Caloric restriction during pregnancy impairs nephrogenesis by modifying epigenetic regulation in nephron progenitor cells

Introduction - Poor intrauterine environment, as maternal malnutrition, impairs offspring nephron endowment and increases the risk of chronic kidney disease. We have previously demonstrated that methionine metabolism has an important role in mediating the negative effects of caloric restriction during pregnancy on nephron endowment. Furthermore, methionine is pivotal in many epigenetic gene expression regulation processes as a methyl donor, leading us to examine malnutrition`s effects on DNA methylation in nephron progenitor cells.

Methods – Caloric intake of pregnant mice was limited to 70% of daily intake. Nephron progenitor cells were FACS-based cell-sorted using transgenic mice, and DNA was extracted. Methylation patterns were characterized using reduced representation bisulfite sequencing. Results were cross-referenced with chromatin accessibility and histone modification available data. The effects of methylation changes in regulatory regions on the expression of identified genes were validated using RT-qPCR. In addition, the effects of methionine supplementation on methylation patterns were evaluated using Bisulfite Amplicon Sequencing.

Results – Caloric restriction during pregnancy leads to a global decrease in DNA methylation in nephron progenitor cells. Most changes in DNA methylation were localized to gene regulatory regions, including genes involved in nephrogenesis and pivotal intracellular signaling pathways. The perturbations in regulatory DNA methylation patterns of these genes were correlated with expression profile changes. Methionine supplementation alleviated the changes in methylation patterns caused by maternal malnutrition.

Conclusion – This is the first evidence that maternal malnutrition during pregnancy impairs nephrogenesis by modifying DNA methylation patterns in nephron progenitor cells, an effect significantly attenuated by methionine supplementation.