Biology subjects

Sun, S.

Publications and source records attributed to Sun, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

A mediterranean-mimicking diet harnesses gut microbiota-derived 3-IAA to rejuvenate T cell

Diet profoundly shapes the tumor microenvironment through metabolite modulation, yet the mechanisms linking diet, gut microbiota, and antitumor immunity remain unclear. Here, we demonstrate that a mediterranean-mimicking diet (MedDiet) suppresses tumor growth by orchestrating a microbiota-metabolite-immune axis. MedDiet selectively enriched Bacteroides thetaiotaomicron (B. thetaiotaomicron) in the gut, whose administration recapitulated tumor suppression. Both MedDiet and B. thetaiotaomicron elevated plasma levels of the tryptophan metabolite indole-3-acetic acid (3-IAA). Mechanistically, 3-IAA enhanced CD8+ T cell cytotoxicity and alleviated exhaustion by inhibiting the integrated stress response, sustaining antitumor immunity in vivo. Importantly, 3-IAA synergized with anti-PD-1 therapy to further restrain tumor progression. Finally, we developed a MedDiet Score to predict patient survival and response to immunotherapy. These findings reveal that dietary modulation of gut microbiota can reshape systemic metabolites to potentiate T cell-mediated antitumor responses. Our study identifies 3-IAA as a metabolite-based adjuvant for immune checkpoint therapy and highlights the translational potential of diet-driven immunomodulation in cancer treatment.

cancer biology↗

bioRxiv2026

Consumption of processed foods impairs memory function through dietary advanced glycation end-products

Consumption of processed foods is associated with dementia, obesity, and other negative health outcomes. Sustained heat treatment, a common food processing approach to enhance flavor, induces the chemical Maillard reaction that promotes the formation of dietary advanced glycation end-products (AGEs). The neurocognitive impacts of consuming dietary AGEs are poorly understood. Here we modeled an AGE-rich diet through heat treatment fed to rats during adolescence, a critical period of neural development, to mechanistically evaluate the long-term impact of early life dietary AGEs on behavioral and neural processes. Consuming the AGE-rich diet impaired hippocampal-dependent memory function and altered the gut microbiome without inducing obesity or nonspecific behavioral deficits. AGE-induced memory deficits were coupled with impaired hippocampal glutamatergic synaptic neurotransmission and altered expression in the synapse-pruning complement system. Hippocampal synaptic deficits likely result from direct AGE-complement interactions, as our extended studies reveal competitive antagonist action of AGEs on complement receptors. Memory impairments were prevented by administration of the AGE-inhibitor, alagebrium, and by supplementation with an AGE-inhibiting bacterial taxon, Lactococcus lactis, which was depleted in the heat-treated diet. These findings reveal a functional connection between early life dietary AGEs, the microbiome, and memory impairments, thus illuminating mechanisms through which food processing negatively impacts neurocognition.

neuroscience↗

bioRxiv2026

A single-cell transcriptomic atlas of the periventricular proliferative zone in the late gestation fetal brain in the pigtail macaque

BackgroundThe fetal brain undergoes rapid changes in late gestation, when waves of neurogenesis and gliogenesis shape cortical circuitry. The periventricular proliferative region and adjacent white matter are enriched in neuroprogenitor cells, newborn neurons, and interneurons, which is challenging to study in the late gestation human fetal brain. The nonhuman primate (NHP) provides a powerful translational model to overcome this limitation, given its close similarity to human neurodevelopmental trajectories. The study objective was to construct a single-cell RNA-Seq (scRNA-Seq) atlas of the late-gestation fetal brain of the pigtail macaque (Macaca nemestrina), focused on the periventricular proliferative zone. MethodsA sample of the lateral ventricular wall, subventricular zone, and overlying white/gray matter was dissociated into single cells and processed through the 10X Genomics pipeline, followed by SoupX removal of ambient RNA, and Seurats pipeline to aggregate, cluster and annotate single-cell populations. Monocle3 was used to determine pseudotime and map lineage progression. ResultsThis analysis captured diverse populations of neuroprogenitors, newborn neurons, developing lineages of excitatory and inhibitory neurons, oligodendrocyte and astrocyte lineages, and resident immune and endothelial cells. ConclusionsSingle-cell populations from the third-trimester nonhuman primate fetal brain are highly similar to those in the human fetus. This late-gestation single-cell atlas of the periventricular proliferative zone provides a unique reference for progenitor, neuronal, glial, vascular, and immune cell states during a critical window of primate neurodevelopment, enabling mechanistic interrogation of how inflammatory, infectious, or hypoxic insults disrupt vulnerable neurogenic niches.

