Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses

Urinary concentrations of phthalate and phthalate alternative metabolites and sperm DNA methylation: A multi-cohort and meta-analysis of men in preconception studies

Phthalates are ubiquitous pollutants in the environment; however, the mechanisms of phthalate-associated reproductive disorders in men are not fully understood. The aim of this study is to investigate associations between urinary phthalate metabolite concentrations and sperm DNA methylation. The study was conducted on 697 men from three prospective pregnancy cohorts: Longitudinal Investigation of Fertility and the Environment (LIFE) Study, Sperm Environmental Epigenetics and Development Study (SEEDS), and Environment and Reproductive Health (EARTH) Study. Eighteen phthalate and two phthalate alternative metabolites were quantified by mass spectrometry in preconception urinary samples and sperm DNA methylation was measured via Illumina EPIC Array (v1). Regional methylation analyses were conducted to identify cohort-specific loci associated with urinary phthalate metabolites. Models were adjusted for age, body mass index (BMI), race, smoking status, urinary creatinine/specific gravity, and analytical batch for phthalate measurements. The cohort-specific results were meta-analyzed using METAL. Participants had an average age of 30 years, most (79.6 %) of whom had BMI>25 kg/m2 and were non-smokers (90.1 %). A total of 7,979 differentially methylated regions (DMRs; 7,979 LIFE-specific DMRs, 72 SEEDS-specific DMRs, and 23 EARTH-specific DMRs) were associated with urinary MBzP, MiBP, MMP, MCNP, MCPP, MBP, and MCOCH. Meta-analysis identified fewer DMRs than cohort-specific models: 946 DMRs were associated with MBzP, 27 DMRs associated with MiBP, and 1 DMR associated with MEHP. The majority of cohort-specific and meta-analysis-derived DMRs displayed a positive association with phthalate metabolite concentrations and were enriched in genes associated with spermatogenesis, response to hormones and their metabolism, embryonic organ development and developmental growth. In conclusion, several preconception urinary phthalate metabolites were associated with increased DNA methylation patterns in sperm. These findings provide an epigenetic pathway by which environmental phthalate exposures can impact couples' reproductive outcomes.

Mixtures of per- and polyfluoroalkyl substances (PFAS) alter sperm methylation and long-term reprogramming of offspring liver and fat transcriptome

Male fertility has been declining worldwide especially in countries with high levels of endocrine disrupting chemicals (EDCs). Per- and polyfluorinated alkyl Substances (PFAS) have been classified as EDCs and have been linked to adverse male reproductive health. The mechanisms of these associations and their implications on offspring health remain unknown. The aims of the current study were to assess the effect of PFAS mixtures on the sperm methylome and transcriptional changes in offspring metabolic tissues (i.e., liver and fat). C57BL/6 male mice were exposed to a mixture of PFAS (PFOS, PFOA, PFNA, PFHxS, Genx; 20 µg/L each) for 18-weeks or water as a control. Genome-wide methylation was assessed on F0 epidydimal sperm using reduced representation bisulfite sequencing (RRBS) and Illumina mouse methylation array, while gene expression was assessed by bulk RNA sequencing in 8-week-old offspring derived from unexposed females. PFAS mixtures resulted in 2,861 (RRBS) and 83 (Illumina) sperm DMRs (q < 0.05). Functional enrichment revealed that PFAS-induced sperm DMRs were associated with behavior and developmental pathways in RRBS, while Illumina DMRs were related to lipid metabolism and cell signaling. Additionally, PFAS mixtures resulted in 40 and 53 differentially expressed genes (DEGs) in the liver and fat of males, and 9 and 31 DEGs in females, respectively. Functional enrichment of DEGs revealed alterations in cholesterol metabolism and mitotic cell cycle regulation in the liver and myeloid leukocyte migration in fat of male offspring, while in female offspring, erythrocyte development and carbohydrate catabolism were affected in fat. Our results demonstrate that exposure to a mixture of legacy and newly emerging PFAS chemicals in adult male mice result in aberrant sperm methylation and altered gene expression of offspring liver and fat in a sex-specific manner. These data indicate that preconception PFAS exposure in males can be transmitted to affect phenotype in the next generation.