{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T09:28:04Z","timestamp":1785403684768,"version":"3.56.0"},"reference-count":108,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T00:00:00Z","timestamp":1779926400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["5UG3OD023285"],"award-info":[{"award-number":["5UG3OD023285"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["5P42ES030991"],"award-info":[{"award-number":["5P42ES030991"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["1P30ES036084"],"award-info":[{"award-number":["1P30ES036084"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"award":["5UG3OD023285"],"award-info":[{"award-number":["5UG3OD023285"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["5P42ES030991"],"award-info":[{"award-number":["5P42ES030991"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["1P30ES036084"],"award-info":[{"award-number":["1P30ES036084"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cells"],"abstract":"<jats:p>Early mammalian embryos are highly sensitive to environmental, metabolic, hormonal, and genomic stress, yet embryo assessment during In Vitro Fertilization (IVF) relies largely on morphology and ploidy for embryo assessment, but these tests incompletely predict miscarriage. We present a transcriptomics based framework to classify and quantify lineage-specific stress in early embryos by benchmarking human preimplantation embryos against dose-, time-, and quality-dependent stress programs defined in Embryonic and placental Trophoblast Stem Cells (ESCs, TSCs) from the implanting blastocyst. Human embryos and stressed ESCs and TSCs are screened using transcriptomic markers from eleven biologically distinct stress Gene Ontology (GO) groups that define functional stress states and enable quantification of pathway presence and upregulation, pathway activity, and downstream outcomes. This framework determines whether the Integrated Stress Response (ISR), once initiated, resolves to enable the Developmentally Associated Stress Response (DASR). High-throughput screening (HTS) titrates stress to define increasingly risky yet biologically equivalent doses for levels of diminished stem cell growth across mechanistically diverse stressors. Then bulk RNA seq derives lineage specific transcriptomic markers putatively respond to common levels of diminished growth and that distinguish weak vs. strong stress and resolved vs. unresolved ISR. These stem cell transcriptomic signatures are applied to bulk RNA seq data from IVF embryos graded for morphology or adhesion, enabling quantitative inference of stress burden, lineage vulnerability, and developmental trajectory.<\/jats:p>","DOI":"10.3390\/cells15110996","type":"journal-article","created":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T03:37:29Z","timestamp":1780544249000},"page":"996","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Systematic Methods to Resolve Lineage-Specific Stress States in Early Mammalian Embryos and That May Enable Miscarriage Prediction"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3674-7854","authenticated-orcid":false,"given":"Ximena L.","family":"Ruden","sequence":"first","affiliation":[{"name":"Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, 275 East Hancock Street, Detroit, MI 48201, USA"},{"name":"Reproductive Stress Inc., Grosse Pointe Farms, MI 48236, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Campbell","family":"Coddington","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Chemistry, University of California, San Diego, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynessa","family":"Asplund","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, 275 East Hancock Street, Detroit, MI 48201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anjie","family":"Dinakin","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, 275 East Hancock Street, Detroit, MI 48201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0864-5394","authenticated-orcid":false,"given":"Awoniyi O.","family":"Awonuga","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, 275 East Hancock Street, Detroit, MI 48201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0070-437X","authenticated-orcid":false,"given":"Douglas M.","family":"Ruden","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, 275 East Hancock Street, Detroit, MI 48201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8895-6052","authenticated-orcid":false,"given":"Steven J.","family":"Korzeniewski","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, 275 East Hancock Street, Detroit, MI 48201, USA"},{"name":"Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI 48201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4974-2745","authenticated-orcid":false,"given":"Lijun","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth