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Frontiers in cell and developmental biology2026; 14; 1840498; doi: 10.3389/fcell.2026.1840498

Matched embryo-endometrium RNA-seq reveals coordinated but asymmetric transcriptomic reprogramming at the onset of early equine pregnancy.

Abstract: Maternal recognition of pregnancy (MRP) in the mare requires coordinated adaptations of both the conceptus and the endometrium during the peri-recognition interval; however, integrated transcriptomic analyses of both compartments within the same biological window remain limited. Here, we analyzed conceptus RNA-seq data across embryonic age (Days 8 and 12 post ovulation) and endometrial RNA-seq data across pregnancy status (pregnant versus non-pregnant mares sampled between Days 8 and 12 post ovulation). In pregnant mares, conceptus recovery and endometrial biopsy collection were performed within the same gestation, allowing biological integration of embryo and maternal transcriptomes while preserving tissue-specific statistical contrasts. Unassigned: RNA-seq analysis followed by TMM normalization and voom-limma modeling identified differential expression in both compartments. Differential expression was defined by an adjusted P-value (FDR threshold 1. Gene-level interpretation was restricted to transcripts with a Bayesian posterior probability of differential expression (B > 1). In the conceptus, high-confidence upregulated genes from day 8 to 12 included steroidogenic enzymes (), extracellular matrix components (), protease regulators (), and selective transporters (). In the endometrium, downregulated genes in pregnant mares included immediate-early transcriptional regulators () and oxidative stress-associated genes (), while upregulated genes in pregnant mares included signaling and regulatory components (), complement regulator , and mitochondrial sulfide metabolism gene . Functional enrichment analysis supported coordinated extracellular matrix organization and signaling modulation without enrichment of inflammatory pathways. Unassigned: Matched transcriptomic profiling reveals coordinated but compartment-specific gene regulation at the onset of early equine pregnancy. The conceptus exhibits endocrine and interface specialization, whereas the endometrium demonstrates attenuation of immediate-early transcriptional programs and selective signaling recalibration. These data define a high-confidence systems-level framework for early embryo-maternal communication that precedes the classical maternal recognition phase and is consistent with early embryo-maternal communication associated with the transition toward maternal recognition.
Copyright © 2026 Da Silva Álvarez, Ortiz-Rodríguez, Martín-Cano, Álvarez-Barrientos, Becerro-Rey, Gil, Redondo, Masot, Aparicio, Peña and Ortega-Ferrusola.
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Publication Date: 2026-06-18 PubMed ID: 42396560PubMed Central: PMC13325742DOI: 10.3389/fcell.2026.1840498Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This study investigates how the RNA expression profiles of both the early embryo (conceptus) and the mother’s uterine lining (endometrium) change and interact during the start of early pregnancy in horses.
  • By analyzing matched samples from both compartments in the same pregnancies, the research reveals coordinated but distinct patterns of gene expression that underlie early embryo-maternal communication before the full maternal recognition of pregnancy occurs.

Background and Purpose

  • Maternal recognition of pregnancy (MRP) in mares is a critical process requiring synchronized physiological changes between the embryo and the maternal uterus during the peri-recognition interval (around Days 8 to 12 post ovulation).
  • Earlier studies often focused on either the embryo or the endometrium separately, limiting understanding of their integrated molecular communication.
  • This research aimed to perform integrated transcriptomic profiling of both conceptus and endometrium from the same pregnancies to capture the coordinated gene regulation events at the onset of early pregnancy.

Methodology

  • Samples were collected from pregnant mares during the early window of pregnancy: embryonic tissues on Days 8 and 12 post ovulation, and endometrial tissues comparing pregnant versus non-pregnant mares sampled between Days 8 and 12.
  • RNA sequencing (RNA-seq) was performed on both the embryo and endometrial tissues.
  • Data analysis involved:
    • TMM normalization (Trimmed Mean of M-values) to normalize RNA-seq counts.
    • A voom-limma modeling framework to identify differentially expressed genes (DEGs) between conditions.
    • Stringent criteria for significance including false discovery rate (FDR) adjusted p-values and Bayesian posterior probabilities to identify high-confidence DEGs.
  • Matching samples from the same pregnancies enabled biologically relevant integration of transcriptomes while keeping tissue-specific differential expression contrasts clear.

