{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:08:43Z","timestamp":1792786123468,"version":"4.5.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"2","funder":[{"name":"Chemical Safety for Sustainability National Research Program"},{"DOI":"10.13039\/100000139","name":"U.S. Environmental Protection Agency","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000139","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>There is growing interest in introducing efficiencies in chemical safety assessment by reducing reliance on conventional chronic toxicity tests. One approach involves benchmark dose (BMD) analysis of gene expression data from short-term adult animal studies to assess chronic toxicity. Whether this approach applies to chemicals that cause developmental and reproductive toxicity (DART), such as dicyclohexyl phthalate (DCHP), is unknown. The present study aimed to (i) investigate how well BMD analysis of gene expression data performed at indicating DART potency using an in utero rat exposure (gestational days 14 to 18 at 0, 100, 300, 600, and 900\u2009mg DCHP\/kg-day), and (ii) inform new key events in phthalate syndrome through use of targeted RNA-sequencing. A sub-aim evaluated the consistency of existing polymerase chain reaction array vs. targeted RNA-sequencing data, which were relatively similar. BMD analysis identified gene set points-of-departure (PODs) of 10.4 and 24.7\u2009mg\/kg-day, which were similar to some of the lowest PODs for DCHP DART endpoints at 10\u2009mg\/kg-day. Further analysis of targeted RNA-sequencing results identified Testin (found in Sertoli cell junctions) as one of a few significantly upregulated genes. Upstream regulator analysis predicted inhibition of SREBPs and gonadotropins, consistent with downregulation of steroidogenesis genes and testosterone production. These results show that transcriptomics can quickly identify a gene set POD comparable to that of DART PODs while also discovering upregulation of Testin as a putative mediator of rodent phthalate syndrome. These data present an important first step to evaluating a transcriptomic approach as an efficient and cost-effective means to assess chemical impacts related to DART.<\/jats:p>","DOI":"10.1093\/toxsci\/kfaf106","type":"journal-article","created":{"date-parts":[[2025,7,19]],"date-time":"2025-07-19T11:56:40Z","timestamp":1752926200000},"page":"372-382","source":"Crossref","is-referenced-by-count":2,"title":["Targeted RNA-sequencing of testes from fetal rats exposed to dicyclohexyl phthalate informs potency and adverse outcome pathway development"],"prefix":"10.1093","volume":"207","author":[{"given":"Carolyn R","family":"Waterbury","sequence":"first","affiliation":[{"name":"Oak Ridge Associated Universities, U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure , Research Triangle Park, NC 27711,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miles N","family":"Crockett","sequence":"additional","affiliation":[{"name":"Oak Ridge Associated Universities, U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure , Research Triangle Park, NC 27711,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6622-5769","authenticated-orcid":false,"given":"Justin M","family":"Conley","sequence":"additional","affiliation":[{"name":"U.S. Environmental Protection Agency, Office of Research and Development, Center for Public Health and Environmental Assessment , Research Triangle Park, NC 27711,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christy S","family":"Lambright","sequence":"additional","affiliation":[{"name":"U.S. Environmental Protection Agency, Office of Research and Development, Center for Public Health and Environmental Assessment , Research Triangle Park, NC 27711,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1529-2387","authenticated-orcid":false,"given":"Leah C","family":"Wehmas","sequence":"additional","affiliation":[{"name":"U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure , Research Triangle Park, NC 27711,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,7,21]]},"reference":[{"key":"2025092615322441600_kfaf106-B1","author":"Alliance of Genome Resources Consortium","year":"2024"},{"key":"2025092615322441600_kfaf106-B2","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1093\/toxsci\/kft182","article-title":"Concordance of transcriptional and apical benchmark dose levels for conazole-induced liver effects in mice","volume":"136","author":"Bhat","year":"2013","journal-title":"Toxicol Sci"},{"key":"2025092615322441600_kfaf106-B3","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1038\/nprot.2009.97","article-title":"Mapping identifiers for the integration of genomic datasets with the r\/bioconductor package