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.)

BACKGROUND Congenital abnormalities of the kidney and the urinary tract are the most common cause of pediatric kidney failure. These disorders are highly heterogeneous, and the etiologic factors are poorly understood. METHODS We performed genomewide linkage analysis and whole-exome sequencing in a family with an autosomal dominant form of congenital abnormalities of the kidney or urinary tract (seven affected family members). We also performed a sequence analysis in 311 unrelated patients, as well as histologic and functional studies. RESULTS Linkage analysis identified five regions of the genome that were shared among all affected family members. Exome sequencing identified a single, rare, deleterious variant within these linkage intervals, a heterozygous splice-site mutation in the dual serine–threonine and tyrosine protein kinase gene (DSTYK). This variant, which resulted in aberrant splicing of messenger RNA, was present in all affected family members. Additional, independent DSTYK mutations, including nonsense and splice-site mutations, were detected in 7 of 311 unrelated patients. DSTYK is highly expressed in the maturing epithelia of all major organs, localizing to cell membranes. Knockdown in zebrafish resulted in developmental defects in multiple organs, which suggested loss of fibroblast growth factor (FGF) signaling. Consistent with this finding is the observation that DSTYK colocalizes with FGF receptors in the ureteric bud and metanephric mesenchyme. DSTYK knockdown in human embryonic kidney cells inhibited FGF-stimulated phosphorylation of extracellular-signal-regulated kinase (ERK), the principal signal downstream of receptor tyrosine kinases. CONCLUSIONS We detected independent DSTYK mutations in 2.3% of patients with congenital abnormalities of the kidney or urinary tract, a finding that suggests that DSTYK is a major determinant of human urinary tract development, downstream of FGF signaling. (Funded by the National Institutes of Health and others.)

Renal agenesis and hypodysplasia (RHD) are major causes of pediatric chronic kidney disease and are highly genetically heterogeneous. We conducted whole-exome sequencing in 202 case subjects with RHD and identified diagnostic mutations in genes known to be associated with RHD in 7/202 case subjects. In an additional affected individual with RHD and a congenital heart defect, we found a homozygous loss-of-function (LOF) variant in SLIT3, recapitulating phenotypes reported with Slit3 inactivation in the mouse. To identify genes associated with RHD, we performed an exome-wide association study with 195 unresolved case subjects and 6,905 control subjects. The top signal resided in GREB1L, a gene implicated previously in Hoxb1 and Shha signaling in zebrafish. The significance of the association, which was p = 2.0 × 10 for novel LOF, increased to p = 4.1 × 10 for LOF and deleterious missense variants combined, and augmented further after accounting for segregation and de novo inheritance of rare variants (joint p = 2.3 × 10). Finally, CRISPR/Cas9 disruption or knockdown of greb1l in zebrafish caused specific pronephric defects, which were rescued by wild-type human GREB1L mRNA, but not mRNA containing alleles identified in case subjects. Together, our study provides insight into the genetic landscape of kidney malformations in humans, presents multiple candidates, and identifies SLIT3 and GREB1L as genes implicated in the pathogenesis of RHD.

Copy number variations associate with different developmental phenotypes and represent a major cause of congenital anomalies of the kidney and urinary tract (CAKUT). Because rare pathogenic copy number variations are often large and contain multiple genes, identification of the underlying genetic drivers has proven to be difficult. Here we studied the role of rare copy number variations in 80 patients from the KIMONO-study cohort for which pathogenic mutations in three genes commonly implicated in CAKUT were excluded. In total, 13 known or novel genomic imbalances in 11 of 80 patients were absent or extremely rare in 23,362 population controls. To identify the most likely genetic drivers for the CAKUT phenotype underlying these rare copy number variations, we used a systematic in silico approach based on frequency in a large dataset of controls, annotation with publicly available databases for developmental diseases, tolerance and haploinsufficiency scores, and gene expression profile in the developing kidney and urinary tract. Five novel candidate genes for CAKUT were identified that showed specific expression in the human and mouse developing urinary tract. Among these genes, DLG1 and KIF12 are likely novel susceptibility genes for CAKUT in humans. Thus, there is a significant role of genomic imbalance in the determination of kidney developmental phenotypes. Additionally, we defined a systematic strategy to identify genetic drivers underlying rare copy number variations.