E.","family":"Puscheck","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, 275 East Hancock Street, Detroit, MI 48201, USA"},{"name":"Reproductive Stress Inc., Grosse Pointe Farms, MI 48236, USA"},{"name":"InVia Fertility, Chicago, IL 60618, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel A.","family":"Rappolee","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, 275 East Hancock Street, Detroit, MI 48201, USA"},{"name":"Reproductive Stress Inc., Grosse Pointe Farms, MI 48236, USA"},{"name":"Department of Physiology, Wayne State University, Detroit, MI 48201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.1002\/bdr2.2079","article-title":"Using high throughput screens to predict miscarriages with placental stem cells and long-term stress effects with embryonic stem cells","volume":"114","author":"Puscheck","year":"2022","journal-title":"Birth Defects Res."},{"key":"ref_2","unstructured":"National Research Council (U.S.) (2007). Committee on Toxicity Testing and Assessment of Environmental Agents. Toxicity Testing in the 21st Century: A Vision and a Strategy, National Academies Press."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1093\/toxsci\/kfn255","article-title":"Toxicity Testing in the 21st Century: Bringing the Vision to Life","volume":"107","author":"Andersen","year":"2008","journal-title":"Toxicol. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1093\/toxsci\/kfp140","article-title":"Cellular Stress Response Pathway System as a Sentinel Ensemble in Toxicological Screening","volume":"111","author":"Simmons","year":"2009","journal-title":"Toxicol. Sci."},{"key":"ref_5","first-page":"1","article-title":"Novel kinetic and developmental transcriptomic pan-stress responses by embryonic stem cells","volume":"15","author":"Singh","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Puscheck, E.E., Awonuga, A.O., Yang, Y., Jiang, Z., and Rappolee, D.A. (2015). Molecular biology of the stress response in the early embryo and its stem cells. Cell Signaling During Mammalian Early Embryo Development, Springer.","DOI":"10.1007\/978-1-4939-2480-6_4"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"10425","DOI":"10.1038\/ncomms10425","article-title":"Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization","volume":"7","author":"Huang","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1089\/scd.2021.0330","article-title":"Using Live Imaging and Fluorescence Ubiquitinated Cell Cycle Indicator Embryonic Stem Cells to Distinguish G1 Cell Cycle Delays for General Stressors like Perfluoro-Octanoic Acid and Hyperosmotic Sorbitol or G2 Cell Cycle Delay for Mutagenic Stressors like Benzo(a)pyrene","volume":"31","author":"Abdulhasan","year":"2022","journal-title":"Stem Cells Dev."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Abdulhasan, M., Ruden, X., You, Y., Harris, S.M., Ruden, D.M., Awonuga, A.O., Alvero, A., Puscheck, E.E., and Rappolee, D.A. (2021). Using Live Imaging and FUCCI Embryonic Stem Cells to Rank DevTox Risks: Adverse Growth Effects of PFOA Compared With DEP Are 26 Times Faster, 1,000 Times More Sensitive, and 13 Times Greater in Magnitude. Front. Toxicol., 3.","DOI":"10.3389\/ftox.2021.709747"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1089\/scd.2018.0157","article-title":"Stress Forces First Lineage Differentiation of Mouse Embryonic Stem Cells; Validation of a High-Throughput Screen for Toxicant Stress","volume":"28","author":"Li","year":"2019","journal-title":"Stem Cells Dev."},{"key":"ref_11","unstructured":"Faqi, A. (2016). High throughput screens for embryonic stem cells; stress-forced potency-stemness loss enables toxicological assays. Methods in Toxicology and Pharmacology, Springer."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1089\/scd.2015.0169","article-title":"Development and Validation of a Rex1-RFP Potency Activity Reporter Assay That Quantifies Stress-Forced Potency Loss in Mouse Embryonic Stem Cells","volume":"25","author":"Li","year":"2015","journal-title":"Stem Cells Dev."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.placenta.2023.12.020","article-title":"Novel high throughput screen reports that benzo(a)pyrene overrides mouse trophoblast stem cell multipotency, inducing SAPK activity, HAND1 and differentiated trophoblast giant cells","volume":"152","author":"Kidder","year":"2024","journal-title":"Placenta"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1038\/nature10291","article-title":"A Jurassic eutherian mammal and divergence of marsupials and placentals","volume":"476","author":"Luo","year":"2011","journal-title":"Nature"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"102419","DOI":"10.1016\/j.stemcr.2025.102419","article-title":"Tracking and mitigating imprint erasure during induction of naive human pluripotency at single-cell resolution","volume":"20","author":"Fischer","year":"2025","journal-title":"Stem Cell Rep."