oEPA
United States
Environmental Protection
Agency
Bottom-Up Exposomics for Ensuring
Chemical Safety
Jon R. Sobus, Ph.D.
Office of Research and Development
Center for Computational Toxicology and Exposure
Jan 24, 2020
-------
oH* Presentation Outline
United States
Environmental Protection
Agency
The Exposome: State-of-the-Science
Top-Down vs. Bottom-Up Exposomics
Bottom-Up Exposomics for Ensuring Chemical Safety
Non-Targeted Analysis (NTA) within EPA's ORD
Efforts to Evaluate and Harmonize NTA Methods
Perspectives for the Future of Exposomics
-------
SERA
United States
Environmental Protection
Agency
Exposomics:
A Paradigm Shift for Exposure and Health Sciences
Traditional Research : Courtship
fit
Exposomics: Online Dating
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SERA
United States
Environmental Protection
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15 Years Later... How Far Have We Come?
Books
Centers
i
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Editorial
Canter Epidemiol Biomarkers Prev 2005; 14(8). August 2005
Complementing the Genome with an "Exposome":
The Outstanding Challenge of Environmental
Exposure Measurement in Molecular Epidemiology
Christopher Paul Wild
Molecular Epidemiology Unit, Centre for Epidemiology and Biostatuktic*, Leeds Institute uf Genetics, Health
and Therapeutics, Faculty of Medicine and Health, University of Leeds., Leeds, United Kingdom
Training
COLUMBIA | K'S
The
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EMERGING SCIENCE
FOR ENVIRONMENTAL
HEALTH DECISIONS
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Emerging Technologies for Measuring
Individual Exposomes
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What Are Researchers Studying?
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Figure adapted from: Wild CP. Int. J. Epidemiol. 2012 Feb;41(l):24-32
-------
oE
United States
Environmental Protection
Agency
What is Different About Exposomics?
Exposure
Source
The 'OmicsRealm
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Exposomics is the one 'omics discipline that puts focus on external exposure
The inherent promise of Exposomics is therefore health protection & disease prevention
-------
Protection
Exposomics Approaches
Top-Down Exposomics
Bottom-Up Exposomics
Perspectives
Editorial
Exposure Science and the Exposome:
An Opportunity for Coherence in the
Environmental Health Sciences
http:lliix.doi.orff 10.1289/efop. 1104387
Measure Important Exposures
Within the Receptor
Measure Important Exposures in All
Relevant Media
Figure adapted from: Rappaport SM. J Expo Sci Environ Epidemiol. 2011 Jan-Feb;21(l):5-9
-------
SERA
United States
Environmental Protection
Agency
Challenges with Top-Down Efforts
Challenges:
1) Always retrospective (start with adverse outcome)
2) Requires relevant banked samples (intra-individual variability)
3) Difficult to show causation
4) Signals of stressors can be low in blood
Potential Positive Outcomes:
1) Biomarkers for early detection
2) Drugs for early treatment
Identifying the most important exposures doesn't require
waiting for an adverse outcome
-------
SERA
United States
Environmental Protection
Agency
Rationale for Bottom-Up Efforts
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AEPA
United States
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SERA
United States
Environmental Protection
Agency
The Need for Chemical Measurement Data
Well-known chemicals
• 100s - 1,000s (e.g., NHANES)
• Quality exposure data
Known but data-poor chemicals
• 1,000s - 1,000,000s (e.g., TSCA)
• Limited exposure data
Chemicals not vet known to exist
• Unknown #
• No exposure data
Targeted Analysis
-------
SERA
United States
Environmental Protection
Agency
Typical Targeted Analysis Workflow
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-------
SERA
United States
Environmental Protection
Agency
Simplified NTA Workflow
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-------
SERA
United States
Environmental Protection
Agency
Integration
Framework
Journal of Exposure Science & Environmental Epidemiology (2018) 28:411-426
https://doi.Org/10.1038/S41370-017-0012-y
REVIEW ARTICLE
Integrating tools for non-targeted analysis research and chemical
safety evaluations at the US EPA
Jon R, Sobus1 • John F. Wambaugh2 • Kristin K. Isaacs1 • Antony J. Williams2 ¦ Andrew D. McEachran3 •
Ann M. Richard2 ¦ Christopher M. Grulke2 ¦ Elin M. Ulrich1 - Julia E. Rager3 4 ¦ Mark J. Strynar1 ¦ Seth R, Newton1
Received: 27 May 2017 / Revised: 4 August 2017 / Accepted: 25 August 2017 / Published online: 29 December 2017
© The Author(s) 2017. This article is published with open access
Abstract
Tens-of-thousands of chemicals are registered in the U.S. for use in countless processes and products. Recent evidence
