2008 hesi emerging issue: identification of
TRANSCRIPT
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January 20, 2009Office of Research and DevelopmentNational Center for Computational Toxicology
2008 HESI Emerging Issue:Identification of Pharmaceuticals for Validation of ToxCastRobert KavlockDirector, National Center for Computational Toxicology, US EPA
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1Office of Research and DevelopmentNational Center for Computational Toxicology
Too Many Chemicals Too High a Cost
Cancer
DevTox
NeuroTox
ReproTox
ImmunoTox
PulmonaryToxMillions $
Change Needed Because …..
1
10
100
1000
10000
100000
Data Collection
IRISTRIPesticide ActivesCCL 1&2Pesticide InertsHPVMPV CurrentMPV HistoricalTSCA Inventory
11,000
90,000
…and not enough data.
Judson, et al EHP submitted
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2Office of Research and DevelopmentNational Center for Computational Toxicology
Future of Toxicity Testing
Bioinformatics/Machine Learning
in silico analysis
Cancer
ReproTox
DevTox
NeuroTox
PulmonaryTox
ImmunoTox
HTS -omics
in vitro testing
$Thousands
EPAs Contribution: The ToxCast Research Programwww.epa.gov/ncct/toxcast
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3Office of Research and DevelopmentNational Center for Computational Toxicology
Cellular Assays
Biochemical Assays
Toxicology Endpoints
Physical chemical properties
Profile Matching
Correlating HTS to Toxicity
Genomic Signatures
In silico Predictions
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4Office of Research and DevelopmentNational Center for Computational Toxicology
Key Challenges
•Find the Toxicity Pathways•Liver vs developmental
•Obtain HTS Assays for Them• Including metabolic capability
•Screen Chemical Libraries• Coverage of chemical properties
•Link Results to in vivo Effects• Gold standard and dosimetry
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5Office of Research and DevelopmentNational Center for Computational Toxicology
Implications for Success
•Hazard Identification•Closing Data Gaps•Reductions in Cost•Hypothesis Generation•Reduced Animal Usage
•Risk Assessment•Providing MOA(s)•Targeted Testing •Identifying Susceptible Populations
•Ancillary Applications•Mixtures•Chirals•Nanomaterials•Green Chemistry•Lot variations
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6Office of Research and DevelopmentNational Center for Computational Toxicology
ToxCastTM Background
• Research program of EPA’s National Center for Computational Toxicology
• Addresses chemical screening and prioritization needs for pesticidal inerts, anti-microbials, CCLs, HPVs and MPVs
• Comprehensive use of HTS technologies to generate
biological fingerprints and predictive signatures
• Coordinated with NTP and NHGRI/NCGC via Tox21
• Committed to stakeholder involvement and public release of data
• Communities of Practice- Chemical Prioritization; Exposure
• NCCT website- http://www.epa.gov/ncct/toxcast
• ACToR- Aggregated Computational Toxicology Resource
http://www.epa.gov/actor/
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7Office of Research and DevelopmentNational Center for Computational Toxicology
Phased Development of ToxCast
FY09-10~$15-20K>200PMN Nanomaterials>12IId
FY09~$20-25k>400ExtrapolationKnown Human Toxicants>100IIb
FY09$10K166PilotNanomaterials15Ib
FY09~$20-25k>400ValidationData Rich Chemicals>300IIa
>300
>400
552
Number of Assays
Data poor
Expanded Structure and Use
Diversity
Data Rich(pesticides)
Chemical Criteria
FY11-12
FY10
FY08
TargetDate
~$15-20k
~$20-25k
$20k
Cost per Chemical
Prediction and Prioritization
Extension
Signature Development
PurposeNumber of ChemicalsPhase
ThousandsIII
>300IIc
320Ia
January 2009
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8Office of Research and DevelopmentNational Center for Computational Toxicology
Phased Development of ToxCast
FY09-10~$15-20K>200PMN Nanomaterials>12IId
FY09~$20-25k>400ExtrapolationKnown Human Toxicants>100IIb
FY09$10K166PilotNanomaterials15Ib
FY09~$20-25k>400ValidationData Rich Chemicals>300IIa
>300
>400
552
Number of Assays
Data poor
Expanded Structure and Use
Diversity
Data Rich(pesticides)
Chemical Criteria
FY11-12
FY10
FY08
TargetDate
~$15-20k
~$20-25k
$20k
Cost per Chemical
Prediction and Prioritization
Extension
Signature Development
PurposeNumber of ChemicalsPhase
ThousandsIII
>300IIc
320Ia
January 2009
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9Office of Research and DevelopmentNational Center for Computational Toxicology
$1B in Toxicology Now Stored in ToxRefDB
Martin, et al EHP, 2008
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10Office of Research and DevelopmentNational Center for Computational Toxicology
ToxCast Phase I Datasets• ToxCast 1.0 (April, 2007)
– Enzyme inhibition/receptor binding HTS (Novascreen)– NR/transcription factors (Attagene, NCGC)– Cellular impedance (ACEA)– Complex cell interactions (BioSeek)– Hepatocelluar HCS (Cellumen)– Hepatic, renal and airway cytotoxicity (IVAL)– In vitro hepatogenomics (IVAL, Expression Analysis)– Zebrafish developmental toxicity (Phylonix)
• ToxCast 1.1 (January, 2008)– Neurite outgrowth HCS (NHEERL)– Cell proliferation (NHEERL)– Zebrafish developmental toxicity (NHEERL)