genomics↗

bioRxiv2026

Characterizing cellular subpopulations critical to treatment response in autoimmune diseases

Single-cell RNA sequencing provides a powerful approach for characterizing cell types, states, and lineages within heterogeneous tissues. However, identifying cell subpopulations that drive phenotypes, particularly treatment responses, remains a challenge. In this study, we performed comprehensive analyses to identify treatment response-associated cell subpopulations in autoimmune diseases by mapping bulk response information onto single-cell data. We integrated single-cell and bulk biopsy data from 314 responders and 619 non-responders treated with six therapeutics targeting tumor necrosis factor (TNF), integrin, or interleukin pathways in inflammatory bowel diseases (IBD) and psoriasis (PsO). Our analyses captured 128,428 interactions among 3,617 differentially expressed genes (DEGs), 852 pathways, and nine cell types spanning immune, stromal, and epithelial compartments. The importance of epithelial barrier integrity and enterocyte-mediated permeability in responses and inflammatory signaling in macrophages in non-responses in all tested therapies were highlighted by the presence of shared DEGs and pathways in both Crohns disease (CD) and ulcerative colitis (UC). In PsO, keratinocytes drove non-response to integrin-targeting therapies via disrupted adhesion, migration, and sustained epidermal inflammation. Additionally we introduce SCTRAD (https://immbioinfoabbv.shinyapps.io/SCTRAD/), an online web-based platform that allows exploration of mechanisms that influence the heterogeneity of cellular responses through DEGs and pathways at the single-cell level, as well as analysis of the cell-type-specific drug-related gene network. Our findings provide a comprehensive analysis of the role of cellular heterogeneity in treatment outcomes and for advancing precision medicine strategies in autoimmune diseases.

immunology↗

bioRxiv2025

A Combinatorial mRNA Therapy for Treating Rheumatoid Arthritis and Osteoarthritis by Inhibiting Inflammation and Promoting Cartilage Regeneration

Rheumatoid arthritis (RA) and osteoarthritis (OA) are debilitating joint disorders with distinct etiologies but share common pathological features of chronic inflammation and progressive cartilage damage. Current therapeutic options are largely palliative and yet fail to achieve desired effect. In this study, we developed a combinatorial mRNA therapy using a rationally engineered lipid nanoparticle (LNP) containing a novel ionizable lipid for enhanced cartilage penetration upon intra-articular administration. This LNP co-delivers mRNAs encoding two complementary therapeutic proteins: interleukin-1 receptor antagonist (IL-1Ra) for inflammation attenuation and a C-terminal truncated derivative of angiopoietin-like 3 (ANL3) for cartilage regeneration. In pre-clinical models including collagen-induced arthritis mice, TNF-transgenic mice with spontaneous RA and destabilization of medial meniscus (DMM) surgical OA model, this "one-shot" combinatorial therapy significantly ameliorated disease severity, reduced synovitis and bone erosion, and potently promoted the regeneration of hyaline-like cartilage. Mechanistically, transcriptomic profiling of joint specimens revealed that the combinatorial therapy concurrently suppressed inflammatory pathways and extracellular matrix degradation pathways, meanwhile upregulating anabolic genes facilitating chondrogenesis. Collectively, our study establishes a versatile and synergistic mRNA therapy that offers a potent disease-modifying immunomodulatory strategy capable of addressing the long-standing unmet needs in arthritis treatment.

immunology↗

bioRxiv2025

Spatiotemporal Atlas of Heart Development Reveals Blood-Flow-Dependent Cellular, Structural, Metabolic, and Spatial Remodeling

Embryonic heart development depends on coordinated interactions between cellular programs, molecular signaling, and biomechanical forces, yet how mechanical cues shape cellular and molecular pathways remains incompletely understood. We perturbed cardiac blood flow by partial left or right atrial ligation (LAL/RAL) in chick embryos, generating chamber-specific hemodynamic gain- or loss-of-function states. Using single-cell and unbiased, high-resolution spatial transcriptomics, we generated a spatiotemporal atlas of flow-dependent tissue development, enabling systematic investigations of bidirectional interactions between blood-flow mechanics and tissue development. Spatially resolved analyses recapitulated key features of normal morphogenesis including regional maturation and the cellular neighborhood. We further revealed flow-specific remodeling across molecular, cellular, and architectural levels. Altered flow induced LOX-expressing cardiomyocyte and endocardial states, disrupted ventricular layer organization, and delayed maturation, alongside transient metabolic and ion-transport adaptations. Together, these findings define how redistributed blood flow reshapes developing cardiac tissues and provide a framework for studying flow-dependent remodeling in morphogenesis and malformation.

