Single-cell multiomic analysis reveals deviations following oocyte maturation in vitro

In vitro maturation of oocytes is a routine step in assisted reproduction, however, it is associated with lower embryo development rates compared to oocyte maturation in vivo. The objective of the current study was to characterize the genomic profile of oocytes derived from the same cow, but submitted to maturation either in vivo or in vitro. To this end single-cell methylome and transcriptome sequencing of individual oocytes and transcriptome analysis of their corresponding cumulus cells was carried out. The resulting data revealed alterations in both the transcriptome and methylome of the oocytes matured in vitro, suggesting compromised oocyte maturation. Notable changes included alterations in CpG islands associated with imprinted genes, including decreased methylation levels in MEST (PEG1), NNAT (both implicated in large offspring syndrome), and MIMT1 following in vitro maturation. Additionally, transcriptomic analysis of their cumulus cells highlighted significant alterations in gene expression linked to impaired mitochondrial function and altered responses to hypoxia and cell adhesion. Our findings highlight the extent to which the maturation environment can influence the key epigenetic regulators and mRNA profiles that affect oocyte quality and subsequent developmental outcomes. The data provides a valuable resource for optimising assisted reproduction technologies. scRNA-seq and scBS-seq were perfomed on bovine MII oocytes after in vivo or in vitro maturation. scRNA-seq was also performed on MII oocytes after in vivo + in vivo maturation. We sequenced 88 MII oocytes and 2 Negative control.

卵母细胞体外成熟是辅助生殖领域的常规操作环节，但相较于体内成熟的卵母细胞，其对应的胚胎发育率普遍偏低。本研究旨在对源自同一母牛、分别经体内与体外成熟的卵母细胞的基因组特征进行系统表征。为此，研究人员对单个卵母细胞开展了单细胞甲基化组与转录组测序，并对其对应的卵丘细胞进行了转录组分析。所得测序数据显示，体外成熟的卵母细胞在转录组与甲基化组层面均存在显著异常，提示其成熟过程受到损伤。其中显著变化包括与印记基因相关的CpG岛的表观遗传改变，具体表现为体外成熟后MEST（PEG1）、NNAT（二者均与巨胎儿综合征相关）以及MIMT1的甲基化水平显著降低。此外，对卵丘细胞的转录组分析显示，其基因表达发生显著改变，涉及线粒体功能受损、缺氧应答异常以及细胞黏附反应失调等通路。本研究结果揭示了成熟环境可在多大程度上影响调控卵母细胞质量及后续发育结局的关键表观遗传调控因子与mRNA表达谱。该数据集为优化辅助生殖技术提供了极具价值的研究资源。研究人员对经体内或体外成熟的牛MII期卵母细胞进行了单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）与单细胞亚硫酸氢盐测序（single-cell bisulfite sequencing, scBS-seq），同时对经体内+体内成熟的MII期卵母细胞开展了单细胞RNA测序。本次测序共纳入88个MII期卵母细胞与2个阴性对照样本。