Systematic Methods to Resolve Lineage-Specific Stress States in Early Mammalian Embryos and That May Enable Miscarriage Prediction

Ruden, Ximena L.; Coddington, Campbell; Asplund, Lynessa; Dinakin, Anjie; Awonuga, Awoniyi O.; Ruden, Douglas M.; Korzeniewski, Steven J.; Zhang, Lijun; Puscheck, Elizabeth E.; Rappolee, Daniel A.

doi:10.3390/cells15110996

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Systematic Methods to Resolve Lineage-Specific Stress States in Early Mammalian Embryos and That May Enable Miscarriage Prediction

by

Ximena L. Ruden

^1,2

,

Campbell Coddington

³,

Lynessa Asplund

¹,

Anjie Dinakin

¹,

Awoniyi O. Awonuga

¹

,

Douglas M. Ruden

¹

,

Steven J. Korzeniewski

^1,4

,

Lijun Zhang

⁵

,

Elizabeth E. Puscheck

^1,2,6 and

Daniel A. Rappolee

^1,2,7,*

¹

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

²

Reproductive Stress Inc., Grosse Pointe Farms, MI 48230, USA

³

Department of Pharmaceutical Chemistry, University of California, San Diego, CA 92093, USA

⁴

Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI 48201, USA

⁵

Department of Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA

⁶

InVia Fertility, Chicago, IL 60618, USA

⁷

Department of Physiology, Wayne State University, Detroit, MI 48201, USA

^*

Author to whom correspondence should be addressed.

Cells 2026, 15(11), 996; https://doi.org/10.3390/cells15110996 (registering DOI)

Submission received: 7 April 2026 / Revised: 14 May 2026 / Accepted: 22 May 2026 / Published: 28 May 2026

(This article belongs to the Special Issue Cellular Stress Responses in Early Embryonic and Stem Cell Development)

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Abstract

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.

Keywords: transcriptomic analyses; stress; developmental stem cells; trophoblast stem cells (TSCs); embryonic stem cells (ESCs); miscarriage; systematic stress classification and prediction; high-throughput screening (HTS); differentially expressed gene (DEG); NOAEL; LOAEL; IC50; gene ontology

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MDPI and ACS Style

Ruden, X.L.; Coddington, C.; Asplund, L.; Dinakin, A.; Awonuga, A.O.; Ruden, D.M.; Korzeniewski, S.J.; Zhang, L.; Puscheck, E.E.; Rappolee, D.A. Systematic Methods to Resolve Lineage-Specific Stress States in Early Mammalian Embryos and That May Enable Miscarriage Prediction. Cells 2026, 15, 996. https://doi.org/10.3390/cells15110996

AMA Style

Ruden XL, Coddington C, Asplund L, Dinakin A, Awonuga AO, Ruden DM, Korzeniewski SJ, Zhang L, Puscheck EE, Rappolee DA. Systematic Methods to Resolve Lineage-Specific Stress States in Early Mammalian Embryos and That May Enable Miscarriage Prediction. Cells. 2026; 15(11):996. https://doi.org/10.3390/cells15110996

Chicago/Turabian Style

Ruden, Ximena L., Campbell Coddington, Lynessa Asplund, Anjie Dinakin, Awoniyi O. Awonuga, Douglas M. Ruden, Steven J. Korzeniewski, Lijun Zhang, Elizabeth E. Puscheck, and Daniel A. Rappolee. 2026. "Systematic Methods to Resolve Lineage-Specific Stress States in Early Mammalian Embryos and That May Enable Miscarriage Prediction" Cells 15, no. 11: 996. https://doi.org/10.3390/cells15110996

APA Style

Ruden, X. L., Coddington, C., Asplund, L., Dinakin, A., Awonuga, A. O., Ruden, D. M., Korzeniewski, S. J., Zhang, L., Puscheck, E. E., & Rappolee, D. A. (2026). Systematic Methods to Resolve Lineage-Specific Stress States in Early Mammalian Embryos and That May Enable Miscarriage Prediction. Cells, 15(11), 996. https://doi.org/10.3390/cells15110996

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Systematic Methods to Resolve Lineage-Specific Stress States in Early Mammalian Embryos and That May Enable Miscarriage Prediction

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