developmental biology↗

bioRxiv2025

The FERM Guild: A Differentially Correlated Microbial Module Drives Hypertension via Metabolic Flux Perturbations

BackgroundHypertension is a major risk factor for cardiovascular diseases, with changes in gut microbiota composition and function being closely associated with its onset and progression. However, the high inter-individual variability in gut microbiota complicates the identification of pathogenic mechanisms using traditional methods. In contrast, the smaller variability in gut microbial metabolites offers a more reliable and consistent basis for cross-individual comparisons. ResultsParsimonious Flux Balance Analysis (pFBA), integrated with Double Machine Learning (DoubleML), identified 17 metabolites significantly associated with hypertension (p < 0.05, RobustnessV alue > 0.1). These included meso-2,6-diaminoheptanedioate, p-hydroxyphenylacetic acid, cellobiose, dextran 40 (1,6--D-glucan), L-glutamic acid, kestopentaose, among others. Differential microbial correlation network analysis identified a key microbial sub-network, the FERM guild, consisting of 19 species, with prominent genera including Faecalibacterium,Enterobacter,Roseburia, and Methanobrevibacter. Using GSEA, the dysregulation of this guild was found to be strongly associated with a set of 17 hypertension-related metabolites(p = 0.017). Further analysis revealed that the contribution of FERM genus to key metabolites is significantly associated with blood pressure (p < 0.05), even without significant differences in their abundance; additionally, an imbalance exists between FERM genus and other species. ConclusionsOur findings reveal that hypertension is associated with a disruption of gut microbial diversity, structure, and metabolic function. Seventeen key metabolites related to blood pressure regulation were identified, exhibiting pro- or anti-hypertensive potential and linked to functional microbial modules. These results highlight the gut microbiota and its metabolites as promising targets for therapeutic intervention in hypertension.

bioinformatics↗

bioRxiv2025

Tri-AD: Hippocampal cell-type-specific responses to age, sex and APOE genotype

Alzheimers disease (AD) risk is strongly shaped by age, sex, and the apolipoprotein E {varepsilon}4 (APOE4) allele--the strongest genetic risk factor for late-onset AD. While each factor has been studied independently, their combined impact on cellular and molecular processes remains unclear. Here, we used single-nucleus RNA sequencing (snRNA-seq) to profile hippocampal cell states in a sex-balanced cohort of human APOE4/4 and APOE3/3 knock-in mice across 6, 12, and 18 months of age. We identify sex as the major driver of variation in cell-type abundance and find that oligodendrocytes exhibit pronounced male-biased transcriptional sensitivity to APOE4. Differential expression and cell-cell communication analyses further reveal sex-divergent temporal trajectories in inhibitory neurons, with females showing early APOE4-associated suppression of synaptic pathways and males displaying a delayed but convergent decline. Together, these findings clarify how age, sex, and APOE genotype jointly regulate cell-type-specific gene expression and intercellular communication in the aging hippocampus, providing an innovative and publicly accessible database for aging and AD research and related precision medicine.

bioinformatics↗

bioRxiv2025

Electrodiffusion active pump model with asymmetric immersed chemical potentials

Electrodiffusion is essential in understanding the mechanisms of electrophysiology. Active exchange pumps are critical regarding volume homeostasis, and are also significant in the mechanisms of cell division, growth, and apoptosis. In the formalism of the immersed boundary (IB) method, we replace classical interface conditions across the membrane with regularized chemical potentials to control the permeation of each ionic species governed by the Poisson-Nernst-Planck equation. In asymmetry, to regulate ionic transport, continuous chemical potential barriers are augmented with energetic gradients represented by smoothed Heaviside kernels specifying the directions of active pumps. We obtain steady-state concentrations from electrodiffusion active pumps using Na+, K+, Cl- ionic species, with background charges in the entire unified domain under periodic boundary conditions. As a consequence of the model simulation, electroneutrality, except for the thin space charge layers along the membrane, is well satisfied. The electrodiffusion active pump model for the exchange of sodium and potassium (NKE) exhibits a good fit to the theoretical formula over a broad range of pertur-bations in ionic concentrations, ensuring volume conservation in the steady state only when active pumps are functioning. It is also shown that vant Hoffs law is satisfied without active pumps. This is a foundation for applying the IB electrodiffusion active pump model for subcellular transport of water and molecules, possibly involving cell motility and migration.

