bims-mazytr 2025-06-29 papers

Issue of 2025–06–29
seven papers selected by
川一刀

Biology (Basel). 2025 Jun 11. pii: 676. [Epub ahead of print]14(6):

Integrative Single-Cell Transcriptomics and Network Modeling Reveal Modular Regulators of Sheep Zygotic Genome Activation.

Xiaopeng Li, Peng Niu, Kai Hu, Xueyan Wang, Fei Huang, Pengyan Song, Qinghua Gao, Di Fang.

Zygotic genome activation (ZGA) marks the critical transition from reliance on maternal transcripts to the initiation of embryonic transcription early in development. Despite extensive characterization in model species, the regulatory framework of ZGA in sheep remains poorly defined. Here, we applied single-cell RNA sequencing (Smart-seq2) to in vivo- and in vitro-derived sheep embryos at the 8-, 16-, and 32-cell stages. Differential expression analysis revealed 114, 1628, and 1465 genes altered in the 8- vs. 16-, 16- vs. 32-, and 8- vs. 32-cell transitions, respectively, with the core pluripotency factors SOX2, NANOG, POU5F1, and KLF4 upregulated during major ZGA. To uncover coordinated regulatory modules, we constructed a weighted gene co-expression network using WGCNA, identifying the MEred module as most tightly correlated with developmental progression (r = 0.48, p = 8.6 × 10-14). The integration of MERed genes into the STRING v11 protein-protein interaction network furnished a high-confidence scaffold for community detection. Louvain partitioning delineated two discrete communities: Community 0 was enriched in ER-Golgi vesicle-mediated transport, transmembrane transport, and cytoskeletal dynamics, suggesting roles in membrane protein processing, secretion, and early signaling; Community 1 was enriched in G2/M cell-cycle transition and RNA splicing/processing, indicating a coordinated network for accurate post-ZGA cell division and transcript maturation. Together, these integrated analyses reveal a modular regulatory architecture underlying sheep ZGA and provide a framework for dissecting early embryonic development in this species.

Keywords: Louvain algorithm; WGCNA; sheep embryos; single cell transcriptomics; zygotic genome activation

DOI: https://doi.org/10.3390/biology14060676

J Cell Biol. 2025 Sep 01. pii: e202503080. [Epub ahead of print]224(9):

PLK-1 suppresses centrosome maturation and microtubule polymerization to ensure faithful oocyte meiosis.

Juhi G Narula, Sarah M Wignall.

Sexual reproduction relies on meiosis, a specialized cell division program that produces haploid gametes. Oocytes of most organisms lack centrosomes, and therefore chromosome segregation is mediated by acentrosomal spindles. Here, we explore the role of Polo-like kinase 1 (PLK-1) in Caenorhabditiselegans oocytes, revealing mechanisms that ensure the fidelity of this unique form of cell division. Previously, PLK-1 was shown to be required for nuclear envelope breakdown and chromosome segregation in oocytes. We now find that PLK-1 is also required for establishing and maintaining acentrosomal spindle organization and for preventing excess microtubule polymerization in these cells. Additionally, our studies revealed an unexpected new role for this essential kinase. While PLK-1 is known to be required for centrosome maturation during mitosis, we found that either removal of PLK-1 from oocytes or inhibition of its kinase activity caused premature recruitment of pericentriolar material to the sperm-provided centrioles following fertilization. Thus, PLK-1 suppresses centrosome maturation during oocyte meiosis, which is opposite to its role in mitosis. Taken together, our work identifies PLK-1 as a key player that promotes faithful acentrosomal meiosis in oocytes and demonstrates that its catalytic activity is required for carrying out these important roles.

DOI: https://doi.org/10.1083/jcb.202503080

bioRxiv. 2025 May 03. pii: 2025.04.29.650984. [Epub ahead of print]

Replication competition drives the selective mtDNA inheritance in Drosophila ovary.

Cheng Zhang, Zhe Chen, Hansong Ma, Hong Xu.

Purifying selection that limits the transmission of harmful mitochondrial DNA (mtDNA) mutations has been observed in both human and animal models. Yet the precise mechanism underlying this process remains undefined. Here, we present a highly specific and efficient in situ imaging method capable of visualizing mtDNA variants that differ by only a few nucleotides at single-molecule resolution in Drosophila ovaries. Using this method, we revealed that selection primarily occurs within a narrow developmental window during germline cysts differentiation. At this stage, the proportion of the deleterious mtDNA variant decreases without a reduction in its absolute copy number. Instead, the healthier mtDNA variant replicates more frequently, thereby outcompeting the co-existing deleterious variant. These findings provide direct evidence that mtDNA selection is driven by replication competition rather than active elimination processes, shedding light on a fundamental yet previously unresolved mechanism governing mitochondrial genome transmission.

