A ‘Broad’ View of Translational Research at the Stanley Center

CDD Community MeetingJanice Kranz, Assistant Director of Stanley Center

for Psychiatric Research at the Broad InstituteOct. 7, 2008

2

Outline

Introduction• Broad Institute• Stanley Center for Psychiatric Research• ‘Genomics to Medicine’

Examples with CDD• Compound Registration System• Mining IC50 Data for Target Selectivity

3

4

Broad Institute mission

Bring the power of genomics to biology and medicine

The Broad Institute is a research collaboration of MIT, Harvard and its affiliated hospitals, and the Whitehead Institute.

More specifically:Empower creative scientists to:• Construct new powerful tools for genomic medicine,• Make them accessible to the global scientific community, and •Apply them to the understanding and treatment of disease.

5

Broad PlatformsThe Broad's Scientific platforms are made up of professional scientists with the expertise and organization to carry out major projects that cannot be done within a single laboratory.

Broad ProgramsThe Broad's Scientific programs bring together research groups with a shared commitment to important biomedical challenges.

Novel Therapeutics

Imaging

RNAi

Chemical Biology

Proteomics

Genetic Analysis

Genome Sequencing

Biological Samples

A unique collaborative structure enables the Broad mission

Broad Faculty6 Core Members in Broad buildings

108 Associate Members: faculty with labs at MIT, Harvard, Whitehead, or affiliated hospitals

Computational Biology

Infectious Disease

Chemical Biology

Medical & Popul’nGenetics

Psychiatric Disease

Metabolic Disease

Cell Circuits

Genome Biology

Cancer

*

**

6

Funded by Ted and Vada Stanley through the Stanley Medical Research Institute

MissionTo discover the human genes that confer risk for bipolar disorder and schizophrenia and to use this information to develop new diagnostic tests and treatments for these illnesses.

HistoryGrew from Psychiatric Disease Initiative (now ‘Program’)

Founding members of Psychiatric Disease Initiative (2005): Ed Scolnick Pamela Sklar Stephen Haggarty

Stanley Center for Psychiatric Research

7

HumanGenetics

Neurobiology

ChemicalBiology

Bipolar Disorder

Schizophrenia

Approaches

Dis

ease

s

Major Depression

Stanley Center for Psychiatric Research

• New approaches to discover potentially different biology and leads for therapeutic development• No assumption about genetic architecture

8

International Schizophrenia Genetics Consortium

Pamela Sklar

Hugh GurlingAndrew McQuillin

Michael OwenMichael O’Donovan

Douglas BlackwoodDavid PorteousWalter Muir

Edward ScolnickPamela Sklar

David St. Clair

Michael GillAiden Corvin

Carlos PatoMichele Pato

Paul LichtensteinChristina Hultman

Patrick F. Sullivan

QuickTime™ and aUncompressed) decomneeded to see this pict

9

International Case-Control Cohort for Bipolar Disorder

Nick Craddock

Christina HultmanMikael Landen

Carlos Pato

Jordan Smoller

Goal: 10,000 cases and controls in ~2 or so yearsFunded by the NIMH and an additional grant from the Stanley Medical Research Institute

10

Genome-Wide Association Studies (GWAS): Examples

Published online July 30 ‘08

Published online August ‘08

11

Follow-up Biology needed to take GWAS Results to ChemBioFor Schizophrenia• Explore role of major deletions—which gene(s) are involved?• Look for measurable effect on biology--cell lines from patients for

protein, mRNA differences; • SNP analysis also revealing individual genes-same follow-up as in

BPFor Bipolar Disorder:• ANK3 and CACNA1C suggest BP may be ‘ion channelopathy’• Pathway analysis to identify ‘best’ targets• Nature of defect (alt. splicing, altered activity, loss-of-function…)• Determine whether agonist or antagonist needed• Develop assays• Test in vivo with RNAi• Explore use of existing

12

CholesterolObesityMyocardial infarctionQT intervalAtrial FibrilliationType 2 DiabetesProstate cancerBreast cancerColon cancer

KCNJ11

20032000

PPARγ

2001

IBD5NOD2

2005 20062002

CTLA4

2004

PTPN22

Age-Related Macular DegenerationCrohn’s DiseaseType 1 DiabetesSystemic Lupus ErythematosusAsthmaRestless leg syndromeGallstone diseaseMultiple sclerosisRheumatoid arthritisGlaucoma

