Targeted exome sequencing integrated with clinicopathological information reveals novel and rare mutations in atypical, suspected and unknown cases of Alport syndrome or proteinuria.

We applied customized targeted next-generation exome sequencing (NGS) to determine if mutations in genes associated with renal malformations, Alport syndrome (AS) or nephrotic syndrome are a potential cause of renal abnormalities in patients with equivocal or atypical presentation. We first sequenced 4,041 exons representing 292 kidney disease genes in a Caucasian woman with a history of congenital vesicoureteral reflux (VUR), recurrent urinary tract infections and hydronephrosis who presented with nephrotic range proteinuria at the age of 45. Her biopsy was remarkable for focal segmental glomerulosclerosis (FSGS), a potential complication of longstanding VUR. She had no family history of renal disease. Her proteinuria improved initially, however, several years later she presented with worsening proteinuria and microhematuria. NGS analysis revealed two deleterious COL4A3 mutations, one novel and the other previously reported in AS, and a novel deleterious SALL2 mutation, a gene linked to renal malformations. Pedigree analysis confirmed that COL4A3 mutations were nonallelic and compound heterozygous. The genomic results in conjunction with subsequent abnormal electron microscopy, Collagen IV minor chain immunohistochemistry and progressive sensorineural hearing loss confirmed AS. We then modified our NGS approach to enable more efficient discovery of variants associated with AS or a subset of FSGS by multiplexing targeted exome sequencing of 19 genes associated with AS or FSGS in 14 patients. Using this approach, we found novel or known COL4A3 or COL4A5 mutations in a subset of patients with clinically diagnosed or suspected AS, APOL1 variants associated with FSGS in African Americans and novel mutations in genes associated with nephrotic syndrome. These studies demonstrate the successful application of targeted capture-based exome sequencing to simultaneously evaluate genetic variations in many genes in patients with complex renal phenotypes and provide insights into etiology of conditions with equivocal clinical and pathologic presentations.

Traditional and targeted exome sequencing reveals common, rare and novel functional deleterious variants in RET-signaling complex in a cohort of living US patients with urinary tract malformations.

Signaling by the glial cell line-derived neurotrophic factor (GDNF)-RET receptor tyrosine kinase and SPRY1, a RET repressor, is essential for early urinary tract development. Individual or a combination of GDNF, RET and SPRY1 mutant alleles in mice cause renal malformations reminiscent of congenital anomalies of the kidney or urinary tract (CAKUT) in humans and distinct from renal agenesis phenotype in complete GDNF or RET-null mice. We sequenced GDNF, SPRY1 and RET in 122 unrelated living CAKUT patients to discover deleterious mutations that cause CAKUT. Novel or rare deleterious mutations in GDNF or RET were found in six unrelated patients. A family with duplicated collecting system had a novel mutation, RET-R831Q, which showed markedly decreased GDNF-dependent MAPK activity. Two patients with RET-G691S polymorphism harbored additional rare non-synonymous variants GDNF-R93W and RET-R982C. The patient with double RET-G691S/R982C genotype had multiple defects including renal dysplasia, megaureters and cryptorchidism. Presence of both mutations was necessary to affect RET activity. Targeted whole-exome and next-generation sequencing revealed a novel deleterious mutation G443D in GFRα1, the co-receptor for RET, in this patient. Pedigree analysis indicated that the GFRα1 mutation was inherited from the unaffected mother and the RET mutations from the unaffected father. Our studies indicate that 5% of living CAKUT patients harbor deleterious rare variants or novel mutations in GDNF-GFRα1-RET pathway. We provide evidence for the coexistence of deleterious rare and common variants in genes in the same pathway as a cause of CAKUT and discovered novel phenotypes associated with the RET pathway.

Expression profiles of podocytes exposed to high glucose reveal new insights into early diabetic glomerulopathy.

Podocyte injury has been suggested to have a pivotal role in the pathogenesis of diabetic glomerulopathy. To glean insights into molecular mechanisms underlying diabetic podocyte injury, we generated temporal global gene transcript profiles of podocytes exposed to high glucose for a time interval of 1 or 2 weeks using microarrays. A number of genes were altered at both 1 and 2 weeks of glucose exposure compared with controls grown under normal glucose. These included extracellular matrix modulators, cell cycle regulators, extracellular transduction signals and membrane transport proteins. Novel genes that were altered at both 1 and 2 weeks of high-glucose exposure included neutrophil gelatinase-associated lipocalin (LCN2 or NGAL, decreased by 3.2-fold at 1 week and by 7.2-fold at 2 weeks), endothelial lipase (EL, increased by 3.6-fold at 1 week and 3.9-fold at 2 week) and UDP-glucuronosyltransferase 8 (UGT8, increased by 3.9-fold at 1 week and 5.0-fold at 2 weeks). To further validate these results, we used real-time PCR from independent podocyte cultures, immunohistochemistry in renal biopsies and immunoblotting on urine specimens from diabetic patients. A more detailed time course revealed changes in LCN2 and EL mRNA levels as early as 6 hours and in UGT8 mRNA level at 12 hours post high-glucose exposure. EL immunohistochemistry on human tissues showed markedly increased expression in glomeruli, and immunoblotting readily detected EL in a subset of urine samples from diabetic nephropathy patients. In addition to previously implicated roles of these genes in ischemic or oxidative stress, our results further support their importance in hyperglycemic podocyte stress and possibly diabetic glomerulopathy pathogenesis and diagnosis in humans.

