Developing a Roadmap for Integrating Computational and In Vitro Approaches in Risk-Based Chemical Safety Decisions Rusty Thomas Director National Center for Computational Toxicology SSCT-SweTox Workshop October 14, 2015 ToxPi PRIORITIZATION Interactive Chemical Safety for Sustainability Web Application TOXCAST iCSS v0.5 Tool Tip Description of Assays (Data) or whatever is being hovered over Prioritization Mode Desc Summary Log 80-05-7 80-05-1 80-05-2 80-05-3 80-05-5 CHEMICAL SUMMARY CASRN Chemical Name 80-05-7 Bisphenol A 80-05-1 Bisphenol B 80-05-2 Bisphenol C 80-05-3 Bisphenol D 80-05-4 Bisphenol E 80-05-5 Bisphenol F 80-05-6 Bisphenol G 80-05-7 Bisphenol H 80-05-8 Bisphenol I 80-05-9 Bisphenol J A B C D E G H F 1 1 1 1 1 1 1 1 SCORING APPLY Studies The views expressed in this presentation are those of the author and do not necessarily reflect the views or policies of the U.S. EPA
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Developing a Roadmap for Integrating Computational and In Vitro Approaches in Risk-Based Chemical Safety Decisions
Rusty ThomasDirectorNational Center for Computational Toxicology
SSCT-SweTox WorkshopOctober 14, 2015
ToxPi
PRIORITIZATION
Interactive Chemical Safety for Sustainability Web
Application
TOXCAST iCSS v0.5
Tool TipDescription of Assays (Data) or whatever is being hovered over Prioritization Mode
Judson et al., Tox Sci. In PressBrowne et al., ES&T. 2015
*Values in parentheses exclude inconclusive chemicals
National Center forComputational Toxicology
AOP Network for Thyroid Hormone Disruption
Paul et al., In Review
Presenter
Presentation Notes
Inorganic iodine enters the body primarily as iodide, I−. After entering the thyroid follicle (or thyroid follicular cell) via a Na+/I− symporter (NIS) on the basolateral side, iodide is shuttled across the apical membrane into the colloid via pendrin, after which thyroid peroxidase oxidizes iodide to atomic iodine (I) or iodinium (I+). The "organification of iodine," the incorporation of iodine into thyroglobulin for the production of thyroid hormone, is nonspecific; that is, there is no TPO-bound intermediate, but iodination occurs via reactive iodine species released from TPO.[4] The chemical reactions catalyzed by thyroid peroxidase occur on the outer apical membrane surface and are mediated by hydrogen peroxide
National Center forComputational Toxicology
Identification of Selective TPO Inhibitors
Paul et al., In Review
National Center forComputational Toxicology
What About the Non-Selective Chemicals?
?????????
Nonselective Chemical
Define Point-of-DepartureBMR
BMDBMDL
0.01 0.1 1 100.0
0.2
0.4
0.6
0.8
1.0
Concentration to Activate First AssayConcentration to Activate 10% of Assays
Cum
ulat
ive
Frac
tion
of C
hem
ical
s
~80% with < 3-fold ratio
Nonselective
Selective
Most sensitive response generally protective on a
dose level
Specific adverse outcome not reliably
predicted
Absence of activity difficult to interpret
National Center forComputational Toxicology
16
Efforts to Ensure HTS Data Quality and Increase Transparency
• Public release of Tox21 and ToxCast data on PubChem and EPA web site (raw and processed data)
• ToxCast data analysis pipeline has been completely revamped
• More statistically rigorous and less prone to outliers
• Data quality flags to indicate concerns with chemical purity and identity, noisy data, systematic assay errors, and activity in range of cytotoxicity
• Available for download as an R package
• Release of ToxCast “Owner’s Manual”• Chemical Procurement and QC
• Data Analysis
• Assay Characteristics and Performance
• External audit on ToxCast data and data analysis pipeline
• Continued offering of webinars and workshops to educate stakeholders on high-throughput screening data analysis and interpretation
FLAGS:Only one conc above baseline, activeBorderline active
National Center forComputational Toxicology
17
Efforts to Address Metabolism Challenge
ToxCast
Concentration
Res
pons
e
~700 Cell & biochemical
assays
~2,000 Chemicals
Limited Xenobiotic
Metabolism
National Center forComputational Toxicology
18
Efforts to Address Metabolism Challenge