DOI: https://doi.org/10.1101/2025.04.29.650984

PLoS Biol. 2025 Jun;23(6): e3003193

Single-cell and spatiotemporal profile of ovulation in the mouse ovary.

Ruixu Huang, Caroline E Kratka, Jeffrey Pea, Cai McCann, Jack Nelson, John P Bryan, Luhan T Zhou, Daniela D Russo, Emily J Zaniker-Gomez, Achla H Gandhi, Alex K Shalek, Brian Cleary, Samouil L Farhi, Francesca E Duncan, Brittany A Goods.

Ovulation is a spatiotemporally coordinated process that involves several tightly controlled events, including oocyte meiotic maturation, cumulus expansion, follicle wall rupture and repair, and ovarian stroma remodeling. To date, no studies have detailed the precise window of ovulation at single-cell resolution. Here, we performed parallel single-cell RNA-seq and spatial transcriptomics on paired mouse ovaries across an ovulation time course to map the spatiotemporal profile of ovarian cell types. We show that major ovarian cell types exhibit time-dependent transcriptional states enriched for distinct functions and have specific localization profiles within the ovary. We also identified gene markers for ovulation-dependent cell states and validated these using orthogonal methods. Finally, we performed cell-cell interaction analyses to identify ligand-receptor pairs that may drive ovulation, revealing previously unappreciated interactions. Taken together, our data provides a rich and comprehensive resource of murine ovulation that can be mined for discovery by the scientific community.

DOI: https://doi.org/10.1371/journal.pbio.3003193

Cell Prolif. 2025 Jun 27. e70088

Lactate Promotes the Second Cell Fate Decision in Blastocysts by Prompting Primitive Endoderm Formation Through an Intercellular Positive Feedback Loop That Couples Paracrine FGF Signalling.

Xiao Hu, Yawen Tang, Wei Zhao, Juan Liu, Zhize Liu, Qianyin Yang, Meiqiang Chu, Jianhui Tian, Lei An, Shumin Wang.

Lactate has been widely recognised as an energy source and metabolic by-product, but increasing evidence supports its critical role as a signalling molecule or epigenetic substrate. During early embryogenesis, lactate production increases during the transition from early to late blastocyst, coinciding with the differentiation of inner mass cell (ICM) into epiblast (EPI) and primitive endoderm (PrE), termed the second cell fate decision. However, the role of this hallmark metabolic change in the second cell fate segregation remains unknown. Herein, using in vitro and in vivo models, we found lactate production is preferentially increased in PrE cells and is essential for ICM differentiation into PrE. Mechanically, increased lactate in PrE precursor cells and FGF signalling in EPI precursor cells reciprocally activate each other and synergise to prompt PrE specification, forming an intercellular positive feedback loop essential for this lineage commitment. Additionally, lactate enhanced histone lactylation levels during differentiation into PrE fate. Thus, our findings construct a complex multilayer model in which intracellular metabolite in PrE cooperates with intercellular growth factor signalling from EPI to regulate early embryonic lineage commitment. Highlighting the multifaceted lactate's function, our findings also advance the current knowledge that bridges epigenetic reprogramming and metabolic remodelling during early embryonic development.

Keywords: FGF4; histone lactylation; lactate; pre‐implantation embryo; primitive endoderm

DOI: https://doi.org/10.1111/cpr.70088

Comput Biol Med. 2025 Jun 21. pii: S0010-4825(25)00988-6. [Epub ahead of print]195 110637

Innovative AI models for clinical decision-making: predicting blastocyst formation and quality from time-lapse embryo images up to embryonic day 3.

Akihiro Yanai, Akihito Horie, Azusa Sakurai, Sachi Imakita, Mitsuhiro Nakamura, Asami Ikeda, Shimpei Shitanaka, Tsutomu Ohara, Baku Nakakita, Akihiko Ueda, Yoshimi Kitawaki, Yusuke Sagae, Asuka Okunomiya, Masaki Mandai.

