Epigenome-wide association study for glyphosate induced transgenerational sperm DNA methylation and histone retention epigenetic biomarkers for disease

ABSTRACT

The herbicide glyphosate has been shown to promote the epigenetic transgenerational inheritance of pathology and disease in subsequent great-grand offspring (F3 generation). This generational toxicology suggests the impacts of environmental exposures need to assess subsequent generations. The current study was designed to identify epigenetic biomarkers for glyphosate-induced transgenerational diseases using an epigenome-wide association study (EWAS). Following transient glyphosate exposure of gestating female rats (F0 generation), during the developmental period of gonadal sex determination, the subsequent transgenerational F3 generation, with no direct exposure, were aged to 1 year and animals with specific pathologies identified. The pathologies investigated included prostate disease, kidney disease, obesity, and presence of multiple disease. The sperm were collected from the glyphosate lineage males with only an individual disease and used to identify specific differential DNA methylation regions (DMRs) and the differential histone retention sites (DHRs) associated with that pathology. Unique signatures of DMRs and DHRs for each pathology were identified for the specific diseases. Interestingly, at a lower statistical threshold overlapping sets of DMRs and DHRs were identified that were common for all the pathologies. This is one of the first observations that sperm histone retention can potentially act as a biomarker for specific diseases. The DMR and DHR associated genes were identified and correlated with known pathology specific-associated genes. Observations indicate transgenerational epigenetic biomarkers of disease pathology can be identified in the sperm that appear to assess disease susceptibility. These biomarkers suggest epigenetic diagnostics could potentially be used to facilitate preventative medicine.

KEYWORDS:

• Glyphosate
• sperm
• diagnostics
• prostate Disease
• kidney Disease
• obesity
• multiple Pathology
• ewas

Supplemental data

Supplemental data for this article can be accessed here.

Availability of Data and Materials

All molecular data have been deposited into the public database at NCBI (GEO # GSE118557 and GSE152678), and R code computational tools are available at GitHub (https://github.com/skinnerlab/MeDIP-seq) and www.skinner.wsu.edu.

Ethics approval

All experimental protocols for the procedures with rats were pre-approved by the Washington State University Animal Care and Use Committee (protocol IACUC # 2568), and all methods were performed in accordance with the relevant guidelines and regulations.

Consent for Publication

Not applicable.

Acknowledgments

We acknowledge Dr. Ingrid Sadler-Riggleman, Ms. Michelle Pappalardo, and Mr. Ryan Thompson for technical assistance. We acknowledge Ms. Amanda Quilty for editing and Ms. Heather Johnson for assistance in preparation of the manuscript. We thank the Genomics Core laboratory at WSU Spokane for sequencing data. This study was supported by John Templeton Foundation (50183 and 61174) (https://templeton.org/) grants to MKS and NIH (ES012974) (https://www.nih.gov/) grant to MKS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author contributions

MBM Molecular analysis, data analysis, wrote and edited manuscript.

DB Bioinformatic analysis, data analysis, edited manuscript.

EN Animal studies, cell isolations, data analysis, edited manuscript.

DK Animal breeding and care, data analysis, edited manuscript.

MKS Conceived, oversight, obtained funding, data analysis, wrote and edited manuscript.

Disclosure of Interest

The authors report no conflict of interest.

Funding

This study was supported by John Templeton Foundation (50183 and 61174) (https://templeton.org/) grants to MKS and NIH (ES012974) (https://www.nih.gov/) grant to MKS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript;National Institutes of Health [ES012974];

Additional information

Funding

This study was supported by John Templeton Foundation (50183 and 61174) (https://templeton.org/) grants to MKS and NIH (ES012974) (https://www.nih.gov/) grant to MKS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript;National Institutes of Health [ES012974];