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"111645","DOI":"10.1016\/j.yexcr.2019.111645","article-title":"Recent insights into the na\u00efve state of human pluripotency and its applications","volume":"385","author":"Dong","year":"2019","journal-title":"Exp. Cell Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e2409","DOI":"10.1002\/bdr2.2409","article-title":"A Single Cell Transcriptomic Fingerprint of Stressed Premature, Imbalanced Differentiation of Embryonic Stem Cells","volume":"116","author":"Ruden","year":"2024","journal-title":"Birth Defects Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1093\/toxsci\/kfq188","article-title":"The Vision of Toxicity Testing in the 21st Century: Moving from Discussion to Action","volume":"117","author":"Andersen","year":"2010","journal-title":"Toxicol. Sci."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Singh, A., Rappolee, D.A., and Ruden, D.M. (2023). Epigenetic Reprogramming in Mice and Humans: From Fertilization to Primordial Germ Cell Development. Cells, 12.","DOI":"10.3390\/cells12141874"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"113701","DOI":"10.1016\/j.celrep.2024.113701","article-title":"Molecular profiling of human blastocysts reveals primitive endoderm defects among embryos of decreased implantation potential","volume":"43","author":"Chousal","year":"2024","journal-title":"Cell Rep."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/j.devcel.2025.08.004","article-title":"Efficient stem cell-derived mouse embryo models for environmental studies","volume":"61","author":"Jorgensen","year":"2025","journal-title":"Dev. Cell"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1584","DOI":"10.1038\/s41596-023-00802-1","article-title":"Generating human blastoids modeling blastocyst-stage embryos and implantation","volume":"18","author":"Khoei","year":"2023","journal-title":"Nat. Protoc."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1016\/j.fertnstert.2013.11.004","article-title":"The nature of aneuploidy with increasing age of the female partner: A review of 15,169 consecutive trophectoderm biopsies evaluated with comprehensive chromosomal screening","volume":"101","author":"Franasiak","year":"2014","journal-title":"Fertil. Steril."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1016\/j.fertnstert.2013.04.039","article-title":"Cleavage-stage biopsy significantly impairs human embryonic implantation potential while blastocyst biopsy does not: A randomized and paired clinical trial","volume":"100","author":"Scott","year":"2013","journal-title":"Fertil. Steril."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"109233","DOI":"10.1016\/j.celrep.2021.109233","article-title":"Probing the signaling requirements for naive human pluripotency by high-throughput chemical screening","volume":"35","author":"Khan","year":"2021","journal-title":"Cell Rep."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.stem.2014.07.002","article-title":"Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency","volume":"15","author":"Theunissen","year":"2014","journal-title":"Cell Stem Cell"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1038\/s41586-021-04267-8","article-title":"Human blastoids model blastocyst development and implantation","volume":"601","author":"Kagawa","year":"2021","journal-title":"Nature"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"103690","DOI":"10.1016\/j.ejmg.2019.103690","article-title":"Endocervical trophoblast for interrogating the fetal genome and assessing pregnancy health at five weeks","volume":"62","author":"Kadam","year":"2019","journal-title":"Eur. J. Med. Genet."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"32382","DOI":"10.1038\/srep32382","article-title":"Altered Biomarkers in Trophoblast Cells Obtained Noninvasively Prior to Clinical Manifestation of Perinatal Disease","volume":"6","author":"Bolnick","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/j.fertnstert.2015.05.010","article-title":"Noninvasive detection of trophoblast protein signatures linked to early pregnancy loss using trophoblast retrieval and isolation from the cervix (TRIC)","volume":"104","author":"Fritz","year":"2015","journal-title":"Fertil. Steril."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1093\/humupd\/dmy008","article-title":"Trophoblast retrieval and isolation from the cervix: Origins of cervical trophoblasts and their potential value for risk assessment of ongoing pregnancies","volume":"24","author":"Moser","year":"2018","journal-title":"Hum. Reprod. Updat."