Ciliogenesis in developing and post-natal human kidneys appears to influence cell proliferation and differentiation, apico-basal cell polarity, and tubular lumen formation. We have analyzed the appearance of primary cilia and differentiation of kidney cells in ten human conceptuses aged 6-22 weeks and in one 5-year-old kidney, using a double immunofluorescence labeling technique for α-tubulin, γ-tubulin, Oct-4, and Ki-67 and by electron microscopy. Immature forms of nephrons and ampullae were characterized by intense cell proliferation, which subsequently decreased during development. Primary cilia appeared on the surfaces of non-proliferating cells in developing nephrons, gradually increasing in length from 0.59 μm in renal vesicles to 0.81 μm in the S-forms of nephrons, ultimately reaching 3.04 μm in length in mature fetal and post-natal nephrons. Ciliary length increased from 0.59 μm in ampullae to 1.28 μm in post-natal collecting tubules. Mesenchymal to epithelial transformation of kidney cells coincided with the appearance of apico-basal polarity, both gap and tight junctions, and lumen formation. Up-regulation of Oct-4 expression correlated with the onset of kidney cell differentiation. Our results demonstrate the importance of proper primary cilia lengthening and Oct-4 expression for the normal development of fetal and post-natal kidneys and of apico-basal polarity for normal tubular lumen formation. Disturbances in these processes are associated with ciliopathies.

Background: Information about renal diseases in children is available from national registries of renal biopsies. Aim of the study was to compare the clinical presentation of glomerular diseases and tubulointerstitial space diseases with pathohistological diagnosis of indicated renal biopsies from pediatric population in the Croatian region of Dalmatia. Methods: Out of 231 pediatric patients with suspected glomerular and tubulointerstitial diseases, 54 underwent ultrasound-guided renal biopsy at University Hospital of Split. Kidney allograft biopsy, and re-biopsy were excluded. The biopsy sections were examined under light microscopy, immunofluorescence and electron microscopy. The data was reviewed to determine the pathohistological spectrum and clinicopathologic correlations. We retrospectively analyzed kidney biopsy data from 2008 to 2017 and compared them to that between 1995 and 2005.Results: The mean age of patients was 9.84 ± 5.4 years. Male:female ratio was 1.2:1. The main indications for biopsy were pure nephrotic syndrome without hematuria (25.9%), non-nephrotic proteinuria with haematuria (22.2%), nephritic syndrome with nephrotic proteinuria (18.5%), and isolated hematuria (16.7%). The most common pathohistological findings were IgA nephropathy (IgAN, 24.1%), minimal change disease (MCD, 16.7%), Henoch-Schönlein purpura glomerulonephritis (HSPN, 14.8%), Alport syndrome and focal segmental glomerulosclerosis (AS and FSGS, 11.1% each), tubulointerstitial nephritis and membranous glomerulopathy (TIN and MGN, 3.7% each), while other cases were diagnosed rarely. Conclusions:Changes in epidemiology of renal diseases in children between the analyzed periods showed an increasing trend of IgAN, MCD, HSPN, AS and FSGS, while mesangioproliferative glomerulonephritis (MesPGN) and endoproliferative glomerulonephritis (EDGN) showed a decreasing trend that can be explained with the new pathohistological classification.

There is low awareness about EBM and The Cochrane Library among physicians in Croatia, which creates a need for educational interventions about EBM for the benefit of health care in Croatia.

Spatio-temporal immunolocalizations of cytokeratin 8 (CK8), vimentin, syndecan-1 and Ki-67 were analyzed in ten human incisors and canine tooth germs between the 7th and 20th developmental weeks. CK8 expression was mild to moderate in the epithelial tooth parts, while it shifted from absent or mild in its mesenchymal parts, but few cells, sparsely distributed throughout the tooth germ, strongly expressed CK8. As development progressed, CK8 expression increased to strong in preameloblasts, while expression of vimentin increased to moderate in the epithelial and mesenchymal tooth parts, particularly in the dental papilla and sac. Co-expression of CK8 and vimentin was observed in some parts of the tooth germ, and was increasing in the differentiating preameloblasts and preodontoblasts. Syndecan-1 showed characteristic shift of expression from epithelial to mesenchymal tooth parts, being particularly strong in dental papilla, sac and cervical loops, while co-expression of Ki-67/syndecan-1 was strong in the dental papilla. Our study demonstrated spatio-temporal expression and restricted co-expression of the investigated markers, indicating participation of CK8 and vimentin in cell proliferation and migration, and differentiation of preodontoblasts and preameloblasts. Our data also suggest involvement of syndecan-1 in morphogenesis of the developing tooth crown and cervical loops, and together with CK8 and vimentin in differentiation of preameloblasts and preodontoblasts.