suggests that many of these chemicals are measureable in environmental and/or biological systems, indicating the potential
for widespread exposures. Traditional public health research tools, including in vivo studies and targeted analytical
chemistry methods, have been unable to meet the needs of screening programs designed to evaluate chemical safety. As
such, new tools have been developed to enable rapid assessment of potentially harmful chemical exposures and their
attendant biological responses. One group of tools, known as "non-targeted analysis" (NTA) methods, allows the rapid
characterization of thousands of never-before-studied compounds in a wide variety of environmental, residential, and
biological media. This article discusses current applications of NTA methods, challenges to their effective use in chemical
screening studies, and ways in which shared resources (e.g., chemical standards, databases, model predictions, and media
measurements) can advance their use in risk-based chemical prioritization. A brief review is provided of resources and
projects within EPA's Office of Research and Development (ORD) that provide benefit to, and receive benefits from, NTA
research endeavors. A summary of EPA's Non-Targeted Analysis Collaborative Trial (ENTACT) is also given, which makes
direct use of ORD resources to benefit the global NTA research community. Finally, a research framework is described that
shows how NTA methods will bridge chemical prioritization efforts within ORD. This framework exists as a guide for
institutions seeking to understand the complexity of chemical exposures, and the impact of these exposures on living
systems.
Keywords Non-targeted analysis • Suspect screening • Exposome • ENTACT
Sample Analysis via NTA Methods
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-------
SERA
United States
Environmental Protection
Agency
The Hrtioiul Academic* 0/
SCIENCES • ENGINEERING • MEDICINE
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21 ST CENTURY
SCIENCE
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United States
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Building an NTA Research Program
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point-of-use filters'*
| Scth R. Newton J-Rebecca L McMahen '•b. Jon R. Sobus Kamel Mansouri '' '.
Antony J. Williams . Andrew D. McEachran " ', Mark J. StrynarJ
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Suspect Screening Analysis of Chemicals in Consumer Products
Katherine A. Phillips. ® Alice Yau, Kristin A. Favela, Kristin K Isaacs, Andrew McEachran,5 '
Christopher Grulke," Ann M. Richard," Antony J. Williams," Jon R. Sobus,' Russell S. Thomas,11
and John F. Wambaugh*
' National Exposure Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, 109 T. W.
Alexander Drive, Research Triangle PaA, North Carolina 27711, United States
'Southwest Research Institute, San Antonio, Texas 78238, United States
5Oak Ridge Institute for Science and Education (OR1SE), Oak Ridge, Tennessee 37830, United Stales
'National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, 109
T. W. Alexander Drive, Research Triangle Park, North Carolina 27711, United States
fr
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McEachran etaLJCheminform 12018! I0.4S
https://doi.org/10.1136-s13321-018-0299-2
Journal of Cheminformatics
| METHODOLOGY
Open Access ¦
"MS-Ready" structures for non-targeted
high-resolution mass spectrometry screening
studies
Andrew D. McEachran1-2", Kamel Mansouri®-23, Chris Grulke2, Emma L Schymanski"1, Christoph Ruttkies5
and Antony 1 Williams2"
'MS Ready" Structures
SCIENTIFIC DATM
0PEN Linking in silico MS/MS spectra
,tadescriptor with chemistry data to improve
identification of unknowns
online: 02 August 2019
In Silico Spectra
2019.
Model Organisms
Hospital Masks
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academlc.oup.com/loxsci
TOJOCOUXaCAl SCIEKCZS, mill. XI19. 109-03
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Spotlight
A Breath Ra. 14 (2020)016006
Triclosan-Selected Host-Associated Microbiota Perform
Xenobiotic Biotransformations in Larval Zebrafish
Chelsea A. Weitekamp Q ,*•' Drake Phelps,'1 Adam Swank,' James McCoid 9 ,*
Jon R. Sobus.1 Tara Catron © ,* Scott Keely © * Nichole Brinkman,4
Todd Zurlinden ©,' Emily Wheaton,5 Mark Strynar,' Charlene McQueen,
Charles E. Wood,1-2 and Tamara Tal 0 111-3
Oak Ridge Institute lor Science and EducaUonAJ.S. EPA/ORQ'NUEERL/tSTD. Research Trainee Park. North
CaroBn»,277U: US EPA/ORD/NHEEJtt/RCU. Research Triangle Park. North Carolina, OTlfcUS EPA/OREV
NERLTMMD. Research Triangle Park, North Carolina. 2771 J; *US. EPA/ORIVNERUSED, Cincinnati. Ohio.