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.molcel.2005.03.027","article-title":"AMP-Activated Protein Kinase Induces a p53-Dependent Metabolic Checkpoint","volume":"18","author":"Jones","year":"2005","journal-title":"Mol. Cell"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1113\/jphysiol.2006.108324","article-title":"AMPK and cell proliferation\u2013AMPK as a therapeutic target for atherosclerosis and cancer","volume":"574","author":"Motoshima","year":"2006","journal-title":"J. Physiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1158\/1541-7786.MCR-15-0479","article-title":"AMPK Causes Cell Cycle Arrest in LKB1-Deficient Cells via Activation of CAMKK2","volume":"14","author":"Fogarty","year":"2016","journal-title":"Mol. Cancer Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/nature11675","article-title":"Coordinated control of replication and transcription by a SAPK protects genomic integrity","volume":"493","author":"Duch","year":"2012","journal-title":"Nature"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3572","DOI":"10.1091\/mbc.e09-02-0129","article-title":"The Stress-activated Protein Kinase Hog1 Mediates S Phase Delay in Response to Osmostress","volume":"20","author":"Yaakov","year":"2009","journal-title":"Mol. Biol. Cell"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1016\/j.fertnstert.2004.08.038","article-title":"Increases in phosphorylation of SAPK\/JNK and p38MAPK correlate negatively with mouse embryo development after culture in different media","volume":"83","author":"Wang","year":"2005","journal-title":"Fertil. Steril."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1093\/molehr\/gal021","article-title":"Effects of SAPK\/JNK inhibitors on preimplantation mouse embryo development are influenced greatly by the amount of stress induced by the media","volume":"12","author":"Xie","year":"2006","journal-title":"Mol. Hum. Reprod."},{"key":"ref_39","first-page":"72","article-title":"Entire mitogen activated protein kinase (mapk) pathway is present in preimplantation mouse embryos","volume":"231","author":"Wang","year":"2004","journal-title":"Dev. Dyn. Off. Publ. Am. Assoc. Anat."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"110359","DOI":"10.1016\/j.isci.2024.110359","article-title":"Stress granules in cancer: Adaptive dynamics and therapeutic implications","volume":"27","author":"Jia","year":"2024","journal-title":"iScience"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1093\/biolre\/ioaf057","article-title":"Diverse roles of stress-responsive RNP granules in oogenesis and infertility","volume":"112","author":"Glineburg","year":"2025","journal-title":"Biol. Reprod."},{"key":"ref_42","first-page":"e111802","article-title":"Cytosolic stress granules relieve the ubiquitin-proteasome system in the nuclear compartment","volume":"42","author":"Xu","year":"2022","journal-title":"EMBO J."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1038\/s41556-024-01418-7","article-title":"Mammalian IRE1\u03b1 dynamically and functionally coalesces with stress granules","volume":"26","author":"Liu","year":"2024","journal-title":"Nat. Cell Biol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1042\/BJ20081386","article-title":"How mitochondria produce reactive oxygen species","volume":"417","author":"Murphy","year":"2009","journal-title":"Biochem. J."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/j.molcel.2012.09.025","article-title":"Physiological roles of mitochondrial reactive oxygen species","volume":"48","author":"Sena","year":"2012","journal-title":"Mol. Cell"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Scial\u00f2, F., Fern\u00e1ndez-Ayala, D.J., and Sanz, A. (2017). Role of Mitochondrial Reverse Electron Transport in ROS Signaling: Potential Roles in Health and Disease. Front. Physiol., 8.","DOI":"10.3389\/fphys.2017.00428"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e000693","DOI":"10.1161\/JAHA.113.000693","article-title":"Dual Modulation of the Mitochondrial Permeability Transition Pore and Redox Signaling Synergistically Promotes Cardiomyocyte Differentiation From Pluripotent Stem Cells","volume":"3","author":"Cho","year":"2014","journal-title":"J. Am. Hear. Assoc."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"11165","DOI":"10.1038\/ncomms11165","article-title":"Mouse model of chromosome mosaicism reveals lineage-specific depletion of aneuploid cells and normal developmental potential","volume":"7","author":"Bolton","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1038\/s41556-021-00660-7","article-title":"Depletion of aneuploid cells in human embryos and gastruloids","volume":"23","author":"Yang","year":"2021","journal-title":"Nat. Cell Biol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1093\/molehr\/5.2.125","article-title":"Detection of benzo[a]pyrene diol epoxide-DNA adducts in embryos from smoking couples: Evidence for transmission by spermatozoa","volume":"5","author":"Zenzes","year":"1999","journal-title":"Mol. Hum. Reprod."