Key Findings in the Conceptus

  • From Day 8 to Day 12, the embryo showed upregulation of several important gene categories:
    • Steroidogenic enzymes: Suggesting increasing steroid hormone biosynthesis activity supporting pregnancy.
    • Extracellular matrix (ECM) components: Indicating remodeling of the conceptus structural interface.
    • Protease regulators: Enzymes involved in controlled degradation/modification of the ECM and signaling molecules.
    • Selective transporters: Proteins facilitating nutrient and signaling molecule exchange at the maternal-fetal interface.
  • These changes reflect endocrine specialization and preparation for interface interactions essential for early pregnancy success.

Key Findings in the Endometrium

  • Comparing pregnant to non-pregnant mares, the endometrium displayed:
    • Downregulation of immediate-early transcriptional regulators: Suggesting a dampening of rapid gene activation signals.
    • Decreased expression of oxidative stress-associated genes: Indicative of reduced damaging reactive oxygen species and a protective environment.
    • Upregulation of signaling and regulatory components: Suggesting selective adjustments in cell communication pathways.
    • Increased expression of complement regulator genes: Potentially involved in controlling immune responses during early pregnancy.
    • Upregulation of mitochondrial sulfide metabolism genes: Possibly supporting cellular energy and redox balance adaptations.
  • Overall, the endometrium shows coordinated modulation of transcription and signaling without activating inflammatory pathways, promoting an environment conducive to embryo acceptance.

Functional Enrichment and Systems-Level Integration

  • Functional enrichment analysis highlighted shared but compartment-specific biological processes, especially extracellular matrix organization and signaling modulation.
  • No significant enrichment of inflammatory pathways was found, supporting the idea that early pregnancy involves immune tolerance rather than activation.
  • The conceptus and endometrium exhibit complementary gene expression changes that together prepare both tissues for the success of pregnancy.

Conclusions and Implications

  • Matched transcriptomic profiling uncovers a coordinated yet asymmetric pattern of gene regulation at the start of early equine pregnancy.
  • The conceptus focuses on developing endocrine functions and remodeling interactions at the maternal interface, while the endometrium attenuates immediate early gene responses and selectively recalibrates signaling pathways.
  • These findings depict a systems-level framework for early embryo-maternal communication that precedes and possibly facilitates the classical phase of maternal recognition of pregnancy.
  • This research provides important molecular insights that could help improve understanding of early pregnancy establishment and potentially aid in managing equine fertility.

Cite This Article

APA
Da Silva Álvarez E, Ortiz-Rodríguez JM, Martín-Cano FE, Álvarez-Barrientos A, Becerro-Rey L, Gil MC, Redondo E, Masot J, Aparicio IM, Peña FJ, Ortega-Ferrusola C. (2026). Matched embryo-endometrium RNA-seq reveals coordinated but asymmetric transcriptomic reprogramming at the onset of early equine pregnancy. Front Cell Dev Biol, 14, 1840498. https://doi.org/10.3389/fcell.2026.1840498

Publication

Frontiers in cell and developmental biology
ISSN: 2296-634X
NlmUniqueID: 101630250
Country: Switzerland
Language: English
Volume: 14
Pages: 1840498
PII: 1840498

Researcher Affiliations

Da Silva Álvarez, Eva
  • Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain.
Ortiz-Rodríguez, José M
  • Department of Veterinary Clinical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy.
Martín-Cano, Francisco E
  • Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain.
Álvarez-Barrientos, Alberto
  • Service of Techniques Applied to Biosciences, University of Extremadura, Badajoz, Spain.
Becerro-Rey, Laura
  • Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain.
Gil, María C
  • Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain.
Redondo, Eloy
  • Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain.
Masot, Javier
  • Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain.
Aparicio, Inés M
  • Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain.
Peña, Fernando J
  • Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain.
Ortega-Ferrusola, Cristina
  • Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain.

Conflict of Interest Statement

The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author FP declared that they were an editorial board member of Frontiers at the time of submission. This had no impact on the peer review process and the final decision.

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