In Development
P450 Glo IPA Assay
National Center forComputational Toxicology
19
Efforts to Address Limited Biological Coverage
ToxCast
Concentration
Res
pons
e
~700 Cell & biochemical
assays
~2,000 Chemicals
In DevelopmentGene Coverage
Pathway Coverage*
ToxCast
Not in ToxCast
*At least one gene from pathway represented
Multiple cell lines/types
~2,000 Chemicals
High-Throughput Transcriptomics
Lamb et al. Science (2006)
Concentration
Res
pons
e
• Low-cost• Whole genome• 384-well• Automatable
National Center forComputational Toxicology
20
Efforts to Address Limited Biological Coverage
Illumina RNA AccessL1000 Illumina Low Coverage WT
Log2
FC
L10
00
Log2 FC Affymetrix Log2 FC Affymetrix Log2 FC Affymetrix
Log1
0 FC
RN
A Ac
cess
Log1
0 FC
Low
Cov
erag
e W
T
r2 = 0.03 r2 = 0.60 r2 = 0.63
National Center forComputational Toxicology
21
Developing a Broad Hazard Screening Platform
Tier 1
Select In VitroHTS Assays
Non-Selective Interacting Chemicals
Tier 0High-Throughput Transcriptomic
Assay
Selective Interacting Chemicals
Tier 2Organotypic Assays and Virtual Tissue
Modeling
Estimate Point-of-Departure Based on AOP
Estimate Point-of-Departure Based on Biological Activity
Rotroff et al., Tox Sci., 2010Wetmore et al., Tox Sci., 2012
Reverse Dosimetry
Oral Exposure
Plasma Concentration
ToxCast AC50 Value
Oral Dose Required to Achieve Steady State
Plasma Concentrations Equivalent to In Vitro
Bioactivity
~700 In Vitro ToxCast Assays
Least Sensitive Assay
MostSensitive
Assay
Human Liver Metabolism
Human Plasma Protein Binding
Population-Based IVIVE Model
Upper 95th Percentile CssAmong 100 Healthy
Individuals of Both Sexes from 20 to 50 Yrs Old
309 EPA ToxCastPhase I Chemicals
National Center forComputational Toxicology
Comparing with Exposure for Risk Context
Rotroff et al., Tox Sci., 2010Wetmore et al., Tox Sci., 2012
Reverse Dosimetry
Oral Exposure
Plasma Concentration
ToxCast AC50 Value
Oral Dose Required to Achieve Steady State
Plasma Concentrations Equivalent to In Vitro
Bioactivity
~700 In Vitro ToxCast Assays
Least Sensitive Assay
Ora
l Equ
ival
ent D
ose
(mg/
kg/d
ay)
What are humans exposed to?
?
?
?
Chemical
In VitroBioactivity
MostSensitive
Assay
Human Liver Metabolism
Human Plasma Protein Binding
Population-Based IVIVE Model
Upper 95th Percentile CssAmong 100 Healthy
Individuals of Both Sexes from 20 to 50 Yrs Old
309 EPA ToxCastPhase I Chemicals
Exposure
National Center forComputational Toxicology
Comparing with Exposure for Risk Context
Wetmore et al., Tox Sci., 2012
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or E
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Exp
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0.00001
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0.1
1
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1000
10000
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clob
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zol
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fen
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0.1
1
10
100
1000
10000
100000
Ora
l Equ
ival
ent D
ose
or E
stim
ated
Exp
osur
e(m
g/kg
/day
)
Assay Bioactivity
Exposure Range
National Center forComputational Toxicology
Certainly the Road Less Traveled…
Dinoseb
2-[2-(
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ethoxy
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Perfluoro
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ide
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Endrin
Heptac
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mer B
Potassiu
m perfluoro
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yl-4,6
-dinitrophen
ol
Pentad
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uoroocta
noic ac
id a
Sulfasa
lazine
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ichloro
benze
ne
Isopro
palin
Potassiu
m nonafluoro
-1-butan
es
Warfari
n
Perfluoro
undecan
oic ac
id
Hexam
ethyl-
p-rosa
niline c
hlori
Di-n-octy
l phthala
te
Perfluoro
heptan
oic ac
id
Perfluoro
nonanoic
acid
Benzy
l hyd
rogen
phthalate
Perfluoro
decan
oic ac
id
Fomesafe
n
Heptad
