Molecular and Genetic Insights Into Human Ovarian Aging From Single-Nuclei Multi-omics Analyses

Ovaries are the crux of the female reproductive system and are the first organs to show signs of aging and thus the slowing of reproductive processes, characterized by a reduced number and quality of oocytes. The more a woman ages, the higher the risk of infertility or aneuploidy and congenital disabilities in their children. Though evidence has shown how aging and ovarian function plays a role in reproductive success, there is little evidence surrounding the mechanisms of ovarian deterioration related to aging. One related factor that could provide valuable insight is age at natural menopause (ANM), which has a large genetic component. This study was designed to present a single-nuclei multi-omics atlas of human ovarian aging, highlighting the ovary-specific role of mTOR signaling and relating the data to ANM-associated genome-wide association study risk variants to identify functional regulatory and noncoding variants across cell types within the ovary. This was meant to be a resource for exploring cellular, molecular, and genetic drivers of ovarian aging. To create this atlas, single-nuclei RNA sequencing (snRNA-seq) and single-nuclei assay for transposase-accessible chromatin sequencing (snATAC-seq) was performed on flash-frozen ovarian tissues from donors with normal histology. A total of 42,568 nuclei were obtained for snRNA-seq, and 41,550 were obtained for snATAC-seq, and all major cell types in the ovary were represented. Differentially expressed genes (DEGs) for each cell type were identified, and many age-related changes were congruous across cell types among DEGs. Further analysis showed that these age-related changes were only strongly present in ovarian tissue, and weak or negligible in other tissues throughout the body. This indicates an accelerated cellular aging in ovarian tissue compared with other tissues. Other changes related to aging in ovarian tissue include differences in cellular communication, cell identity, and signaling networks. Signaling pathways that were significantly changed showed a difference in probability of communication between young and aged ovaries; a total of 46 pathways with these altered levels of signaling were identified. Evidence shows that certain molecules are susceptible to changes in ovarian tissue that come with aging, including the CEBPD molecule, and that cell signaling also plays a significant role in the accelerated nature of ovarian aging regardless of cell type. This study also identified several ANM genetic variants associated with ovarian aging, consistent with previous literature on the topic. These have the potential to help understand through future study the mechanisms surrounding ovarian aging as it relates to ANM. This multi-omics atlas represents a valuable resource for future studies in identifying particular molecules of interest that may drive the process of accelerated ovarian aging, and future research using this resource could have major impacts such as extending female reproductive lifespan and improving overall health outcomes as women age.