The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations

Epidemiological research suggests that paternal obesity may increase the risk of fathering small for gestational age offspring. Studies in non-human mammals indicate that such associations could be mediated by DNA methylation changes in spermatozoa that influence offspring development in utero. Human obesity is associated with differential DNA methylation in peripheral blood. It is unclear, however, whether this differential DNA methylation is reflected in spermatozoa. We profiled genome-wide DNA methylation using the Illumina MethylationEPIC array in a cross-sectional study of matched human blood and sperm from lean (discovery n = 47; replication n = 21) and obese (n = 22) males to analyse tissue covariation of DNA methylation, and identify obesity-associated methylomic signatures. We found that DNA methylation signatures of human blood and spermatozoa are highly discordant, and methylation levels are correlated at only a minority of CpG sites (~1%). At the majority of these sites, DNA methylation appears to be influenced by genetic variation. Obesity-associated DNA methylation in blood was not generally reflected in spermatozoa, and obesity was not associated with altered covariation patterns or accelerated epigenetic ageing in the two tissues. However, one cross-tissue obesity-specific hypermethylated site (cg19357369; chr4:2429884; P = 8.95 × 10−8; 2% DNA methylation difference) was identified, warranting replication and further investigation. When compared to a wide range of human somatic tissue samples (n = 5,917), spermatozoa displayed differential DNA methylation across pathways enriched in transcriptional regulation. Overall, human sperm displays a unique DNA methylation profile that is highly discordant to, and practically uncorrelated with, that of matched peripheral blood. We observed that obesity was only nominally associated with differential DNA methylation in sperm, and therefore suggest that spermatozoal DNA methylation is an unlikely mediator of intergenerational effects of metabolic traits.
Author summary Research primarily conducted in mice suggests that obesity in fathers can have effects on the health of their offspring via changes in the fathers’ sperm. It is not confirmed whether this is true for humans. In this study, we examined sperm and blood from lean and obese men to understand whether obesity affects DNA methylation in both tissues. DNA methylation can impact on gene function and therefore may affect offspring health. We found that there was almost no association between obesity and DNA methylation in sperm. We also showed that DNA methylation patterns found in the blood of obese individuals are not present in sperm from obese men. Generally, DNA methylation patterns across the whole genome were completely different and uncorrelated between the two tissues. Lastly, we compared DNA methylation patterns in sperm to those in many other tissues, including for example blood and brain samples, and found that sperm has a unique signature of DNA methylation—one that points to genes involved in regulating overall levels of transcription. We conclude that obesity probably does not affect DNA methylation in sperm and that, although more research is needed, if obesity in fathers does influence the health of their children, this process is unlikely to be mediated by spermatozoal DNA methylation.