ecafl
uoroocta
nesulfo
nic
Surinab
ant
Dibutyl se
bacate
Coumarin
Tamoxif
en
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x
Didecyl
dimeth
yl am
monium chlo
Di(ethyle
ne glyc
ol) diben
zoate
1,2-B
enzis
othiazolin
-3-one
Benz[a
]anthrac
ene
Tris(1,
3-dich
loro-2-
propyl)
ph
Safrole
2,4-D
initrophen
ol
p,p'-DDT
Perfluoro
hexan
oic ac
id
7,12-D
imeth
ylben
z(a)an
thracen
e
Pirinixi
c acid
Naphthale
ne
Methyl
laurat
eMire
x
1,2,3-
Trichloro
benze
ne
5,5-D
iphenylh
ydan
toin
N,N-D
iethyl
anilin
e
Butaned
ioic ac
id
9-Phen
anthro
l
Benzo
[b]fluoran
thene
0.00001
0.0001
0.001
0.01
0.1
1
10
100
1000
10000Gen. USMHE
Ora
l Equ
ival
ent D
ose
or E
stim
ated
Exp
osur
e(m
g/kg
/day
)
O-Ethyl
O-(p-nitr
ophenyl)
phen
o,p'-DDT
1,3-D
iisopro
pylben
zene
Triphen
yl phosp
hate
Biphenyl
6-Pro
pyl-2-t
hiouracil
Diphenyle
nemeth
ane
Isoeu
genol
Dibenzo
furan
3-Buten
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3-meth
yl-4-(
2,6
Acenap
hthylene
Acenap
hthene
4-(2-m
ethylb
utan-2-
yl)phen
ol
Diethyls
tilbes
trol (D
ES)
Octrizo
le
4-Octy
lphenol
4-(1,1
,3,3-T
etram
ethylb
utyl)ph
Carbosu
lfan
Dieldrin
Kepone (
Chlordec
one)
Tebuco
nazole
Benodan
il
4-Aminoaz
obenze
ne
Propan
ol, 1 (o
r 2)-(
2-meth
oxym
4,4'-m
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nebis(
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Chlorpyri
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imeth
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2,4-D
initrotoluen
e
Ethoxyquin
2,4,5-
Trichloro
phenol
Diisobutyl
adipate
2,4,6-
Trichloro
phenol
Carbofuran
Benzo
phenone
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Fluoranthen
e
4,4'-O
xydian
iline
Proges
terone
Diphenhyd
ramine h
ydro
chlorid
e
methyl
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zimidaz
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car
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butylphen
ol
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hanol
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nitroan
iline
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xyad
enosin
e
1,5-D
iaminonap
hthalene
0.00001
0.0001
0.001
0.01
0.1
1
10
100
1000
10000 Gen. USMHE
Ora
l Equ
ival
ent D
ose
or E
stim
ated
Exp
osur
e(m
g/kg
/day
)
N-[(3R
)-1-az
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zene
Predniso
ne
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phenol
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ylphen
ol
Phosmet
Quinoline
Volinan
serin
Cyclopam
ine
Methyl
octanoate
Butylpara
ben
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-Butyl
phenol
2,6-D
initrotoluen
e
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-butylam
ine
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e
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4,5,5,
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8-Trid
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ugenol
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araben
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yl-1,4
-benze
nediam
ine
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imeth
oxyben
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2,6-D
imeth
ylphen
ol
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otinine
4-Nitr
otoluene
Oxytet
racyc
line h
ydro
chlorid
e
Eugenol
2,4-D
i-tert-
butylphen
ol
N,N'-M
ethyle
nebis(
acryl
amide)
Candoxa
tril
p-Cres
idine
Propylp
araben
Dibutyl hex
aned
ioate
Ethylpara
ben
Tannic
acid
Resorci
nol
Dimeth
yl glutar
ate
N,N-D
imeth
ylocty
lamine
Erythro
mycin
Triethyle
ne Glyc
ol Diac
etate
Triethyl
citrat
e
Diallyl
phthalate
Dimeth
yl su
ccinate
0.00001
0.0001
0.001
0.01
0.1
1
10
100
1000
10000Gen. USMHE
Ora
l Equ
ival
ent D
ose
or E
stim
ated
Exp
osur
e(m
g/kg
/day
)
1-Hyd
roxy
pyrene
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c acid
di(2-et
hylhex
yl)
Tridem
orph
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e
Triamcin
olone
Acetam
inophen
Octhilin
one
2-Ben
zylid
eneo
ctanal
Tri(eth
ylene g
lycol) b
is(2-e
th
N-Nitr
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Aldrin
