High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations

Abstract

Background Children of aged fathers are at a higher risk of developing mental disorders. Alterations in sperm DNA methylation have been implicated as a potential cause. However, age-dependent modifications of the germ cells’ epigenome remain poorly understood. Our objective was to assess the DNA methylation profile of human spermatozoa during aging. Results We used a high throughput, customized methylC-capture sequencing (MCC-seq) approach to characterize the dynamic DNA methylation in spermatozoa from 94 fertile and infertile men, who were categorized as young, 48 men between 18–38 years or old 46 men between 46–71 years. We identified more than 150,000 age-related CpG sites that are significantly differentially methylated among 2.65 million CpG sites covered. We conducted machine learning using our dataset to predict the methylation age of subjects; the age prediction accuracy based on our assay provided a more accurate prediction than that using the 450 K chip approach. In addition, we found that there are more hypermethylated (62%) than hypomethylated (38%) CpG sites in sperm of aged men, corresponding to 798 of total differential methylated regions (DMRs), of which 483 are hypermethylated regions (HyperDMR), and 315 hypomethylated regions (HypoDMR). Moreover, the distribution of age-related hyper- and hypomethylated CpGs in sperm is not random; the CpG sites that were hypermethylated with advanced age were frequently located in the distal region to genes, whereas hypomethylated sites were near to gene transcription start sites (TSS). We identified a high density of age-associated CpG changes in chromosomes 4 and 16, particularly HyperDMRs with localized clusters, the chr4 DMR cluster overlaps PGC1α locus, a protein involved in metabolic aging and the chr16 DMR cluster overlaps RBFOX1 locus, a gene implicated in neurodevelopmental disease. Gene ontology analysis revealed that the most affected genes by age were associated with development, neuron projection, differentiation and recognition, and behaviour, suggesting a potential link to the higher risk of neurodevelopmental disorders in children of aged fathers. Conclusion We identified thousands of age-related and sperm-specific epigenetic alterations. These findings provide novel insight in understanding human sperm DNA methylation dynamics during paternal aging, and the subsequently affected genes potentially related to diseases in offspring.

Single-Cell Analysis of Human Testis Aging, and Impact of Elevated Body Mass Index

“…This apparent lack of major impact on the spermatogonia has clinical implications, as improvements to the function of the somatic niche may then allow proper spermatogenesis from a healthy pool of spermatogonia. However, we note that distinguishable from young germ cells, aging germ cells demonstrate higher levels of DNA fragmentation, and display certain epigenetic changes (e.g., hyper DNA methylation) (Cao et al, 2020;Pohl et al, 2021). Consistent with the modest transcriptional changes in spermatogonia, we find no significant change in overall SSC transplant efficiency in both older groups, which also holds true in mice (Oatley and Brinster, 2012;Ryu et al, 2006).…”

“…Agingassociated subfertility is linked to increased time to pregnancy and higher miscarriage rates (du Fossé et al, 2020;Hassan and Killick, 2003). Aging adversely affects sperm genome integrity (DNA fragmentation, telomere length, chromosomal aneuploidy), genome fidelity (DNA mutations), epigenetic status (e.g., DNA methylation), and sperm parameters (e.g., sperm motility, semen volume) (Broer et al, 2013;Cao et al, 2020;Griffin et al, 1996;Kong et al, 2012;Nguyen-Powanda and Robaire, 2020;Pohl et al, 2021;Sharma et al, 2015;Singh et al, 2003). Aging also impacts the entire endocrine system, including the hypothalamic-pituitary-gonadal (HPG) axis which is critical for the production of hormones such as testosterone (T) and leads to changes in testis physiology as well as fertility status (Decaroli and Rochira, 2016;Pincus et al, 1996;Sampson et al, 2007;Wu et al, 2008).…”

HIF1A modulate glycolysis function to governs mouse ovarian microenvironment metabolic plasticity in aging single cell resolution

“…During parental age increased, aging-associated problems are related to multiple risk factors including reduced fertility and higher miscarriage rates 5 . Aging adversely affects genome integrity, epigenetic status and endocrine disorder in both male and female 6 . Thus, the ovary and testis are indispensable for the maintenance fertility and endocrine homeostasis 7–9 .…”

Emerging rejuvenation strategies—Reducing the biological age

“…It is also important to note that gametes are not immune to age‐relate damage‐they do age. Therefore, it would be particularly interesting to find out how gametes are affected by these cellular maintenance machineries (Cao et al, 2020 ).…”