biophysics↗

bioRxiv2025

Anionic Lipid Trafficking and Cell Mechanics RegulateMembrane Electrical Potential in Non-Excitable Tissue Cells

1The membrane potential of eukaryotic cells, classically described by the Goldman-Hodgkin-Katz model, is conventionally attributed to the steady-state balance of transmembrane ionic fluxes. Here, we demonstrate that non-excitable cells maintain stable, spatially heterogeneous membrane voltage gradients. Using the ratiometric voltage indicator JEDI-2P-cyOFP1, we quantitatively map membrane potential in live cells and find that cellular protrusions are consistently depolarized, whereas lateral membrane regions are hyperpolarized. These voltage gradients strongly correlate with anisotropic distributions of anionic lipids, including phosphatidylserine (PS) and phosphatidylinositol 3,4,5-trisphosphate (PIP3). Perturbation of cytoskeletal integrity, the ion exchanger NHE1, or vesicular trafficking disrupts both voltage anisotropy and lipid polarization, revealing an uncharacterized electromechanical regulatory mechanism. Moreover, membrane potential dynamically responds to cell shape, substrate stiffness, external electric fields, and cell cycle progression. To account for these phenomena, we develop a quantitative model that integrates ionic fluxes and lipid charge distributions, thereby explaining the emergence of voltage gradients. This framework establishes that membrane potential is governed not solely by ionic currents but also by lipid dynamics and mechanical signaling. Collectively, these findings identify membrane voltage as a global integrator of electrochemical and mechanical cues in eukaryotic cells.

biophysics↗

bioRxiv2025

Dissecting the homeodomain MAT locus and engineering novel tripolar and bipolar mating systems in Cryptococcus amylolentus

Sex in fungi is governed by the mating-type (MAT) locus, which exists as bipolar, pseudobipolar, or tetrapolar systems. The significance and impact of MAT on sexual reproduction, however, remain understudied. Furthermore, the evolution of fungal MAT loci shares features with the evolution of sex chromosomes in plants and animals. Pathogenic Cryptococcus species harbor a bipolar system with a large contiguous MAT locus, whereas closely related species, such as the non-pathogen C. amylolentus possess a tetrapolar system with unlinked P/R and HD loci. The HD locus encodes homeobox domain containing proteins that play an important and evolutionarily conserved role in sexual reproduction. Here, we explored the roles of HD genes in sexual reproduction and determined the implications of a tetrapolar to bipolar MAT transition. With a CRISPR-Cas9 system we developed for C. amylolentus, we generated gene deletion mutants and demonstrated that a single compatible Sxi1-Sxi2 pair is necessary and sufficient for mating. By relocating the HD genes to the P/R locus, we found that the artificially generated bipolar configuration led to defective sexual development, which could be partially restored through additional rounds of sexual reproduction. Transcriptomic profiling further revealed that a Sxi1-Sxi2 heterodimeric complex drives expression of genes required for DNA replication and ergosterol biosynthesis during sexual reproduction. These findings provide the first experimental demonstration of a tetrapolar-to-bipolar transition in a tetrapolar mating species, illuminating MAT locus evolution and homeodomain protein functions in Cryptococcus. ImportanceSexual reproduction is critical for fungal survival and adaptation, yet the mechanisms driving transitions between mating systems remain unclear. With Cryptococcus amylolentus, we provide the first experimental validation of a mating system transition from its original tetrapolar to an intermediate tripolar to a derived bipolar in a tetrapolar species. We show that HD heterodimers phenotypically govern dikaryotic filamentation and also transcriptionally modulate DNA replication. These findings establish a mechanistic basis for how MAT locus reorganization drives bipolar evolution from an ancestral tetrapolar state and reinforce that fertility depends on the coordinated control of MAT locus architecture and regulatory functions.

microbiology↗

bioRxiv2025

Scaling up orphan crop research: A global genetic perspective of cowpea (Vigna unguiculata) diversity from 10,617 accessions