CD25IRF5

PCSK9CFH

NOS1APIFIH1

PCSK9CFB/C2

LOC3877158q24IL23R

TCF7L2

2007

CDKN2B/A8q24 #28q24 #38q24 #48q24 #58q24 #6ATG16L15p1310q21IRGMNKX2-3IL12B3p211q24PTPN2TCF2CDKN2B/AIGF2BP2CDKAL1

FGFR2TNRC9MAP3K1LSP18q24LOXL1IL7RTRAF1/C5STAT4ABCG8GALNT2PSRC1NCANTBL2TRIB1KCTD10ANGLPT3GRIN3A

HHEXSLC30A8MEIS1LBXCOR1BTBD9C38q24ORMDL34q25TCF2GCKRFTOC12orf30ERBB3KIAA0350CD22616p13PTPN2SH2B3

GWAS: Progress In The Identification OfGene Variants For Common Diseases

13

Common Variants in Established Drug Targets Identified by GWAS

Frayling, Nature Reviews Genetics’07; 8:657

odds ratio 1.14 per allele95% CI (1.10-1.19)

5x10-1135%E23Krs215Sulfon-ylureas

Type 2 diabetesKCNJ11

Diabetes Genetics Initiative, Science ’07; 316:1341

odds ratio 1.14 per allele95% CI (1.08-1.20)

2x10-687%P12Ars1801282

thiazolidinediones

Type 2 diabetesPPARG

Kathiresan, Nature Genetics’08; 40:189

4 mg/dLdifference in LDL cholesterol between homozygote classes

1x10-2039%A/Trs12654264StatinsLDL

cholesterolHMGCR

ReferenceEffect sizeStatistical evidence (p-value)

Allele freq-uency

AlleleSNP*(rsnumber)

DrugTrait or Disease

Gene Name

14

Lesson from HMGCR on Genetic Variation vs. Potential Therapeutic Effect

The frequency and effect size (4 mg/dL) of genetic variation bears no clear relationship to therapeutic impact of mechanism-driven intervention (>40 mg/dL)

Evolution vs. Therapy:Alleles are limited by natural selection,

developmental biology, and pleiotropy

Drugs aimed at the same pathway are not necessarily limited in the same way

15

HumanGenetics

Neurobiology

ChemicalChemicalBiologyBiology

Bipolar Disorder

Schizophrenia

Approaches

Dis

ease

s

Major Depression

Stanley Center for Psychiatric Research

• New approaches to discover potentially different biology and leads for therapeutic development• No assumption about genetic architecture

16

Laboratory Operations

MGHCHGR

MITBroad

Chemical Neurobiology Laboratory of the Stanley Center: Haggarty Lab

Assay Development +Follow-up Neurobiology

High-Throughput Screening, Chemistry + Target ID

17

Synthetic ChemistryComputational Chemistry

Medicinal Chemistry

BiologyChemicalScreens

Follow-upFrom Screens

Medicine

Genetics

Broad Novel Therapeutics

+ Optimization(ADME-PK, Tox)

Core Drug Design Team

• assay dev.• access to cpds

• multiple assays• behavior (in vivo)

hit lead

• outsourced animals• outsourced chem.

Dr. Mike MoyerDr. Mike FoleyDr. Robert Gould

Chemical Neurobiology Laboratory: Chemistry Activities

Project #1: Cognitive Disorders(HDAC/chromatin remodeling)

Project #2: Bipolar Disorder(lithium/valproate pathways)

19

Reversible Changes in Chromatin Structure Control Gene Expression in the Brain

Tsankova et al. (2007) Nat. Neuro.

CBP

20

de Ruijter et al. (2003) Biochem J.

catalytic domainNLS

Key Role for Histone Acetylation: HDACs

HAT HDAC

21

Evidence from the literature: HDAC inhibitors are beneficial for learning + memory in mice

- CBP+/- (HAT) or CBPDN+/- mice display impaired LTP and learning.

The impairment can be ameliorated by administration of HDAC inhibitors Alarcon et al., 2004 Neuron; Korzus et al., 2004 Neuron

- Non-selective HDAC inhibitors increased histone H3 and H4 acetylation, facilitated spatial and associative learning and synaptic plasticity in WT mice Levenson et al., 2004 JBC

- Histone deacetylase inhibitors enhance memory and synaptic plasticity via CREB:CBP-dependent transcription activation Vecsey et al., 2007 J Neurosci

22

Goal: Isoform-specific HDAC Inhibitors with Desired Activities in Multiple Secondary Assays

Neurobiology and behavior suggest different HDACs are targets for learning/memory vs. mania/ depressionScreening Plan:

• Enzymatic--end point and kinetic; panel of Class I and II HDACs• Cell-based Assays

• Cell lines: reporter genes to monitor desired specific gene or protein expression

