Genetic Drivers of Kidney Defects in the DiGeorge Syndrome

Abstract

BACKGROUND The DiGeorge syndrome, the most common of the microdeletion syndromes, affects multiple organs, including the heart, the nervous system, and the kidney. It is caused by deletions on chromosome 22q11.2; the genetic driver of the kidney defects is unknown. METHODS We conducted a genomewide search for structural variants in two cohorts: 2080 patients with congenital kidney and urinary tract anomalies and 22,094 controls. We performed exome and targeted resequencing in samples obtained from 586 additional patients with congenital kidney anomalies. We also carried out functional studies using zebrafish and mice. RESULTS We identified heterozygous deletions of 22q11.2 in 1.1% of the patients with congenital kidney anomalies and in 0.01% of population controls (odds ratio, 81.5; P=4.5×10−14). We localized the main drivers of renal disease in the DiGeorge syndrome to a 370-kb region containing nine genes. In zebrafish embryos, an induced loss of function in snap29, aifm3, and crkl resulted in renal defects; the loss of crkl alone was sufficient to induce defects. Five of 586 patients with congenital urinary anomalies had newly identified, heterozygous protein-altering variants, including a premature termination codon, in CRKL. The inactivation of Crkl in the mouse model induced developmental defects similar to those observed in patients with congenital urinary anomalies. CONCLUSIONS We identified a recurrent 370-kb deletion at the 22q11.2 locus as a driver of kidney defects in the DiGeorge syndrome and in sporadic congenital kidney and urinary tract anomalies. Of the nine genes at this locus, SNAP29, AIFM3, and CRKL appear to be critical to the phenotype, with haploinsufficiency of CRKL emerging as the main genetic driver. (Funded by the National Institutes of Health and others.)

Urinary Anomalies in 22q11.2 Deletion (DiGeorge syndrome): From Copy Number Variations to Single-Gene Determinants of Phenotype

“…In the study from Lopez-Rivera et al, 10 a large cohort of patients referred with a diagnosis of CAKUT (isolated CAKUT and syndromic CAKUT) were subjected to whole-genome copy number variation analysis followed by: (1) critical examination of the area of overlap in patients with 22q11.2 microdeletion, (2) molecular genetic characterization of the pathogenicity of candidate genes using high-throughput in vivo phenotyping in zebrafish, (3) statistical analysis to determine the mutation burden in candidate genes, and (4) recapitulation of the CAKUT phenotype using global and tissue-specific knockout of the candidate genes in murine models. Using the multitiered strategy, 9 candidate genes were linked to the renal phenotype in DiGeorge syndrome.…”

“…10 This is the most common microdeletion syndrome in humans, 11 and patients classically present with malformations in multiple organs, including facial anomalies, cardiac defects, neurologic malformations and learning disability, thymic hypoplasia resulting in T-cell deficiency, hypoparathyroidism, and CAKUT, among others. 11–13 The prevalence of CAKUT in 22q11.2 microdeletion is ~30%.…”

“…Using the multitiered strategy, 9 candidate genes were linked to the renal phenotype in DiGeorge syndrome. 10 Knockdown of 3 of these genes ( snap29 , aifm3 , and crkl ) was found to be associated with renal anomalies in zebrafish. Most importantly, it was shown that targeted knockdown in crkl alone was enough to induce the CAKUT phenotype in zebrafish, and patients with isolated CAKUT were found to have pathogenic mutations in the human homolog ( CRKL ), thus establishing this gene as a new cause of both syndromic and isolated CAKUT.…”

“…Most importantly, it was shown that targeted knockdown in crkl alone was enough to induce the CAKUT phenotype in zebrafish, and patients with isolated CAKUT were found to have pathogenic mutations in the human homolog ( CRKL ), thus establishing this gene as a new cause of both syndromic and isolated CAKUT. 10 …”

“…One innovative multistep approach was recently reported by a group of investigators in the United States and Europe. 10 …”