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1093\/humupd\/6.2.122","article-title":"Smoking and reproduction: Gene damage to human gametes and embryos","volume":"6","author":"Zenzes","year":"2000","journal-title":"Hum. Reprod. Updat."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1289\/ehp.99107s3451","article-title":"Molecular epidemiologic research on the effects of environmental pollutants on the fetus","volume":"107","author":"Perera","year":"1999","journal-title":"Environ. Heal. Perspect."},{"key":"ref_53","first-page":"207","article-title":"Association between polycyclic aromatic hydrocarbon-DNA adduct levels in maternal and newborn white blood cells and glutathione s-transferase p1 and cyp1a1 polymorphisms","volume":"9","author":"Whyatt","year":"2000","journal-title":"Cancer Epidemiol. Biomark. Prev."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1016\/j.fertnstert.2014.11.013","article-title":"Benzo(a)pyrene disrupts mouse preimplantation embryo development","volume":"103","author":"Zhan","year":"2015","journal-title":"Fertil. Steril."},{"key":"ref_55","first-page":"84","article-title":"Exposure to phthalate mixtures impairs mouse preimplantation embryonic development in an in vitro model","volume":"114","author":"Richardson","year":"2025","journal-title":"Biol. Reprod."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1093\/humupd\/dmab046","article-title":"DNA damage in preimplantation embryos and gametes: Specification, clinical relevance and repair strategies","volume":"28","author":"Musson","year":"2022","journal-title":"Hum. Reprod. Updat."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1374","DOI":"10.15252\/embr.201642195","article-title":"The integrated stress response","volume":"17","author":"Koryga","year":"2016","journal-title":"EMBO Rep."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1038\/s41586-025-08794-6","article-title":"Plasticity of the mammalian integrated stress response","volume":"641","author":"Chen","year":"2025","journal-title":"Nature"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"eaat5314","DOI":"10.1126\/science.aat5314","article-title":"The integrated stress response: From mechanism to disease","volume":"368","author":"Walter","year":"2020","journal-title":"Science"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1016\/S1097-2765(00)00108-8","article-title":"Regulated Translation Initiation Controls Stress-Induced Gene Expression in Mammalian Cells","volume":"6","author":"Harding","year":"2000","journal-title":"Mol. Cell"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.tcb.2003.11.001","article-title":"A trip to the ER: Coping with stress","volume":"14","author":"Rutkowski","year":"2004","journal-title":"Trends Cell Biol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.molcel.2017.06.017","article-title":"The Unfolded Protein Response and Cell Fate Control","volume":"69","author":"Hetz","year":"2018","journal-title":"Mol. Cell"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/nrm2199","article-title":"Signal integration in the endoplasmic reticulum unfolded protein response","volume":"8","author":"Ron","year":"2007","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1126\/science.1209038","article-title":"The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation","volume":"334","author":"Walter","year":"2011","journal-title":"Science"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.1016\/j.celrep.2013.03.024","article-title":"Stress-independent activation of xbp1s and\/or atf6 reveals three functionally diverse er proteostasis environments","volume":"3","author":"Shoulders","year":"2013","journal-title":"Cell Rep."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/nrm.2017.110","article-title":"The mitochondrial UPR: Mechanisms, physiological functions and implications in ageing","volume":"19","author":"Shpilka","year":"2017","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1062","DOI":"10.1126\/science.1219855","article-title":"Mitochondrial fission, fusion, and stress","volume":"337","author":"Youle","year":"2012","journal-title":"Science"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"102145","DOI":"10.1016\/j.arr.2023.102145","article-title":"Mitochondria as a sensor, a central hub and a biological clock in psychological stress-accelerated aging","volume":"93","author":"Liu","year":"2023","journal-title":"Ageing Res. Rev."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1097\/PSY.0000000000000545","article-title":"Psychological Stress and Mitochondria: A Systematic Review","volume":"80","author":"Picard","year":"2018","journal-title":"Psychosom. Med."