• Primary neuronal cultures to measure reporter gene activity and/or measure in vivo histone acetylation

• ADME/PK of desired compounds• In Vivo

• Behavior (multiple paradigms)• Follow-up assay of brain regions for histone acetylation/ other phenotypes

Ideally, all assay data stored in, and mined from, a DB

23

Our Challenge: Research and Med ChemProgress ‘ahead’ of Broad’s ChemBio Informatics

Broad ChemBio Platform focus on Cmpd Mgmt & HTS first

Our main immediate need: classic medchem: small number of molecules screened against panel of diverse assays

Spreadsheets and Spotfire only work so far for sharing data with biologists/ chemists/ screeners

Our research program is a ‘mixture’ of Broad-registered compounds and some ‘external’--hence, need for separate compound registration system (CDD--in progress; as separate ‘collaborative’development contract)

No current mechanism to readily view, mine and compare data frommultiple types of assays

Solution (‘interim’?): CDD

24

Mine for Selectivity: Examples of IC50 Curves in CDD

25

IC50 Reproducibility between Batches

26

Ability to Discern Batch-Specific Effects

27

A Picture’s Worth 1000 Lines of Excel

28

Acknowledgments, part 1Genetics

(MGH/SC)Pamela SklarShaun PurcellRoy PerlisJordan SmollerMark DalyJennifer BarnettKimberly ChambertJinbo FanManuel FerreiraAndrew KirbyYan MengJennifer MoranMatt OgdieDouglas RuderferJennifer StoneKathe Todd-BrownLori ThomasLauren Weiss

Chemical BiologySteve Haggarty

(MGH/SC)Jen PanJon MadisonDan FassKrista HennigJosh KettermanIren KurtserXiulin Liu Cat LuceThomas NielandStephanie NortonSurya ReisKraig Thierault

NeurobiologyLi-Huei Tsai(MIT/SC)Ji-Song GuanYingwei Mao

BehaviorTracey Petryshen

(MGH/SC)Erin BerryMelanie LeussisMike LewisMai SaitoAl Schroeder

Med. ChemistryMike MoyerEd HolsonFlorence WagnerDavid Pearlman

Broad/MIT/MGH CollaboratorsEric LanderMPG/GAP/BSP

Stacey GabrielDavid AltshulerPaul deBakkerKristen ArdlieScott MahanCasey Gates

ChemBioJay BradnerRalph MazitschekAndy SternFrank AnRobert Gould

RNAi/ ImagingDavid RootAnne CarpenterDavid Logan

Et al…

Ed Scolnick, Director of the Stanley Center

29

Informatics and compoundmanagementDave DeCaprioLakshmi AkellaJacob AsieduNurgees Banu SulthanBob Brady Ph.D.Steve BrudzDan DurkinGreg GeorgeMary Pat Happ Ph.D.Santhosh KumaraswamyDennis MocciaJoshua NicholsGreg WendelDavid HoweAlex OrlovskyKaren Rose

Analytical ChemistryStephen Johnston Ph.D.Galina BeletskyChris Johnson

DOS ChemistryLisa Marcaurelle Ph.D.Damian Young Ph.D.Eamon Comer Ph.D.Siva Dandapani Ph.D.Jeremy Duvall Ph.D.Baudouin Gerard Ph.D.Ann Kelly Ph.D.Sarathy Kesevan Ph.D.Haibo Liu Ph.D.Bo Pandya Ph.D.Troy Ryba Ph.D.Byung-Chul Suh Ph.D.Jingqiang Wei Ph.D.Maurice Lee Ph.D.Carol Mulrooney Ph.D.Mark Fitzgerald Ph.D.Jean-Charles Marie Ph.D

Target IDXiaoyu Li Ph.D.Monica Schenone Ph.D.

Screening Michelle Palmer Ph.D.Nicky Tolliday Ph.D.Andy Stern Ph.D.John McGrathMyra PoleyAnita VrcicLynn VerPlank Ph.D.Frank An Ph.D.Vipat RaksakulthaiJason BurbankMelanie deSilvaPeter AspesiBrandon RahhalTyler AldredgeJosh Bittker, Ph.D.

Medicinal ChemistryMikel Moyer Ph.D.David Pearlman Ph.D.Ed Holson Ph.D.Lawrence MacPherson Ph.D.

Director, Chemical Biology Platform Michael A. Foley Ph.D.Director, Novel Therapeutics Robert Gould Ph.D.

