Genetic Variants in ARHGEF6 Cause Congenital Anomalies of the Kidneys and Urinary Tract in Humans, Mice, and Frogs

Significance Statement About 40 disease genes have been described to date for isolated CAKUT, the most common cause of CKD during childhood. However, mutations in these genes explain only 20% of cases. The authors performed exome sequencing in an international cohort of individuals with CAKUT. They identified genetic variants in ARHGEF6 (a gene on the X chromosome in humans that encodes a guanine nucleotide exchange factor) as a potential novel cause of this disease. Using a multifaceted approach, including cellular and independent animal models, they found evidence that ARHGEF6 variants cause disease, potentially via dysregulation of integrin/parvin/RAC1/CDC42 signaling. These findings further link ARHGEF6 function to integrin/parvin/RAC1/CDC42 signaling, thereby strengthening this pathway's relevance for renal development. Background About 40 disease genes have been described to date for isolated CAKUT, the most common cause of childhood CKD. However, these genes account for only 20% of cases. ARHGEF6, a guanine nucleotide exchange factor that is implicated in biologic processes such as cell migration and focal adhesion, acts downstream of integrin-linked kinase (ILK) and parvin proteins. A genetic variant of ILK that causes murine renal agenesis abrogates the interaction of ILK with a murine focal adhesion protein encoded by Parva , leading to CAKUT in mice with this variant. Methods To identify novel genes that, when mutated, result in CAKUT, we performed exome sequencing in an international cohort of 1265 families with CAKUT. We also assessed the effects in vitro of wild-type and mutant ARHGEF6 proteins, and the effects of Arhgef6 deficiency in mouse and frog models. Results We detected six different hemizygous variants in the gene ARHGEF6 (which is located on the X chromosome in humans) in eight individuals from six families with CAKUT. In kidney cells, overexpression of wild-type ARHGEF6 —but not proband-derived mutant ARHGEF6 —increased active levels of CDC42/RAC1, induced lamellipodia formation, and stimulated PARVA-dependent cell spreading. ARHGEF6-mutant proteins showed loss of interaction with PARVA. Three-dimensional Madin-Darby canine kidney cell cultures expressing ARHGEF6-mutant proteins exhibited reduced lumen formation and polarity defects. Arhgef6 deficiency in mouse and frog models recapitulated features of human CAKUT. Conclusions Deleterious variants in ARHGEF6 may cause dysregulation of integrin-parvin-RAC1/CDC42 signaling, thereby leading to X-linked CAKUT.