A common exonic variant of interleukin21 confers susceptibility to atopic asthma.

BACKGROUND: Interleukin (IL)-21, an IL-2 family multifunctional cytokine, is produced by activated CD4+ T cells and is known to potentially affect growth, survival and function of numerous immune cells. As IL-21 regulates IgE production, a key mediator of various allergic disorders and asthma, it is a prime candidate gene for studying atopic asthma. METHODS: In atopic asthma, analyses of four single nucleotide polymorphisms (SNP; C1455T, G1472T, C5250T and C8381T), a tetranucleotide microsatellite repeat (GAAT)(n) and their haplotypes were performed, and serum total IgE (TsIgE) was determined in ethnically matched unrelated patients (n = 255), unrelated controls (n = 245) and nuclear families (n = 140). Correlation between an exonic SNP C5250T in the asthmatics with serum IL-21 levels was also made. RESULTS: In both the case-control and family study groups, the exon-3 polymorphism C5250T of the IL21 gene was significantly associated with atopic asthma and TsIgE. The C5250T polymorphism was found to affect the concentration of serum IL-21 levels in atopic asthmatics. Also, this observation was supported by the structural alteration in IL21 mRNA as predicted by mfold software. Further, our haplotypic studies indicated that while minor haplotypes 4_C_T_C_C and two locus haplotype T_C were associated with asthma in the case-control cohort, none of the major haplotypes was found to be associated with either asthma or TsIgE levels. CONCLUSION: Our study provides evidence that IL21 is associated with atopic asthma, TsIgE and serum IL-21 levels. Thus, it may initiate further research to elucidate the role of the IL21 gene in asthma pathogenesis.

Genetic association of acidic mammalian chitinase with atopic asthma and serum total IgE levels.

BACKGROUND: In view of the hygiene hypothesis and the involvement of acidic mammalian chitinase (CHIA) in the effector responses of IL-13 with asthma, CHIA (GeneID-27159) is a potential asthma candidate gene. OBJECTIVE: To investigate the association of CHIA polymorphisms with atopic asthma and serum total IgE levels. METHODS: Twenty-one single nucleotide polymorphisms were identified by sequencing DNA of 60 individuals. On the basis of linkage disequilibrium, 6 polymorphisms were selected and genotyped in unrelated atopic patients with asthma (N = 270) and controls (N = 292) and an independent pediatric cohort (patients, 150; controls, 101). Electrophoretic mobility shift assay and reporter gene assays were also performed. RESULTS: The rs3806448G/A promoter polymorphism showed significant association with atopic asthma (P(adult) = .00001 and P(pediatric) = .0002) and serum total IgE (P < .05). Also rs2282290G/A was associated with atopic asthma (P(adult) = .00009 and P(pediatric) = .00003), whereas the rs10494132C/T polymorphism was associated with serum total IgE in the patients (P < .05). We also showed that the promoter single nucleotide polymorphisms altered the transcriptional activity of CHIA promoter and the C to T substitution at rs10494132 abrogated the Octamer transcription factor-1 (Oct-1) binding site. CONCLUSION: Our results establish a significant association of CHIA with atopic asthma and serum total IgE levels in the Indian population.

Inducible nitric oxide synthase (iNOS): role in asthma pathogenesis.

Asthma is one of the most common chronic inflammatory disorder of the airways of the lungs, affecting more than 300 million people all over the world. Nitric oxide (NO) is endogenously produced in mammalian airways by nitric oxide synthase (NOS) and is known to regulate many aspects of human asthma, including the modulation of airway and vascular smooth muscle tone and the inflammation. Asthmatic patients show an increased expression of inducible nitric oxide synthase (iNOS) in airway epithelial cells and an increased level of NO in exhaled air. Using various NO inhibitors (non-specific or iNOS-specific) and gene knock-out experiments, controversial results have been obtained regarding iNOS's beneficial and deleterious effects in the disease. In the present review, we have attempted to summarize the results of these experiments and also the genetic studies being undertaken to understand the role of iNOS in asthma. It is argued that extensive biochemical, clinical and genetic studies will be required to assess the precise role of NO in the asthma. This may help in designing selective and more potent iNOS inhibitors and NO donors for developing novel therapeutics for the asthma patients.