Aberrations in Sperm DNA Methylation Patterns Are Associated with Abnormalities in Semen Parameters of Subfertile Males

Infertility affects about 15% of couples worldwide, with approximately 7% of males suffering from infertility problems. This study was designed to assess the relationship between alterations in sperm DNA methylation patterns and semen parameters in subfertile males. Of a total of 108 males, 30 samples were subjected to 450K BeadChip arrays to evaluate the variation in DNA methylation level between cases and controls. Three CpG sites showed the highest difference in methylation levels (cg09737095, cg14271023, and cg17662493), which are located in the KCNJ5, MLPH, and SMC1β genes, respectively; these were selected for further analysis using deep bisulfite sequencing in 78 independent samples (21 proven fertile "controls", and 57 subfertile "cases"). The results of a validation study showed that variation in methylation levels was found in more than one CpG site: there was a significant decrease in methylation levels at six CpGs (CpG1, CpG3, CpG4, CpG6, CpG7, and CpG8) in the KCNJ5 gene-related amplicon (p≤0.001, p≤0.009, p≤0.007, p≤0.007, p≤0.020, and p≤0.016, respectively), and at (CpG1, CpG2, and CpG4) in the MLPH gene-related amplicon (p≤0.003, p≤0.005, and p≤0.0001, respectively), while there was a significant increase in the methylation level at six out of eight CpGs in the SMC1β gene-related amplicon in cases compared to controls. Our results show that three CpGs have a significant difference in sperm DNA methylation levels in subfertile males compared to proven fertile males.