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iethyla
niline
Vernolat
e
Genist
ein
5-Hep
tyldihyd
ro-2(
3H)-f
uranone
Terbuthyla
zin
Mepan
ipyrim
2-Anisi
dine
Tributyl
phosphate
Pyrene
3-Hyd
roxy
fluoren
e
Pyrimeth
amine
2-Nap
hthylamine
Bisphen
ol B
Rifampici
n
Di(2-et
hylhex
yl)ad
ipate
Simva
statin
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-Butyl
-4-meth
oxy-phen
ol
Monuron
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Trimeth
ylanilin
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iphenylg
uanidine
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hlor
Benzid
ine
Caffein
e
Haloperi
dol
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tin
Carbam
azep
ine
PK 1119
5
Chlorthal-
dimeth
yl
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8-Hyd
roxy
quinoline
3-Nitr
otoluene
2-Meth
ylphen
ol
4,4'-M
ethyle
ne bis(
2-meth
ylani
Androste
nedione
Diisopro
pyl meth
ylphosp
honate
Phenolphthale
in0.00001
0.0001
0.001
0.01
0.1
1
10
100
1000
10000Gen. USMHE
Ora
l Equ
ival
ent D
ose
or E
stim
ated
Exp
osur
e(m
g/kg
/day
)
Bioactivity from Wetmore et al., Tox Sci., 2015
National Center forComputational Toxicology
27
Developing High-Throughput Exposure Models
(Bio) Monitoring
Dataset 1
Dataset 2…
e.g., CDC NHANES study
Wambaugh et al., Environ Sci Technol., 2014
Predicted Exposures
…
Use
Production Volume
Inferred Exposures
Pharmacokinetic Models
Estimate Uncertainty
Calibrate models
Infe
rred
Exp
osur
e
Predicted Exposure
National Center forComputational Toxicology
28
High-Throughput Exposure Heuristics
Wambaugh et al., Environ Sci Technol., 2014
Heuristic DescriptionACToR “Consumer use &
Chemical/Industrial Process use”Chemical substances in consumer products (e.g., toys, personal care products, clothes, furniture, and home-care products) that are also used in industrial manufacturing processes. Does not include food or pharmaceuticals.
ACToR “Chemical/Industrial Process use with no Consumer use” Chemical substances and products in industrial manufacturing processes that are not
used in consumer products. Does not include food or pharmaceuticals
ACToR UseDB “Pesticide Inert use”Secondary (i.e., non-active) ingredients in a pesticide which serve a purpose other than repelling pests. Pesticide use of these ingredients is known due to more stringent reporting standards for pesticide ingredients, but many of these chemicals appear to be also used in consumer products
ACToR “Pesticide Active use” Active ingredients in products designed to prevent, destroy, repel, or reduce pests (e.g., insect repellants, weed killers, and disinfectants).
TSCA IUR 2006 Total Production Volume Sum total (kg/year) of production of the chemical from all sites that produced the
chemical in quantities of 25,000 pounds or more per year. If information for a chemical is not available, it is assumed to be produced at <25,000 pounds per year.
National Center forComputational Toxicology
29
Comparing Bioactivity with Exposure Predictions for Risk Context
Wetmore et al., Tox Sci., 2015
Chemicals
National Center forComputational Toxicology
30
Work In Progress to Address Exposure Data Gaps
ExpoCast
Estimate Uncertainty
EDSP Chemicals
QSARs and HTE Data
BiomonitoringData
Infe
rred
(Rev
erse
) Exp
osur
e
Model 1
Model 2…
Calibrate models
Apply calibration and uncertainty to other chemicals
Evaluate Model Performanceand Refine Models
Forward Predictions
Exposure Inference
Dataset 1
Dataset 2…
• Limited domain of applicability of existing biomonitoring data
• Limited knowledge of qualitative and quantitative composition of chemical ingredients and emissivity of consumer products and home goods
• Limited experimental measurements of physical chemical properties
National Center forComputational Toxicology
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Non-Targeted Analysis of Consumer Products (Baby Products Pilot)
Brand #1 Brand #2 Brand #3 Brand #4 Brand #5
Category Number Peak Area Number Peak Area Number Peak Area Number Peak Area Number Peak AreaReported peaks with reviewed library matches 98 430366619 106 123796416 114 1439691153 67 189430603 56 88784398