4S220. *U.S EPA/ORtWNCCT, Research Triangle Park, North Carolina, 27711, University of AHxona.
Department of Pharmacology and Toxicology. Tucson, Arizona, 85721, and
Research Triangle Park. North Caroline, 27711
Journal of Breath Research
How do cancer-sniffing dogs sort biological samples? Exploring
case-control samples with non-targeted LC-Orbitrap, GC-MS, and
immunochemistry methods
Joachim D Plcil1 , M Ariel Geer Wallace , James McCord , Michael C Madden , Jon Sobus and
Glenn Ferguson
' US Environmental Protection Agency, Ofliceor Research and Development, National Exposure Research Laboratory. 109T. W.
Alexander Drive, Research T riangk Park, NC. 27709, United Slates of America
1 ConcerDogs, 25 irapdercxcur&km, Gatineau, Quebec, J9H6L9, Canada
E-mail: pleiLjoacliim@Vpa.gov
Supplementary material for this article is available online
Exposure
Networks
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Methods
EPA NTA
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2020
Recycled
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Blood
Human
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-------
SERA
United States
Environmental Protection
Agency
NTA State-of-the-Science
Science of the Total Environment 670 (2019) 814-825
Contents lists available at ScienceDirect
Science of the Total Environment
journal homepage: www.elsevier.com/locate/scitotenv
Prioritizing potential endocrine active high resolution mass spectrometry
Check for
(HRMS) features in Minnesota lakewater
Meaghan E. Guyader3, Les D. Warren b, Emily Greena, Craig Buttc, Gordana Ivosev d, Richard L. Kieslinge
Heiko L. Schoenfuss b, Christopher P. Higginsl*
a Colorado School of Mines. Golden, CO, USA
b St. Cloud State University. St. Cfoud. MN, USA
c Sciex, Boston, MA, USA
d Sciex, Toronto, Canada
e US. Geological Survey. Mounds View. MN, USA
ences
e
L
cnnoiogg
Cite This: Environ. Sci. Techno/. 2018, 52, 11975-11976
Viewpoint
pubs.acs.org/est
Is Nontargeted Screening Reproducible?
Ronald A. Hites*
School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, United States
Karl J. Jobst*
Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
"The novelty of nontarget analysis, particularly its
current lack of implementation by regulatory agencies,
has prevented the establishment of streamlined quality
assurance and quality control (QA/QC) procedures."
"A/o single analytical technique is suitable for the
analysis of all compounds, and successful
nontargeted screening will require the development
of multiplatform approaches, facilitated and validated
through interlaboratory collaborations."
-------
SERA
United States
Environmental Protection
Agency
EPA Takes a Leadership Role
2015...
Non-Targeted Analysis Workshop
Home Agenda Registration | Abstract Submission Logistics
t
2018...
Environmental Protection Agency
(EPA) 2018
The U.S. Environmental Protection Agency (EPA) hosted a workshop
focused on EPA's Non-Targeted Analysis Collaborative Trial (EMTACT).
ENTACT was designed to assess the characteristics and performance
of cutting-edge non-targeted analysis (NTA) methods using a set of
highly controlled synthetic mixtures and reference samples. This
workshop brought together ENTACT participants, NTA experts, and
key stakeholders to discuss findings from ENTACT as well as next
steps for the NTA research community.
t
2016...
The U.S. Environmental Protection Agency (EPA) will host the Non-Targeted Analysis Workshop
August 18-19, 2015 at EPA's Research Triangle Park Campus.
n
August 13-15,2018
Durham, NC, USA
oEPA
United States
Environmental Protection
Agency
Environmental Topics Laws & Regulations About EPA
Related Topics: Science Matters
Search EPA.gov
CONTACT US SHARE (J) (*) ($T) (g)
EPA's ENTACT Study Breaks New Ground with
Non-Targeted Research
Published July 30,2018
EPA scientists are leading a multi-phase project to evaluate the ability of
non-targeted analysis laboratory methods to consistently and correctly
identify unknown chemicals in samples. EPA's Non-Targeted Analysis
Collaborative Trial (ENTACT) was formed in late 2015 and includes nearly
30 academic, government, and industry groups. Non-targeted analysis
involves analyzing water, soil and other types of samples to identify
unknown chemicals that may be present, without having a preconceived
idea of what chemicals may be in the samples.
"One of our main goals is to figure out what scientists are doing with non-
targeted analysis as a group at large, particularly which chemicals we
correctly identify and why," says Elin Ulrich, an EPA scientist who co-leads
ENTACT with EPA's Jon Sobus.