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.tem.2015.12.001","article-title":"Mitochondrial Dynamics and Metabolic Regulation","volume":"27","author":"Wai","year":"2016","journal-title":"Trends Endocrinol. Metab."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1038\/35041687","article-title":"Oxidants, oxidative stress and the biology of ageing","volume":"408","author":"Finkel","year":"2000","journal-title":"Nature"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"R453","DOI":"10.1016\/j.cub.2014.03.034","article-title":"ROS Function in Redox Signaling and Oxidative Stress","volume":"24","author":"Schieber","year":"2014","journal-title":"Curr. Biol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"2977","DOI":"10.1016\/j.bbamcr.2016.09.012","article-title":"Activation of apoptosis signalling pathways by reactive oxygen species","volume":"1863","year":"2016","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1023\/A:1009616228304","article-title":"Role of reactive oxygen species (ROS) in apoptosis induction","volume":"5","author":"Simon","year":"2000","journal-title":"Apoptosis"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1126\/science.1160809","article-title":"Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation","volume":"324","author":"Cantley","year":"2009","journal-title":"Science"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1016\/j.stem.2016.08.008","article-title":"Glycolytic Metabolism Plays a Functional Role in Regulating Human Pluripotent Stem Cell State","volume":"19","author":"Gu","year":"2016","journal-title":"Cell Stem Cell"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1111\/j.1749-6632.2009.05039.x","article-title":"Mitochondrial metabolism and cancer","volume":"1177","author":"Weinberg","year":"2009","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"3412","DOI":"10.1038\/s41596-024-01137-1","article-title":"CellPhoneDB v5: Inferring cell\u2013cell communication from single-cell multiomics data","volume":"20","author":"Petryszak","year":"2025","journal-title":"Nat. Protoc."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"1484","DOI":"10.1038\/s41596-020-0292-x","article-title":"CellPhoneDB: Inferring cell\u2013cell communication from combined expression of multi-subunit ligand\u2013receptor complexes","volume":"15","author":"Efremova","year":"2020","journal-title":"Nat. Protoc."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/nmeth.4463","article-title":"SCENIC: Single-cell regulatory network inference and clustering","volume":"14","author":"Aibar","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"4010","DOI":"10.1016\/j.cell.2024.05.051","article-title":"The primitive endoderm supports lineage plasticity to enable regulative development","volume":"187","author":"Sell","year":"2024","journal-title":"Cell"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"eabj3725","DOI":"10.1126\/sciadv.abj3725","article-title":"Primary specification of blastocyst trophectoderm by scRNA-seq: New insights into embryo implantation","volume":"8","author":"Liu","year":"2022","journal-title":"Sci. Adv."},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Khatri, P., Sirota, M., and Butte, A.J. (2012). Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges. PLoS Comput. Biol., 8.","DOI":"10.1371\/journal.pcbi.1002375"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1093\/bioinformatics\/btl633","article-title":"Enrichment or depletion of a GO category within a class of genes: Which test?","volume":"23","author":"Rivals","year":"2006","journal-title":"Bioinformatics"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/ng1180","article-title":"PGC-1\u03b1-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes","volume":"34","author":"Mootha","year":"2003","journal-title":"Nat. Genet."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1038\/s41586-019-0933-9","article-title":"A single-cell molecular map of mouse gastrulation and early organogenesis","volume":"566","author":"Griffiths","year":"2019","journal-title":"Nature"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nbt.2859","article-title":"The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells","volume":"32","author":"Trapnell","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1038\/s41596-018-0103-9","article-title":"Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap","volume":"14","author":"Reimand","year":"2019","journal-title":"Nat. Protoc."},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"H\u00e4nzelmann, S., Castelo, R., and Guinney, J. (2013). GSVA: Gene set variation analysis for microarray and RNA-Seq data. