DNA Methyltransferase 1 Controls Nephron Progenitor Cell Renewal and Differentiation.

Abstract

Nephron number is a major determinant of long-term renal function and cardiovascular risk. Observational studies suggest that maternal nutritional and metabolic factors during gestation contribute to the high variability of nephron endowment. However, the underlying molecular mechanisms have been unclear. We used mouse models, including DNA methyltransferase (<i>Dnmt1, Dnmt3a,</i> and <i>Dnmt3b</i>) knockout mice, optical projection tomography, three-dimensional reconstructions of the nephrogenic niche, and transcriptome and DNA methylation analysis to characterize the role of DNA methylation for kidney development. We demonstrate that DNA hypomethylation is a key feature of nutritional kidney growth restriction <i>in vitro</i> and <i>in vivo,</i> and that DNA methyltransferases <i>Dnmt1</i> and <i>Dnmt3a</i> are highly enriched in the nephrogenic zone of the developing kidneys. Deletion of <i>Dnmt1</i> in nephron progenitor cells (in contrast to deletion of <i>Dnmt3a</i> or <i>Dnm3b</i>) mimics nutritional models of kidney growth restriction and results in a substantial reduction of nephron number as well as renal hypoplasia at birth. In <i>Dnmt1</i>-deficient mice, optical projection tomography and three-dimensional reconstructions uncovered a significant reduction of stem cell niches and progenitor cells. RNA sequencing analysis revealed that global DNA hypomethylation interferes in the progenitor cell regulatory network, leading to downregulation of genes crucial for initiation of nephrogenesis, <i>Wt1</i> and its target <i>Wnt4.</i> Derepression of germline genes, protocadherins, <i>Rhox</i> genes, and endogenous retroviral elements resulted in the upregulation of IFN targets and inhibitors of cell cycle progression. These findings establish DNA methylation as a key regulatory event of prenatal renal programming, which possibly represents a fundamental link between maternal nutritional factors during gestation and reduced nephron number.