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SERA
United States
Environmental Protection
Agency
Science Questions for the Research Community
How variable are tools and results from lab to lab?
Are some methods/tools better than others?
How does sample complexity affect performance?
What chemical space does a given method cover?
How sensitive are specific instruments/methods?
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-------
SERA
United States
Environmental Protection
Agency
Original ENTACT Concept
ToxCast
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chemicals chemicals chemicals chemicals chemicals chemicals chemicals chemicals chemicals
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interaction products
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behaviors?
Can we expand
coverage?
Lab C measurement space
? "other" space (missing chemicals)
-------
SERA
ENTACT Part 1 ENTACT Part 2
United States
Environmental Protection
Agency
Chemicals from ToxCast Library
~1200 ToxCast Chemicals
(highest quality)
10 Mixtures ,
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-------
SERA
United States
Environmental Protection
Agency
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Contractors:
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UNIVERSITY OF WISCONSIN-MADISON
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California Environmental
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NC STATE
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-------
SERA
United States
Environmental Protection
Agency
EPA Lab Results
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1200
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True Positives -> ~1,000
False Positives? -> ~11,000
Pass
Other
10 15
RT (min)
20
Sobus et al. 2019. https://doi.org/10.1007/s00216-018-1526-4
-------
SERA
United States
Environmental Protection
Agency
Cross-Lab Comparison
3 Labs, 6 Methods. All LC-HRMS
Obs. = 69% Obs. = 45% Obs. = 42% Obs. = 39% Obs. = 22% Obs. = 21%
ID'd = 5% ID'd = 37% ID'd = 33% ID'd = 21% ID'd = 17% ID'd = 14%
12% Not Observed by Any Method
1ZUU
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tl
§
•
•
Compound #
M
4^ CI 00 O
O O O O
O O O O
2-Ie*t-Butyl-4-nietfty1ph«nol
TOXCAST:2M/Ui
OehyOiwptantfrosterone
TOXCA5I:62/713
*'
<'
Y
j^ucx
Cfckwpropftam
200 -
3% Observed by All 6 Methods
n
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COOu
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4
V
%
x
4
4
4
4
%
%
V
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Observed
Not Observed
4
-------
SERA
United States
Environmental Protection
Agency
Evaluating In SilicoSpectra with ENTACT Data
McUibolomics (2015) I l:9R-l 10
DOI 10.1007/s 11306-014-0676-4
ORIGINAL ARTICLE
Competitive fragmentation modeling of ESI-MS/MS spectra
for putative metabolite identification
Felicity Allen • Russ Greiner * David Wishart
Fragmentation
Prediction Model
DSSTox structures
DSSTox MS2
spectra
liLJ
SCIENTIFIC DATA!'-
0PEN Linking in silico MS/MS spectra
tadescriptor with chemistry data to improve
identification of unknowns
Accepted: t July 2019
Published online: 02 August 2019
Andrew D. McEachran 'J1-2, llya Balabin1, Tommy Cathey4, Thomas R. Transue',
Hussein Al-Ghoul5, Chris Grulke2, ion R. Sobus6 & Antony J. Williams2
10 Synthetic Mixtures:
1,269 Unique ToxCast Substances
F LC-QTOF HRMS:
Data Dependent Acquisition
II
MS2
Reference
Library
Probable
Structures
No Library
Matches
MS2 in silico Library
(~765,000 DSSTox Substances)
Tentative
Structures
Analytical and Bioanalytical Chemistry
https://doi.Org/10.1007/S00216-019-02351 -7
RESEARCH PAPER
In silico MS/MS spectra for identifying unknowns: a critical
examination using CFM-ID algorithms and ENTACT mixture samples
Alex Chao1'2 • Hussein Al-Ghoul1,2 • Andrew D. McEachran1,3 • llya Balabin4 • Tom Transue4 • Tommy Cathey4
Jarod N. Grossman2,3 • Randolph Singh1,5 • Elin M. Ulrich2 • Antony J. Williams6 • Jon R. Sobus2
Top
Reference
Library
Match
377 ENTACT Compounds
with MS2 Spectra
88
111
77
101
Not Top Match
Top in
silico
L brary
Match
-------
SERA
United States
Environmental Protection
Agency
ENTACT Publications to Date