Prior industrial experience

Acknowledgments, part 2: ChemBio at the Broad

30

STEP collaboratorsBernie Devlin, Steve Faraone,Nan Laird, Matt McQueen, Vishwajit Nimgaonkar, Jordan SmollerGary Sachs, Roy Perlis

UK-US Bipolar DisorderHugh Gurling, Andrew McQuillin, Nick Bass, Jacob LawrenceU. of EdinburghDouglas Blackwood, Walter Muir, Kevin McGheeTrinity CollegeMichael Gill, Aiden Corvin, Derek Morris

NIMH Genetics InitiativeControl CollectionPablo Gejman, Alan SandersFarooq Amin, Nancy BuccolaWilliam Byerley, Robert Cloninger, Raymond Crowe, Donald Black, Robert Freedman, Douglas Levinson, Bryan Mowry, Jeremy Silverman

ISC (International Schiz. Consortium)http://pngu.mgh.harvard.edu/isc/

ICCBDUSC: Carlos and Michelle Pato, MGH: Jordan Smoller, Pamela Sklar and Roy PerlisCardiff University: Nick CraddockKarolinska: Mikael Landen, Christina Hultman, Paul Lichtenstein

Funded by:NIH, NARSAD, Herman Foundation, J&J, Merck Genome Research Foundation,Stanley Medical Research Institute

Acknowledgments, part 3

31

Chemical Biology Program Model: Molecular Genetics Of Human Cognition

1) Known human illnesses with firm genetic basis and unmet medical need

2) Translation of human genetics into animal disease neurobiology

3) Develop cell + biochemical assays

Eg. Rubinstein-Taybi syndrome with mutations in CBP implicating histone acetylation in cognition

Weeber et al. (2002) Mol Interv.

32

Academic Science with NIH

MLI

Prob

abili

ty

of s

ucce

ssC

umul

ativ

e C

ost

Ph IV-V(Additional indications, Safety monitoring)

Dedicated Chem-Biol

Project Team formed

Compound accepted into

Clinical Development

Target identification

Assay develop-ment Hit-to-

Probe

Screening (HTS or otherwise)

1 yr 1 yr 1 yr ~ 3 yrs 1 yr 2 yrs ~3 yrs

Ph III (Efficacy and safety in large populations)

Ph II (Dose finding, initial efficacy

in patient pop.)

Ph I (Safety)

Lead Development, Optimization

Indefinite Indefinite1.5 yrs

Regulatory review

Academic Probe/Drug Development Efforts

Dr. Chris Austin, NIH Chemical

Genomics Center

33

34

High-throughput/high-content screening modules

• Execution of primary screens and secondary follow-up assays• Capabilities for biochemical and cell-based assays • Capabilities for high-content (imaging) and plate reader assays• Capabilities to support the early stages of GE-HTS • Throughput of ~200,000 wells/day

Dr. Nicky TollidayDr. Frank AnDr. Lynn VerPlankMeghan Bliss-

MoreauJason BurbankMelanie DeSilvaStephanie NortonJohn McGrathJessie PerksMyra PoleyKaren Rose

Broad Screening Group

Dr. Mike FoleyDr. Andy Stern

(est. Dec. 2007)

Sample size (compounds) = 100,000 - 300,000 composed of bioactives, natural products, DOS

35

Lithium + Valproate: Potential Cellular Pathways Relevant to Mania + Mood

HDACvalproate

1) Inositol depletion” hypothesis (Berridge 1982)2) Inhibition of GSK-3β (Klein & Melton 1996; Beaulieu et al. 2008)

PP2A

36

GOAL: Test Selective HDACi with Good PK Properties in Mania + Other Animal Models

AmphetamineInduced

Hyperactivity(other assays)

Lithium

valproate vs. HDACi

amphetamine

NH2HN

O

NH

O

O

N

Dr. Tracey PetryshenBehavioral Neurogenetics Group

37

Summary: lithium/valproate project

Live-cell based assay of potentially disease relevant pathway (TCF/LEF reporter)

Have identified targets; pursuing HDACs

Insight that different HDACs may be involved in mood and memory; key assays for selectivity in place

Can look for other targets and probes

38

valproate (valproic acid)

Valproate: Use In Bipolar Disorder

O

OH

1965, Lambert initiated VPA therapy for mania, using the amide salt developed for epilepsy

1975, Lambert published report emphasizing anti-manic activity and synergism with lithium

1995, FDA approval for anti-manic effects

Relevant therapeutic mechanism unknown(reported inhibition: SSA-DH, GABA-T, a-KG)

Therapeutic plasma levels of ~200-600 mM

Attenuates amphetamine-induced subjective and psychological changes in humans (energy, alertness, blood pressure)

divalproex sodium (Depakote)