biomart","volume":"4","author":"Durinck","year":"2009","journal-title":"Nat Protoc"},{"key":"2025092615322441600_kfaf106-B4","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1038\/s41598-017-01617-3","article-title":"Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data","volume":"7","author":"Everaert","year":"2017","journal-title":"Sci Rep"},{"key":"2025092615322441600_kfaf106-B5","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1093\/toxsci\/kfab053","article-title":"Genomic and hormonal biomarkers of phthalate-induced male rat reproductive developmental toxicity part II: a targeted RT-qPCR array approach that defines a unique adverse outcome pathway","volume":"182","author":"Gray","year":"2021","journal-title":"Toxicol Sci"},{"key":"2025092615322441600_kfaf106-B6","doi-asserted-by":"crossref","first-page":"100180","DOI":"10.1016\/j.crtox.2024.100180","article-title":"Using targeted fetal rat testis genomic and endocrine alterations to predict the effects of a phthalate mixture on the male reproductive tract","volume":"7","author":"Gray","year":"2024","journal-title":"Curr Res Toxicol"},{"key":"2025092615322441600_kfaf106-B7","doi-asserted-by":"crossref","first-page":"21040","DOI":"10.1074\/jbc.273.33.21040","article-title":"Testin secreted by Sertoli cells is associated with the cell surface, and its expression correlates with the disruption of Sertoli-germ cell junctions but not the inter-Sertoli tight junction","volume":"273","author":"Grima","year":"1998","journal-title":"J Biol Chem"},{"key":"2025092615322441600_kfaf106-B8","doi-asserted-by":"crossref","first-page":"109551","DOI":"10.1016\/j.envint.2025.109551","article-title":"Dose-response assessment of dipentyl phthalate effects on testosterone production and morphogenesis of late-gestation fetal rat testis","volume":"200","author":"Gupta","year":"2025","journal-title":"Environ Int"},{"key":"2025092615322441600_kfaf106-B9","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1093\/toxsci\/kfaa081","article-title":"Evaluation of 5-day in vivo rat liver and kidney with high-throughput transcriptomics for estimating benchmark doses of apical outcomes","volume":"176","author":"Gwinn","year":"2020","journal-title":"Toxicol Sci"},{"issue":"Spec No","key":"2025092615322441600_kfaf106-B10","doi-asserted-by":"crossref","first-page":"79","DOI":"10.2131\/jts.30.S79","article-title":"A two-generation reproductive toxicity study of dicyclohexyl phthalate in rats","volume":"30","author":"Hoshino","year":"2005","journal-title":"J Toxicol Sci"},{"key":"2025092615322441600_kfaf106-B11","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1002\/bdr2.2046","article-title":"A microrna or messenger RNA point of departure estimates an apical endpoint point of departure in a rat developmental toxicity model","volume":"114","author":"Johnson","year":"2022","journal-title":"Birth Defects Res"},{"key":"2025092615322441600_kfaf106-B12","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1093\/toxsci\/kfr020","article-title":"Species-specific dibutyl phthalate fetal testis endocrine disruption correlates with inhibition of SREBP2-dependent gene expression pathways","volume":"120","author":"Johnson","year":"2011","journal-title":"Toxicol Sci"},{"key":"2025092615322441600_kfaf106-B13","doi-asserted-by":"publisher","author":"Kassambara","year":"2023","DOI":"10.32614\/CRAN.package.rstatix"},{"key":"2025092615322441600_kfaf106-B14","doi-asserted-by":"crossref","first-page":"104655","DOI":"10.1016\/j.yrtph.2020.104655","article-title":"Short-term toxicogenomics as an alternative approach to chronic in vivo studies for derivation of points of departure: a case study in the rat with a triazole fungicide","volume":"113","author":"LaRocca","year":"2020","journal-title":"Regul Toxicol Pharmacol"},{"key":"2025092615322441600_kfaf106-B15","doi-asserted-by":"crossref","first-page":"246","DOI":"10.3390\/ijerph13030246","article-title":"Effects of in utero exposure to dicyclohexyl phthalate on rat fetal Leydig cells","volume":"13","author":"Li","year":"2016","journal-title":"Int J Environ Res Public Health"},{"key":"2025092615322441600_kfaf106-B16","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1095\/biolreprod.104.039404","article-title":"Gene expression profiling following in utero exposure to phthalate esters reveals new gene targets in the etiology of testicular dysgenesis","volume":"73","author":"Liu","year":"2005","journal-title":"Biol Reprod"},{"key":"2025092615322441600_kfaf106-B17","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for rna-seq data with deseq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2025092615322441600_kfaf106-B18","doi-asserted-by":"crossref","first-page":"12735","DOI":"10.3390\/ijms222312735","article-title":"The roles of