The genetic architecture of membranous nephropathy and its potential to improve non-invasive diagnosis

Membranous Nephropathy (MN) is a rare autoimmune cause of kidney failure. Here we report a genome-wide association study (GWAS) for primary MN in 3,782 cases and 9,038 controls of East Asian and European ancestries. We discover two previously unreported loci, NFKB1 (rs230540, OR = 1.25, P = 3.4 × 10−12) and IRF4 (rs9405192, OR = 1.29, P = 1.4 × 10−14), fine-map the PLA2R1 locus (rs17831251, OR = 2.25, P = 4.7 × 10−103) and report ancestry-specific effects of three classical HLA alleles: DRB1*1501 in East Asians (OR = 3.81, P = 2.0 × 10−49), DQA1*0501 in Europeans (OR = 2.88, P = 5.7 × 10−93), and DRB1*0301 in both ethnicities (OR = 3.50, P = 9.2 × 10−23 and OR = 3.39, P = 5.2 × 10−82, respectively). GWAS loci explain 32% of disease risk in East Asians and 25% in Europeans, and correctly re-classify 20–37% of the cases in validation cohorts that are antibody-negative by the serum anti-PLA2R ELISA diagnostic test. Our findings highlight an unusual genetic architecture of MN, with four loci and their interactions accounting for nearly one-third of the disease risk

Genetic Drivers of Kidney Defects in the DiGeorge Syndrome

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.)

The genetic architecture of membranous nephropathy and its potential to improve non-invasive diagnosis

Membranous Nephropathy (MN) is a rare autoimmune cause of kidney failure. Here we report a genome-wide association study (GWAS) for primary MN in 3,782 cases and 9,038 controls of East Asian and European ancestries. We discover two previously unreported loci, NFKB1 (rs230540, OR = 1.25, P = 3.4 × 10-12) and IRF4 (rs9405192, OR = 1.29, P = 1.4 × 10-14), fine-map the PLA2R1 locus (rs17831251, OR = 2.25, P = 4.7 × 10-103) and report ancestry-specific effects of three classical HLA alleles: DRB1*1501 in East Asians (OR = 3.81, P = 2.0 × 10-49), DQA1*0501 in Europeans (OR = 2.88, P = 5.7 × 10-93), and DRB1*0301 in both ethnicities (OR = 3.50, P = 9.2 × 10-23 and OR = 3.39, P = 5.2 × 10-82, respectively). GWAS loci explain 32% of disease risk in East Asians and 25% in Europeans, and correctly re-classify 20-37% of the cases in validation cohorts that are antibody-negative by the serum anti-PLA2R ELISA diagnostic test. Our findings highlight an unusual genetic architecture of MN, with four loci and their interactions accounting for nearly one-third of the disease risk

Genomic analyses to guide diagnosis and treatment in congenital anomalies of the kidney and urinary tract (CAKUT)

Congenital anomalies of the kidneys and urinary tract are the leading cause of end stage renal disease (ESRD) in children and young adults. CAKUT diagnosis is currently based on imaging studies and It is classified using descriptive anatomic criteria which omit the underlying pathogenetic and molecular mechanisms. Studies from our group indicate that a large fraction of CAKUT is attributable to rare genetic variants with large effect size. In particular, both point mutations and structural genomic variants (copy number variations, CNVs), detectable by whole exome sequencing (WES) or DNA microarrays, respectively, account for 10 to 30% of the cases. Nevertheless, genetic tests are often not performed or not clinically indicated, thus limiting prognosis and medical management. Here we present a new multi-institutional Italian study group on CAKUT, composed of a network of clinical and basic investigators in adult and pediatric nephrology and urology. The group aims at the recruitment and clinical characterization of 5,000 patients affected by CAKUT to conduct detailed clinical characterization and perform research DNA microarrays and WES in all patients (in collaboration with Columbia University). To date, 30 Italian centers have an approved IRB are actively enrolling for these studies or they are in the process of submitting or activating the IRB in order to start enrolling patients. We currently recruited and characterized 1,482 independent index patients. We plan to reach the target goal of 5,000 patients in four years. The deep clinical and phenotypic characterization will allow precise anatomical classification of disease. Genetic data will be use to guide deep phenotyping (ex imaging studies, metabolic tests, neurodevelopmental tests). The longitudinal design will allow identification of both genetic and non genetic prognostic factors. Finally, this project aims at a reclassification of CAKUT based on underlying molecular genetics mechanisms, in order to improve renal and overall patient outcom

Surgical validation of functional magnetic resonance urography in the study of ureteropelvic junction obstruction in a pediatric cohort

Introduction: Ureteropelvic junction obstruction (UPJO) is one of the most common urological diseases in children. The etiology can be intrinsic, extrinsic (crossing vessel [CV] or adhesions), or mixed. To date, ultrasonography and scintigraphy are considered gold-standard imaging techniques for the study of UPJO. Functional magnetic resonance urography (fMRU) combines anatomical and functional information and has been recently evaluated for the detection of CVs in UPJO. Objective: The objective of the study was to evaluate the concordance between fMRU and surgery in determining the etiology of UPJO and the presence of obstructing/non-obstructing CVs. Study design: Patients with unilateral hydronephrosis who underwent surgery after an fMRU were included in the sample. Surgical data regarding the etiology of UPJO were compared with radiological results. The etiology was divided into intrinsic, extrinsic due to CV, extrinsic due to adhesions, and mixed or cicatricial (postoperative). The concordance was calculated by means of the Cohen's kappa coefficient. Results: The observed agreement between fMRU and surgical findings regarding the etiology and the presence of CV were 83.2% and 89.4%, respectively (with substantial Cohen's kappa coefficient). The sensitivity and specificity of fMRU were 0.84 and 0.93, respectively; the positive predictive value (PPV) and negative predictive value (NPV) were 0.889 and 0.897, respectively. The observed agreement regarding the type of vessel was 88.3% with a Cohen's kappa coefficient of 0.787 (substantial). Discussion: In children with hydronephrosis, it is very important for the surgeon to quantify the extent of dilation, define the etiology of the obstruction, and the presence or absence of CVs. fMRU is a \u2018one-stop-shop\u2019 technique which provides both anatomical and functional information showing a high concordance with surgical findings, avoiding radiation exposure. Conclusions: fMRU should be considered a valid imaging technique in the study of pediatric UPJO, as it provides the surgeon with important information regarding the etiology of the obstruction for the preoperative planning.[Figure presented