Analytical arid Bioanalytical Chemistry (2019) 411:853-866
https^/doi jorg/10.1007/S00216-018-1435-6
RESEARCH PAPER
#
Cross Mark
EPA's non-targeted analysis collaborative trial (ENTACT): genesis,
design, and initial findings
Elin M. Ulrich1 ¦ Jon R. Sobus1 • Christopher M. Grulke2 ¦ Ann M. Richard2 • Seth R. Newton1 ¦ Mark J. Strynar1
Kamel Mansoun3'4 • Antony J. Williams2
Received: 30 July 2018/Revised: 14 September 2018 / Accepted: 17 October 2018/Published online: 6 December 2018
<: This is a U.S. Government work and not ur>der copyright protection in the US; foreign copyright protection may apply 2018
£°J CHROMATOGRAPHY . , L
¦mi—— Tnn*v February / March 2018
Comprehensive, Non-Target
Characterisation of Blinded
Environmental Exposome Standards
Using GCxGC ana High Resolution
Time-of-Flight Mass Spectrometry
by Lome Fell\ Todd Rjcbards andJoe Btnkley
LECO, &i tut Joseph, AUcbt&tn, USA
* Corresponding Author: lorne JeB@ Jei o.t om
Analytical and Bioanalytical Chemistry (2019) 4113835-851
hltps J'/dOLOrg/lO.10O7/SOO216-01 &-1526-4
RESEARCH PAPER
Crcss.Vlajk
Using prepared mixtures of ToxCast chemicals to evaluate non-targeted
analysis (NTA) method performance
Jon R. Sobus '© • Jarod N. Grossman2,3 • Alex Chao2 • Randolph Singh" • Antony J. Williams5 ¦ Christopher M. Grulke5 ¦
Ann M. Richard5 * Seth R. Newton1 • Andrew D, McEachran4 • Elin M. Ulrich1
Received: 19 September 2018 /Revised: 14 hkivember 2018 / Accepted: 27 November 2018 /Published online: 5 January 2019
f This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2019
JCIM
JOURNAL OF
CHEMICAL INFORMATION
AND MODELING & Cite This: J. Chem. inf. Model. 2D19, 59, 4052-4060
pubs.acs.ocg/jcim
Evaluation of In Silico Multifeature Libraries for Providing Evidence
for the Presence of Small Molecules in Synthetic Blinded Samples
Jamie R. Nunez, Sean M. Colby, Dennis G. Thomas, Malak M. Tfaily, ~ Nikola Tolic,
Elin M. Ulrich, Jon R. Sobus, Thomas O. Metz,* " Justin G. Teeguarden,* ' ^
and Ryan S. Renslow
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
~U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Research
Triangle Park, North Carolina 27711, United States
^Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon 97331, United States
"""Department of Environmental Science, University of Arizona, Tucson 85712, United States
-------
SERA
United States
Environmental Protection
Agency
Future Focus Areas Within EPA/ORD
Semi-Quant. NTA:
NTA for UVCBs:
120 -
100 -
>, 80 H
u
c
-------
AEPA
United States
Environmental Protection
Agency
NTA and Exposomics Moving Forward
Exposomics Litmus Test:
Definitely Not
Exposomics
Definitely
Exposomics
Does it advance knowledge of the totality of exposures?
• If focused on measurements, is it non-targeted (or "untargeted")?
• If external, can measures be quantitatively linked to a receptor?
• If internal, can measures be linked to a source?
Good examples of exposomics research should be featured
Integrated studies (external and internal) should be encouraged
Explicit curricula should be developed and disseminated
-------
SERA
United States
Environmental Protection
Agency
sS
^DS7"^,
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s
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w
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^ PRO^°
This work was
supported, in
part, by ORD's
Pathfinder
Innovation
Program (PIP)
and an ORD
EMVL award
Contributing Researchers
EPA ORD
Hussein Al-Ghoul*
Alex Chao*
Louis Groff*
Jarod Grossman*
Kristin Isaacs
Sarah Laughlin*
Hannah Liberatore
Charles Lowe
James McCord
Kelsey Miller
Jeff Minucci
Seth Newton
Katherine Phillips
Allison Phillips*
Tom Purucker
Randolph Singh*
Mark Strynar
Elin Ulrich
Nelson Yeung*
EPA ORD (cont.)
Chris Grulke
Kamel Mansouri*
Andrew McEachran*
Ann Richard
Adam Swank
John Wambaugh
Antony Williams
Agilent
Jarod Grossman
Andrew McEachran
GDIT
llya Balabin
Tom Transue
Tommy Cathey
* = ORISE/ORALJ
-------
Questions?
sobus.jon@epa.gov
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The views expressed in this presentation are those of the
author and do not necessarily represent the views or policies
of the U.S. Environmental Protection Agency.
------- |