Cowpea (Vigna unguiculata L. Walp) is a dryland legume crop, providing essential food and nutritional security for millions of people across the semi-arid tropics, in Africa, Asia, and Latin America. However, as a typical "orphan crop", cowpea has long remained underrepresented in global genomic research to support crop improvement. Here, we conducted the largest genetic diversity analysis of cowpea to date, comprising 10,617 accessions sourced from seven international collections. Using genotyping-by-sequencing, we characterized the global patterns of genetic diversity, assessed redundancy within and across collections, and examined the geographic structure of the cowpea global allele pool. Our results revealed nine distinct genetic groups with clear geographic associations and fine-scale population differentiation, reflecting dispersal history, regional adaptation and the influence of modern breeding. Duplication across collections was detected, highlighting the need for improved curation and integration of germplasm resources. Landraces from sub-Saharan Africa do not fully capture the genetic diversity present in several other geographic regions, indicating the existence of abundant and untapped genetic resources worldwide. These findings not only provide insights into the genetic structure and evolutionary history of cowpea but also offer a valuable foundation for harnessing global germplasm diversity to enhance breeding potential and accelerate crop improvement.

plant biology↗

bioRxiv2025

A unifying model of LAT condensates in reconstitution experiments

The formation of condensates by the Linker for the Activation of T-cells (LAT) is a key signal gating and amplification step in the T-cell receptor signaling pathway. LAT condensation is challenging to study in-vivo and is therefore often investigated using reconstitution experiments. While these experiments recapitulate key aspects of LAT condensation, they also exhibit some puzzling features. Here, we describe the mechanisms underlying these observations using two complementary models. First, we employ a Smoluchowski aggregation model to show that the delay time before condensation is observed arises from a low effective binding probability between LAT monomers. Second, we propose a field-theoretic model that reproduces all condensate morphologies observed in experiments, showing that they can arise from common underlying dynamics modulated by variations in experimental conditions. This result unifies different experimental observations reported previously. While this article addresses open questions regarding the formation of LAT condensates, our results also provide a common framework for understanding condensation of other multivalent membrane proteins such as EGFR, FGFR2, and nephrin.

biophysics↗

bioRxiv2025

Programmed DNA elimination was present in the last common ancestor of Caenorhabditis nematodes

In most organisms, all cells inherit the same genome, and many mechanisms exist to preserve its integrity across cell divisions. Programmed DNA elimination (PDE), the targeted removal of specific genomic regions from somatic cell lineages during early embryogenesis, is a striking exception. Since its discovery in parasitic nematodes over a century ago, PDE has been observed in diverse eukaryotes, including ciliates, arthropods, and vertebrates. However, the mechanisms, functions, and evolutionary origins of PDE remain poorly understood. Here, we describe the discovery of PDE in three species of the free-living nematode genus Caenorhabditis. Multiple genomic regions are precisely eliminated from somatic cells during early embryogenesis, resulting in chromosome fragmentation and the loss of key germline genes. The sites of elimination are strongly associated with conserved sequence motifs that likely direct DNA breakage. Comparative analyses indicate that PDE was present in the last common ancestor of Caenorhabditis and subsequently lost early during the evolution of many species, including C. elegans. The presence of PDE in the ancestors of one of biologys most important model organisms, together with recent discoveries in other eukaryotic lineages, reveals PDE to be a far more widespread and significant feature of evolution and development than previously recognised.

evolutionary biology↗

bioRxiv2025

Maternal Influenza A Virus Infection Induces Antiviral and Immune Dysregulation in the Placenta and Fetus Without Vertical Transmission

Influenza A virus (IAV) infection during pregnancy is associated with stillbirth and preterm birth, but the degree to which IAV alters placental and fetal immunity is poorly understood. The objective of our study was to determine the immunologic impact of maternal IAV infection on the placenta and fetus in a pigtail macaque (Macaca nemestrina) model. Pregnant pigtail macaques were inoculated with 107 plaque forming units (PFU) of IAV [A/California/07/2009 (H1N1)] and underwent necropsy 5 days post-infection (N=11). Results were compared to uninfected historical controls (N=16). IAV inoculation induced maternal pneumonia in all cases. Stillbirth occurred in 18% (2/11) of IAV-infected pregnancies, but not in controls. While vertical transmission was not observed, low-level IAV viral RNA was detected in two placentas. In the placenta, maternal IAV infection was associated with increased IL-1{beta}, IL-18, and IFN-{beta} levels, and an upregulated type I interferon (IFN) transcriptional response. IAV infection was also associated with significantly higher frequencies of intermediate and non-classical monocytes, plasmacytoid dendritic cells, CD4 T cells, and NKT cells in the fetus (lung, lymph node, blood). Although placental immune and transcriptional perturbations were rarely correlated with maternal IAV disease indicators (e.g., maternal lung viral load/IFN-/IFN-{beta}/IL-6), there were consistent and significant correlations between these metrics and perturbed immune cell populations in the fetus (CD4+ and CD8+ T cells, plasmacytoid dendritic cells, monocyte sub-populations). Maternal IAV infection disrupted both placental and fetal immune environments, but only fetal immune alterations correlated with maternal lung disease severity. One Sentence SummaryMaternal influenza A virus infection in pregnant pigtail macaques dysregulates placental and fetal immunity, with disease severity correlating strongly with fetal, but not placental, immune perturbations.

