Mutations of the SLIT2–ROBO2 pathway genes SLIT2 and SRGAP1 confer risk for congenital anomalies of the kidney and urinary tract

Abstract

Congenital anomalies of the kidney and urinary tract (CAKUT) account for 40–50% of chronic kidney disease that manifests in the first two decades of life. Thus far, 31 monogenic causes of isolated CAKUT have been described, explaining ~12% of cases. To identify additional CAKUT-causing genes, we performed whole exome sequencing followed by a genetic burden analysis in 26 genetically unsolved families with CAKUT. We identified two heterozygous mutations in SRGAP1 in 2 unrelated families. SRGAP1 is a small GTPase activating protein in the SLIT2-ROBO2 signaling pathway, which is essential for development of the metanephric kidney. We then examined the pathway-derived candidate gene SLIT2 for mutations in cohort of 749 individuals with CAKUT and we identified 3 unrelated individuals with heterozygous mutations. The clinical phenotypes of individuals with mutations in SLIT2 or SRGAP1 were cystic dysplastic kidneys, unilateral renal agenesis, and duplicated collecting system. We show that SRGAP1 is expressed in early mouse nephrogenic mesenchyme and that it is coexpressed with ROBO2 in SIX2-positive nephron progenitor cells of the cap mesenchyme in developing rat kidney. We demonstrate that the newly identified mutations in SRGAP1 lead to an augmented inhibition of RAC1 in cultured human embryonic kidney cells and that the SLIT2 mutations compromise the ability of the SLIT2 ligand to inhibit cell migration. Thus, we report on two novel candidate genes for causing monogenic isolated CAKUT in humans.

Exome Sequencing Discerns Syndromes in Patients from Consanguineous Families with Congenital Anomalies of the Kidneys and Urinary Tract

“…4 Recently, it was shown that a monogenic cause can be detected in approximately 12% of patients. 2,[5][6][7][8] The documented mode of inheritance in most published pedigrees is compatible with an autosomal dominant inheritance with variable expressivity and incomplete penetrance. 2 However, several CAKUT-causing genes with autosomal recessive mode of inheritance have been recently identified.…”

Identification of 8 Novel Mutations in Nephrogenesis-Related Genes in Chinese Han Patients with Unilateral Renal Agenesis

“…Furthermore, certain recently discovered disease-causing genes, such as SRGAP1, SLIT2 [39,] and TBC1D1 [40] were not included because they were described in the literature only after the completion of our study. The functional relevance of the identified mutations was not explored, which was a limitation of the study, and we intend to explore this topic further in the future.…”

Slit-Robo signaling

“…Slit-Robo signaling has also been implicated in kidney development in humans. Whole exome-sequencing of patients suffering from congenital abnormalities of the kidney and urinary tract (CAKUT) identified mutations in SRGAP1 and SLIT2 (Hwang et al, 2015); the SRGAP1 mutation results in a gain-of-function phenotype with increased RAC1 inhibition, whereas the SLIT2 mutations all cluster in the regions encoding the LRR domains and hence may interfere with ROBO binding.…”