Large-Scale Heterogeneous Disruption of Sperm Dna-Methylation in Infertile Individuals is Associated with Genes Implicated in Sperm Chemotaxis, Acrosome Reaction and Egg-Binding.

The standard of care for assessing male fertility is the semen analysis. In addition to checking for low sperm counts, gross morphological disruptions or a lack of progressive motility can be examined for. However, many infertile men have normal semen parameters. In these cases, sperm function may be impacted in less visually obvious ways. To identify and characterize patterns of aberrant DNA methylation in sperm samples from infertile males suspected of impacting genes associated with sperm functions other than morphology and motility. We defined a reference sperm methylomes from 156 samples derived from 98 unique donors of known fertility. We compared the DNA methylation profiles of 336 sperm samples from 292 unique infertile men to identify loci with substantial variation from the reference. Sperm DNA methylation was measured using Illumina’s 450k HM array. We called a gene differentially methylated in an infertile sample if two or more probes in the gene body or 5kb upstream of the transcription start site showed a methylation level that was 0.2 higher/lower than 95% of the fertile control samples, and showed statistically significant association with fertility potential under hold-one-out cross-validation. The analyzed samples were a combination of those used in Aston et. al (2015), and 264 new samples collected from Episona’s partner sperm banks (known-fertile samples) and fertility clinics (infertile samples). Infertile samples were collected from couples with no known female-factor impacting their infertility and normal semen analysis parameters. 37% of infertile samples examined had one or more genes differentially methylated by the above criteria. Most samples with differential methylation had only 1 or 2 differentially methylated genes (145 samples), while a minority had very large counts (16 samples had more than 100 differentially methylated genes). Common differentially methylated genes included FCGBP (differentially methylated in 22 samples; putatively involved in sperm–zona pellucida interaction), ID3 (20 samples; known role in murine male infertility) and a region containing two taste receptors-TAS2R60 and TAS2R41 (28 samples; speculated to be involved in sperm chemotaxis). In other cases, such as the gene TBCD (37 cases), the role in fertility is less clear. Our data support the hypothesis that male-factor infertility is multi-faceted, with many different potential underlying causes. We have taken initial steps to identify common epigenetic disruptions that are likely to be associated with male-factor infertility, but which don’t impact morphology or motility and hence may be difficult or impossible to identify by standard semen analysis methods.