research • Central theme • Combined expertise and effort of the investigators

2. Genomics Research CenterGoals • Novel discoveries • International recognition • Impact on the Taiwan new economy based on biotech.

3. Genomics Research CenterResearch Theme • Search for Novel Genes Associated with Human Diseases

4. Human Genome Landscape --Surprise • Human gene count is much lower than expected: 30,000-40,000 in human, only twice as many genes as the worm or the fly

5. Gene Number in EukaryotesSpecies # of Gene Genome Size Human 32,000 2.9 Gb Mustard weed 25,498 115 Mb Worm 19,099 97 Mb Fly 13,601 116 Mb Yeast 5,800 12 Mb

6. Human Genome Landscape --Highlights • Human gene make more proteins than worm: 90,000 in human as compared to 20,000 in worm • Human proteins are more complex than other species: richer collection of domain architectures

7. Human Genome Project- Where We Are 30,000-40,000 genes >90 % sequences completed 40% genes : function totally unknown 60% genes: function could be inferred from sequence similarity to protein of known function, the exact function yet to be proven

8. Genomic Medicine-Search for novel genes associated with human diseases • 1,000 genes for 100-150 common diseases Largely unknown • 5,000 genes for rare single-gene disorders 1/3, responsible genes identified Improve diagnosis Improve therapy

9. Research Theme Genetic epidemiology ENU mouse Bioinformatics Proteomics System biology Novel disease genes Diagnostics Preventive medicine Proteins, pathways, biology Pharmacogenetics Drug therapy Gene therapy

10. Search for Novel Genes Associated with Human Diseases- Approaches • Genetic epidemiology: map and identify novel disease genes • Mouse mutant: screen phenotypes resembling human diseases to map and identify novel disease genes • Bioinformatics: linked genes, comparative genomics • Proteomics: interacting proteins, protein expression profile

12. Genetic epidemiology approach-Common disease due to common DNA variants • Large genetic component: Young-onset Hypertension Early-onset Breast cancer Adverse reaction to drugs • Unique population: Susceptibility to chronic HBV infection Gout Alcoholism

14. ENU Mouse Mutagenesis Program • Ethyl nitrosourea (ENU) is a chemical mutagen • ENU induces point mutations • Mutations are genome-wide and random with frequency: 1/750/locus/gamete

15. Mouse Mutagenesis Program-Applications • Screen for disease phenotypes: disease models and novel drug targets for human diseases • Screen for genes that modify the disease: enhances, suppressors and interacting proteins that modify the existing disease models • Screen ENU mouse library for mouse carrying mutation in the gene of interest

16. ENU mouse library construction and screen for disease phenotypes Dominant screen Recessive screen ENU ENU X Go Go X G1 G1 X & G2 Random matings G3 Map & clone the disease gene Screen for desired phenotypes

17. Mouse mutant screening protocol-Neuro-psychiatric disorders • MRI, micro PET scan: neuro-degenerative, neuro-metabolic and neuro-development disorders, including Alzheimer and cancer • Neurobehaviour screen: psychiatric, pain, memory/learning disorders • drug tolerance/dependence screen • Eye (retina) disorders

18. Why Neuro-psychiatric disorders? • Current drugs for these disorders are simply ineffective • No good drug targets • Symptoms rather than underlying diseases • Needs of identifying disease gene for novel drug targets

19. Mouse Mutant -Screening Protocol-continued • Blood and Urine markers screen: metabolic, immunologic disorders • EKG, Echo and biomarkers screen: cardiovascular disorders, including hypertension, atherosclerosis

20. Mouse Mutagenesis Program • Large-scale production of mutant mice by chemical mutagenesis covering whole genome • Rapid screening for disease phenotypes • 2% recovery of dominant mutations • Genotyping to map the disease genes • Conserved synteny allow rapid identification of the corresponding human gene

21. Mouse Mutagenesis Program-Applications • Screen for disease phenotypes: disease models and novel drug targets for human diseases • Screen for genes that modify the disease: enhances, suppressors and interacting proteins that modify the existing disease models • Screen ENU mouse library for mouse carrying mutation in the gene of interest

22. Screen for genes that modify the disease ENU-treated male X Tumor bearing mouse carries dominant oncogene mutation Genotyping mice carry oncogene mutation Mapping and cloning genes suppress the tumor formation

23. Mouse Mutagenesis Program-Applications • Screen for disease phenotypes: disease models and novel drug targets for human diseases • Screen for genes that modify the disease: enhances, suppressors and interacting proteins that modify the existing disease models • Screen ENU mouse library for mouse carrying mutation in the gene of interest

24. Screen ENU mouse library for mouse carrying mutation in the gene of interest ENU Go X G1 HTP mutation detection

25. Worthwhile targets in screening ENU mutant mouse library • Methuselah: a longevity gene involved in synaptic function in fly • Indy, a longevity gene involved in di- and tri-carboxylate transport • Spoll, a yeast meiotic gene • TPD1, a yeast gene involve in genome stability

26. Research Theme Genetic epidemiology ENU mouse Bioinformatics Proteomics System biology Novel disease genes Diagnostics Preventive medicine Proteins, pathways, biology Pharmacogenetics Drug therapy Gene therapy

27. Where is the BEEF • Intellectual property: novel disease- genes can be patented • Patent license fee: up-front and milestones payments, 140 millions for obesity gene • Royalty: 1-10% royalty of net revenue • Average sale per drug: 1-2 billions/year • Assume 5 % royalty, 1.5 billions/year = 75 millions/yr.

28. Glycogen Storage Disease Type II (Pompe, Acid Maltase Deficiency) • A single gene disorder • Deficiency of lysosomal acid alpha- glucosidase (GAA), the lysosomal glycogen degrading enzyme • Progressive glycogen accumulation • Progressive cardiomyopathy and myopathy • Three clinical forms: Infantile, Juvenile, Adult

29. Recombinant Enzyme Therapy for Pompe Disease (Chen’s Lab. Duke) • 1993, genetically engineered a cell line overproducing the enzyme • 1995, prove enzyme works in vitro • 1996, prove enzyme works in vivo in an animal model • 1997, Duke obtained FDA Orphan Drug Designation for Pompe therapy

30. Recombinant Enzyme Therapy for Pompe Disease (Chen’s Lab. Duke) • 1997, Synpac obtained licensing from Duke • 1999, phase I/II clinical trial • 2000, Genzyme obtained licensing from Synpac/Duke • 2001, Phase II/III clinical trial

31. Affected deceased sibling at same age Pt3-8 months old

32. Genomics Proteomics Structural Biology Systems Biology Gene protein pathway Network Cells Organs Individuals Genes are critical, however, genomics must be incorporated into biology