luteinizing hormone, follicle-stimulating hormone and testosterone in spermatogenesis and folliculogenesis revisited","volume":"22","author":"Oduwole","year":"2021","journal-title":"Int J Mol Sci"},{"key":"2025092615322441600_kfaf106-B19","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1002\/jat.1436","article-title":"Differential developmental toxicities of di-n-hexyl phthalate and dicyclohexyl phthalate administered orally to rats","volume":"29","author":"Saillenfait","year":"2009","journal-title":"J Appl Toxicol"},{"key":"2025092615322441600_kfaf106-B20","doi-asserted-by":"crossref","first-page":"1758","DOI":"10.1091\/mbc.E21-03-0156","article-title":"Stress fiber strain recognition by the LIM protein testin is cryptic and mediated by RhoA","volume":"32","author":"Sala","year":"2021","journal-title":"Mol Biol Cell"},{"key":"2025092615322441600_kfaf106-B21","doi-asserted-by":"crossref","first-page":"E5685","DOI":"10.1073\/pnas.1611424113","article-title":"SCAP\/SREBP pathway is required for the full steroidogenic response to cyclic AMP","volume":"113","author":"Shimizu-Albergine","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025092615322441600_kfaf106-B22","author":"The R Core Team","year":"2024"},{"key":"2025092615322441600_kfaf106-B23","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1093\/toxsci\/kfm092","article-title":"A method to integrate benchmark dose estimates with genomic data to assess the functional effects of chemical exposure","volume":"98","author":"Thomas","year":"2007","journal-title":"Toxicol Sci"},{"key":"2025092615322441600_kfaf106-B24","author":"US Consumer Product Safety Commission","year":"2011"},{"key":"2025092615322441600_kfaf106-B25","volume-title":"Benchmark dose technical guidance. Risk Assessment Forum","author":"US EPA","year":"2012"},{"key":"2025092615322441600_kfaf106-B26","author":"US EPA","year":"2019"},{"key":"2025092615322441600_kfaf106-B27","volume-title":"High-Priority Substance Designations Under the Toxic Substances Control Act and Initiation of Risk Evaluation on High-Priority Substances. EPA-HQ-OPPT-2019-0131-0026","author":"US EPA","year":"2019"},{"key":"2025092615322441600_kfaf106-B28","author":"US EPA","year":"2023"},{"key":"2025092615322441600_kfaf106-B29","volume-title":"Scientific studies supporting development of transcriptomic points of departure for EPA transcriptomic assessment products (ETAPs).","author":"US EPA","year":"2024"},{"key":"2025092615322441600_kfaf106-B30","doi-asserted-by":"publisher","author":"US EPA","year":"2024","DOI":"10.23645\/epacomptox.25365496"},{"key":"2025092615322441600_kfaf106-B31","volume-title":"Value of information case study: human health and economic trade-offs associated with the timeliness, uncertainty, and costs of the draft EPA transcriptomic assessment product (ETAP).","author":"US EPA","year":"2024"},{"key":"2025092615322441600_kfaf106-B32","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.toxlet.2009.04.023","article-title":"Effects of in utero through lactational exposure to dicyclohexyl phthalate and p,p'-DDE in Sprague-Dawley rats","volume":"189","author":"Yamasaki","year":"2009","journal-title":"Toxicol Lett"},{"key":"2025092615322441600_kfaf106-B33","doi-asserted-by":"crossref","first-page":"e0178302","DOI":"10.1371\/journal.pone.0178302","article-title":"A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling","volume":"12","author":"Yeakley","year":"2017","journal-title":"PLoS One"},{"key":"2025092615322441600_kfaf106-B34","doi-asserted-by":"crossref","first-page":"3230","DOI":"10.1038\/ncomms4230","article-title":"A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages","volume":"5","author":"Yu","year":"2014","journal-title":"Nat Commun"}],"container-title":["Toxicological Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/toxsci\/advance-article-pdf\/doi\/10.1093\/toxsci\/kfaf106\/63811764\/kfaf106.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/toxsci\/article-pdf\/207\/2\/372\/63811764\/kfaf106.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/toxsci\/article-pdf\/207\/2\/372\/63811764\/kfaf106.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T19:32:34Z","timestamp":1758915154000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/toxsci\/article\/207\/2\/372\/8209935"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,21]]},"references-count":34,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,7,21]]},"published-print":{"date-parts":[[2025,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/toxsci\/kfaf106","relation":{},"ISSN":["1096-6080","1096-0929"],"issn-type":[{"value":"1096-6080","type":"print"},{"value":"1096-0929","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,10]]},"published":{"date-parts":[[2025,7,21]]}}}