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dc.contributor.authorBasili, Danilo
dc.contributor.authorReynolds, Joe
dc.contributor.authorHoughton, Jade
dc.contributor.authorMalcomber, Sophie
dc.contributor.authorChambers, Bryant
dc.contributor.authorLiddell, Mark
dc.contributor.authorMuller, Iris
dc.contributor.authorWhite, Andrew
dc.contributor.authorShah, Imran
dc.contributor.authorEverett, Logan J
dc.contributor.authorMiddleton, Alistair
dc.contributor.authorBender, Andreas
dc.date.accessioned2022-04-26T01:02:44Z
dc.date.available2022-04-26T01:02:44Z
dc.date.issued2022-04-18
dc.identifier.issn0893-228X
dc.identifier.other35333521
dc.identifier.otherPMC9019810
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/336443
dc.descriptionFunder: Unilever
dc.description.abstractEstimation of points of departure (PoDs) from high-throughput transcriptomic data (HTTr) represents a key step in the development of next-generation risk assessment (NGRA). Current approaches mainly rely on single key gene targets, which are constrained by the information currently available in the knowledge base and make interpretation challenging as scientists need to interpret PoDs for thousands of genes or hundreds of pathways. In this work, we aimed to address these issues by developing a computational workflow to investigate the pathway concentration-response relationships in a way that is not fully constrained by known biology and also facilitates interpretation. We employed the Pathway-Level Information ExtractoR (PLIER) to identify latent variables (LVs) describing biological activity and then investigated in vitro LVs' concentration-response relationships using the ToxCast pipeline. We applied this methodology to a published transcriptomic concentration-response data set for 44 chemicals in MCF-7 cells and showed that our workflow can capture known biological activity and discriminate between estrogenic and antiestrogenic compounds as well as activity not aligning with the existing knowledge base, which may be relevant in a risk assessment scenario. Moreover, we were able to identify the known estrogen activity in compounds that are not well-established ER agonists/antagonists supporting the use of the workflow in read-across. Next, we transferred its application to chemical compounds tested in HepG2, HepaRG, and MCF-7 cells and showed that PoD estimates are in strong agreement with those estimated using a recently developed Bayesian approach (cor = 0.89) and in weak agreement with those estimated using a well-established approach such as BMDExpress2 (cor = 0.57). These results demonstrate the effectiveness of using PLIER in a concentration-response scenario to investigate pathway activity in a way that is not fully constrained by the knowledge base and to ease the biological interpretation and support the development of an NGRA framework with the ability to improve current risk assessment strategies for chemicals using new approach methodologies.
dc.languageeng
dc.publisherAmerican Chemical Society (ACS)
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.sourcenlmid: 8807448
dc.sourceessn: 1520-5010
dc.subjectEstrogens
dc.subjectBayes Theorem
dc.subjectRisk Assessment
dc.subjectToxicogenetics
dc.subjectTranscriptome
dc.titleLatent Variables Capture Pathway-Level Points of Departure in High-Throughput Toxicogenomic Data.
dc.typeArticle
dc.date.updated2022-04-26T01:02:43Z
prism.endingPage683
prism.issueIdentifier4
prism.publicationNameChem Res Toxicol
prism.startingPage670
prism.volume35
dc.identifier.doi10.17863/CAM.83860
rioxxterms.versionofrecord10.1021/acs.chemrestox.1c00444
rioxxterms.versionVoR
rioxxterms.licenseref.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.contributor.orcidBasili, Danilo [0000-0003-4830-7848]
dc.contributor.orcidShah, Imran [0000-0003-0808-0140]
dc.contributor.orcidBender, Andreas [0000-0002-6683-7546]
dc.identifier.eissn1520-5010
cam.issuedOnline2022-03-25


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Attribution-NonCommercial-NoDerivatives 4.0 International
Except where otherwise noted, this item's licence is described as Attribution-NonCommercial-NoDerivatives 4.0 International