• ToxCast 1.2 (June, 2008)– XME Gene Regulation (CellzDirect)– HTS Genotoxicity (Gentronix)– Organ toxicity; dosimetry (Hamner Institutes)– Toxicity and signaling pathways (Invitrogen)– C. elegans WormTox (NIEHS)– Gene markers from microscale cultured hepatocytes (MIT)– 3D Cellular Zebrafish vascular/cardiotoxicity (Zygogen)– microarray with metabolism (Solidus)– HTS stress response (NHEERL+NCGC)
20 Assay sources554 Endpoints
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11Office of Research and DevelopmentNational Center for Computational Toxicology
ToxCast Assays
• Cell lines– HepG2 human hepatoblastoma– A549 human lung carcinoma– HEK 293 human embryonic kidney
• Primary cells– Human endothelial cells– Human monocytes– Human keratinocytes– Human fibroblasts– Human proximal tubule kidney cells– Human small airway epithelial cells
• Biotransformation competent cells– Primary rat hepatocytes– Primary human hepatocytes
• Assay formats– Cytotoxicity– Reporter gene – Gene expression– Biomarker production– High-content imaging for cellular
phenotype
• Protein families– GPCR– NR– Kinase– Phosphatase– Protease– Other enzyme– Ion channel– Transporter
• Assay formats– Radioligand binding– Enzyme activity– Co-activator recruitment
Cellular AssaysBiochemical Assays
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12Office of Research and DevelopmentNational Center for Computational Toxicology
Cellular Assays
• Types of Assays– Known toxicity pathways and targets
• biomarker measurements • reporter gene assays
– General cytotoxicity– Toxicity cellular phenotypes
• Cell lines and primary cells• Generally screened at up to 100 μM or used maximally
tolerated concentration defined by general cytotoxicity determination
• Concentration-response format used and EC50 generated
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13Office of Research and DevelopmentNational Center for Computational Toxicology
Biochemical Assay Results228 A
ssays
320 Chemicals
Log IC50 (M)
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14Office of Research and DevelopmentNational Center for Computational Toxicology
Methods described in:Judson et al 2008A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model.BMC Bioinformatics 9:241
N1 A1 E1 A2 N2 N3 N4 N5 C1 B1 B2 B3 G1 A3 E2HTS Assays
Positivecluster
Negativecluster
In Vivo
In VitroToxCastPredictive Modeling
of ChronicRat Liver
Apoptosis/Necrosis
(15)
(23)
A
B
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15Office of Research and DevelopmentNational Center for Computational Toxicology
Beyond the Proof of Concept
Chemicals
ToxCast_320HighThroughput
Assay DataToxRef in vivobioassay data
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17
Universe 13,247With structures 8,277Plausible P-chem (logP) 7,116
Current Additional
NTP 1353 ~1400
EPA 1330 ~2800
NCGC ~3000 drugs -
Target library, Summer 2009 ~10,000
* Sources include NTP, EPA HPV, CCL, OPPIN, OW, Inerts, ToxCast, DSSTox, EU Carcinogenomics, Pharmaceuticals, others
Tox21 Existing and Candidate Chemicals*
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18Office of Research and DevelopmentNational Center for Computational Toxicology
Source to Outcome ContinuumSource to Outcome Continuum
Source/Stressor FormationSource/Stressor Formation
Environmental Conc.
External Dose Target Dose
Biological Event
Effect/OutcomeEffect/Outcome
ToxRefDB
ToxCast
ToxMiner
rTK
ACToR
ExpoCast
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19Office of Research and DevelopmentNational Center for Computational Toxicology
Current Status of ToxCast and Tox21
• ToxRefDB - Relational phenotypic databases– Chronic rat and mouse studies (Martin, et al, EHP 2008)– Rat multigenerational studies (Martin, et al, submitted)– Rat and Rabbit developmental studies (Knudsen, et al, internal review)
• ToxCast– Submit manuscripts on v1.0 by Feb 1 2009– Data Summit
• RTP, May 14-15– Phase II launch
• Mid summer 2009• Major Pharma is considering supply +100 candidate drugs
• ACToR (Aggregated Computational Toxicology Resource) - www.epa.gov/actor– Released Jan 2009– Portal for public toxicity information, ToxRef and ToxCast data
• Tox21 – qHTS on +6000 chemicals starting in mid 2009
• Includes large collection of pharmaceuticals• One to two assays per week
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20Office of Research and DevelopmentNational Center for Computational Toxicology
Emerging Issues Proposal
• SPECIFIC ACTIONS
– Coordinate Public-Private sector involvement in ToxCast predictions– Scoping meeting to articulate needs, timelines and boundaries of
involvement by participants
• DESIRED OUTCOME
– Successful deliberations and negotiations would result in:• Identify and provide chemicals (~100mg) for screening • Sharing of relevant pre-clincal and clinical data• [Cost sharing of screening costs]• Co-publications on predictive models
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21Office of Research and DevelopmentNational Center for Computational Toxicology
Benefits of Proposal
• Creates a government – private sector effort with potential to significantly improve predictive basis of toxicity evaluations
• Enables utilization of a unique private sector knowledge
• Builds on the experience of EPA in computational toxicology
• Brings direct human relevance to HTS screening on environmental chemicals, which already involves the use of many human protein targets and cell types
• Significantly enables progress at reaching the vision of toxicity testing in the 21st envisioned by the National Research Council