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-7"},{"key":"ref_91","doi-asserted-by":"crossref","unstructured":"Foroutan, M., Bhuva, D.D., Lyu, R., Horan, K., Cursons, J., and Davis, M.J. (2018). Single sample scoring of molecular phenotypes. BMC Bioinform., 19.","DOI":"10.1186\/s12859-018-2435-4"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","article-title":"Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets","volume":"161","author":"Macosko","year":"2015","journal-title":"Cell"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.placenta.2008.10.009","article-title":"Hyperosmolar Stress Induces Global mRNA Responses in Placental Trophoblast Stem Cells that Emulate Early Post-implantation Differentiation","volume":"30","author":"Liu","year":"2009","journal-title":"Placenta"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/1471-2105-7-30","article-title":"WholePathwayScope: A comprehensive pathway-based analysis tool for high-throughput data","volume":"7","author":"Yi","year":"2006","journal-title":"BMC Bioinform."},{"key":"ref_96","doi-asserted-by":"crossref","unstructured":"Toro-Dom\u00ednguez, D., Wang, C., Ellson-Lancho, I., Martorell-Marug\u00e1n, J., L\u00f3pez-Dom\u00ednguez, R., Carmona-S\u00e1ez, P., Alarc\u00f3n-Riquelme, M.E., and Baribaud, F. (2025). Benchmarking single-sample gene set scoring methods for application in precision medicine. Brief. Bioinform., 26.","DOI":"10.1093\/bib\/bbaf684"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1093\/bioinformatics\/btl567","article-title":"Using GOstats to test gene lists for GO term association","volume":"23","author":"Falcon","year":"2006","journal-title":"Bioinformatics"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using david bioinformatics resources","volume":"4","author":"Sherman","year":"2009","journal-title":"Nat. Protoc."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"D419","DOI":"10.1093\/nar\/gky1038","article-title":"PANTHER version 14: More genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools","volume":"47","author":"Mi","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"W191","DOI":"10.1093\/nar\/gkz369","article-title":"g:Profiler: A web server for functional enrichment analysis and conversions of gene lists (2019 update)","volume":"47","author":"Raudvere","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1016\/j.celrep.2017.07.009","article-title":"Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation","volume":"20","author":"Mohammed","year":"2017","journal-title":"Cell Rep."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1016\/j.devcel.2011.10.019","article-title":"Primitive Endoderm Differentiates via a Three-Step Mechanism Involving Nanog and RTK Signaling","volume":"21","author":"Frankenberg","year":"2011","journal-title":"Dev. Cell"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1016\/j.devcel.2017.05.003","article-title":"Lineage Establishment and Progression within the Inner Cell Mass of the Mouse Blastocyst Requires FGFR1 and FGFR2","volume":"41","author":"Kang","year":"2017","journal-title":"Dev. Cell"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/s41586-019-1127-1","article-title":"The emergent landscape of the mouse gut endoderm at single-cell resolution","volume":"569","author":"Nowotschin","year":"2019","journal-title":"Nature"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.ydbio.2011.10.015","article-title":"BMP4 signaling directs primitive endoderm-derived XEN cells to an extraembryonic visceral endoderm identity","volume":"361","author":"Artus","year":"2012","journal-title":"Dev. Biol."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.ydbio.2023.07.002","article-title":"Transcriptional network governing extraembryonic endoderm cell fate choice","volume":"502","author":"Pham","year":"2023","journal-title":"Dev. Biol."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.1002\/j.1460-2075.1986.tb04383.x","article-title":"Evidence from molecular cloning that SPARC, a major product of mouse embryo parietal endoderm, is related to an endothelial cell \u2018culture shock\u2019 glycoprotein of Mr 43,000","volume":"5","author":"Mason","year":"1986","journal-title":"EMBO J."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"e2205371120","DOI":"10.1073\/pnas.2205371120","article-title":"Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development","volume":"120","author":"Kim","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Cells"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4409\/15\/11\/996\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T04:12:15Z","timestamp":1780719135000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4409\/15\/11\/996"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,28]]},"references-count":108,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2026,6]]}},"alternative-id":["cells15110996"],"URL":"https:\/\/doi.org\/10.3390\/cells15110996","relation":{},"ISSN":["2073-4409"],"issn-type":[{"value":"2073-4409","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,28]]}}}