systems biology↗

bioRxiv2025

LINE1 RNA dysregulation impairs chromatin accessibility in C9ORF72- and TDP-43-linked ALS/FTD

The long interspersed element-1 (LINE1) retrotransposon RNAs are abnormally elevated in various neurodegenerative disorders, but their pathogenic roles remain unclear. Here we investigated the mechanism of LINE1 RNA accumulation and its function in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) associated with C9ORF72 repeat expansion and TDP-43 loss-of-function, the leading causes of familial and sporadic forms of these neurodegenerative diseases. We show that LINE1 RNA is dysregulated due to an impaired nuclear exosome targeting (NEXT) degradation pathway. Its elevation epigenetically increases chromatin accessibility, enhancing global transcription via a retrotransposon-independent mechanism. Reducing LINE1 RNA mitigates chromosomal abnormalities and improves the survival of disease-relevant neurons. These findings uncover an essential noncoding RNA function and regulatory mechanism of LINE1 in neurons, providing insights into disease pathogenesis and highlighting potential therapeutic targets for neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Cancer cells surviving cisplatin chemotherapy increase stress-induced OMA1 activity and mitochondrial fragmentation

Cancer is one of the leading causes of deaths worldwide. Once cancer cells acquire therapy resistance, they become the main driver of cancer lethality in patients. Thus, mechanisms of therapy resistance must be investigated to improve patient outcomes. Mitochondria are critical organelles in the cellular stress responses, undergoing dynamic morphological and functional changes in response to external stimuli. We and others have identified a chemotherapy-resistant cancer cell state where cells that survive treatment exhibit a dramatic increase in cell size and remain non-proliferative for weeks. In this study, we demonstrate that cancer cells that enter this resistant cell state in response to cisplatin increase OMA1 activity and decrease mitochondrial fusion and function to combat oxidative stress. These findings contribute to further understanding the role of the mitochondrial stress responses in therapy resistance in cancer and provide a potential therapeutic avenue to targeting cancer cells that enter this chemotherapy-resistant cell state.

cancer biology↗

bioRxiv2025

Uterine immune dysregulation after asynchronous transfer induced embryonic apoptosis in mice

Asynchronous embryo transfer is widely used in assisted reproduction, yet its adverse effects and mechanisms remain unclear. This study investigates implantation failure in D1.5 pseudopregnant mice to elucidate mechanisms underlying asynchronous transfer. Blastocysts were transferred into uterine horns of D1.5 (Group A), D2.5 (Group B), and D3.5 (Group C) recipients. Implantation sites were counted at D7.5, and embryos were recovered within 3 hours post-transfer for analysis. Multibarcode single-cell RNA sequencing was applied to embryos and uterine tissues. Embryo recovery rate in Group A was significantly lower than in Groups B and C (p<0.01), with an abnormal embryo rate of 68.67%. Hoechst 33342/PI double staining revealed dead-cell features in abnormal embryos. Transcriptomic analysis of embryos showed downregulated DNA damage repair and structural maintenance genes in Group A. GO and KEGG analyses highlighted enrichment in transcriptional regulation and cell cycle pathways. GSEA identified activated apoptosis pathways, with intrinsic (mitochondrial) and extrinsic (death receptor TNFR-mediated) apoptosis genes significantly upregulated (p<0.05). Uterine transcriptome analysis revealed downregulated collagen family genes (ECM maintenance) but upregulated immune-related genes (IL family, CDs, C3) in Group A. Functional enrichment confirmed ECM and immune regulation pathway involvement. Gene network analysis identified Clca1, Smpdl3a, Tmprss4, Muc4, Cfb, and Nupr1 as key regulators of D1.5 uterine immunity/inflammation. D1.5 uterine immune dysregulation induces embryonic stress and inflammation. Impaired DNA damage repair activates intrinsic apoptosis, while upregulated TNFR signaling triggers extrinsic apoptosis, collectively blocking embryonic development toward implantation competence. These findings provide mechanistic insights into optimizing embryo transfer timing and improving reproductive outcomes.

immunology↗