Accurate embryo assessment on embryonic day 3 of assisted reproductive technology (ART) is crucial for deciding whether to continue the culture until day 5 (blastocyst stage) or opt for earlier transfer or cryopreservation. Prolonged culture often improves pregnancy outcomes in patients with multiple high-quality embryos, but may offer limited benefits for older patients or those with few available embryos. In Japan, where donor eggs are rarely used, cleavage-stage vitrification remains common in poor-prognosis cases, making early embryo assessment clinically relevant. To address this clinical challenge, analyzing embryo quality in early stages by artificial intelligence (AI) can be useful. We retrospectively analyzed images of 7111 two-pronuclear embryos (Veeck grade ≤3) using four different time-lapse incubators. We fine-tuned ImageNet-1k-pretrained NASNet-A Large to automatically classify each time-lapse image into 17 morphological categories, including cell stages and Veeck grades 1-3. This model achieved 95 % cell-stage accuracy on the test set. We combined these annotations with age at egg retrieval in a gradient boosting framework (XGBoost) to predict blastocyst formation, good blastocysts, and poor blastocyst + arrested embryos (PBAE). The ROC AUCs were 0.87, 0.88, and 0.87 for blastocyst formation, good blastocysts, and PBAE, respectively, indicating good predictive performance for day 3 embryo assessment. Notably, the PBAE model reached a precision-recall AUC of 0.90, accurately identifying embryos unlikely to benefit from extended culture. This novel AI prediction model could ensure transparency and addresses the "black box" limitation often associated with AI. By integrating a high-accuracy auto-annotation pipeline with interpretable AI (via SHapley Additive exPlanations), our device-independent approach supports appropriate embryo-specific decisions, potentially reducing unnecessary culture, optimizing workflows, and improving clinical outcomes in ART.

Keywords: Artificial intelligence; Assisted reproductive technology; Blastocyst; Machine learning; Prediction model; Reproductive medicine; Time-lapse

DOI: https://doi.org/10.1016/j.compbiomed.2025.110637

Mol Hum Reprod. 2025 Jun 16. pii: gaaf029. [Epub ahead of print]

A matrix-free 3D in vitro follicle culture system in mice exhibits enhanced oocyte meiotic and developmental competence compared to hydrogel encapsulation.

Aimilia Zisiadi, Katy Billooye, Ellen Anckaert.

In vitro follicle culture (IFC) is an emerging fertility preservation alternative for women and children with cancer. Because two-dimensional (2D) IFC results in oocytes of suboptimal quality in mice and cannot support follicle growth in humans, the search for an optimal three-dimensional (3D) method that preserves the follicular structure is ongoing and both matrix-free and hydrogel encapsulation systems are being explored. Our aim was to compare several 3D mouse IFC systems, including matrix-free and hydrogel encapsulation approaches. Secondary follicles were cultured for 12 days in a matrix-free non-attachment (NA) system, a Poly-Ethylene-Glycol (PEG) hydrogel, an extracellular-matrix-derived soft hydrogel (ES) and a 2D attachment (AT) control. We assessed follicle growth, survival, hormone secretion, theca cell localization, oocyte meiotic competence and diameter, gene expression in oocytes and cumulus cells, as well as oocyte fertilization potential. Metaphase II oocyte rates were significantly higher in the NA (75 ± 12.4%, n = 79) and AT system (77 ± 12.6%, n = 109) compared to the ES (33.4 ± 9.5%, n = 40, p < 0.01), while low antral follicle rates from the PEG system led to its exclusion from the comparison. Similarly, following IVF, 2-cell rates were significantly higher in the NA (47.7 ± 17.6%, n = 147, p < 0.01) and AT (40.2 ± 9.7%, n = 132, p < 0.05) systems compared to the ES (23.5 ± 9.3%, n = 63). Furthermore, cumulus cells from the NA condition displayed a more in-vivo-like gene expression profile than other conditions. No differences were detected in follicle survival, oocyte diameter, blastocyst rate or quality between conditions. Lastly, we observed major differences in theca cell localization and hormone secretion levels that require further investigation. Our findings demonstrate the efficiency of the NA system over complex encapsulation methodologies, as it enhanced oocyte meiotic and developmental competence compared to the ES. However, as the study is limited by the lack of human data and the use of Fetal Bovine Serum (FBS) in the culture medium, further research is required to translate our findings to humans. Comparison of 3D and 2D in vitro culture systems for mouse secondary follicles. Follicle survival and growth were evaluated across all culture conditions. Oocyte meiotic and developmental competence, hormone secretion levels in spent culture media, gene expression in oocytes and cumulus cells and theca cell localization were assessed in the NA, the ECM-derived hydrogel and the 2D control conditions. NA, non-attachment; MII, metaphase II; E2, estradiol; GV, germinal vesicle; ECM, extracellular-matrix; 2D, two-dimensional; 3D, three-dimensional. Created in BioRender. Anckaert, E. (2025) https://BioRender.com/z4ic7wh.

Keywords: 3D culture; developmental competence; fertility preservation; follicle culture; hydrogel; matrix-free; mouse; oocyte

DOI: https://doi.org/10.1093/molehr/gaaf029