Papers by Virginia Vega-warner
Research Square (Research Square), Oct 5, 2022
Kidney organoids are a promising model to study kidney disease, but use is constrained by limited... more Kidney organoids are a promising model to study kidney disease, but use is constrained by limited knowledge of their functional protein expression pro le. We aimed to de ne the organoid proteome and transcriptome trajectories over culture duration and upon exposure to TNFα, a cytokine stressor. Older organoids increased deposition of extracellular matrix but decreased expression of glomerular proteins. Single cell transcriptome integration revealed that most proteome changes localized to podocytes, tubular and stromal cells. TNFα-treatment of organoids effected 320 differentially expressed proteins, including cytokines and complement components. Transcript expression of these 320 proteins was signi cantly higher in individuals with poorer clinical outcomes in proteinuric kidney disease. Key TNFαassociated protein (C3 and VCAM1) expression was increased in both human tubular and organoid kidney cell populations, highlighting the potential for organoids to advance biomarker development. By integrating kidney organoid omic layers, incorporating a disease-relevant cytokine stressor and comparing to human data, we provide crucial evidence of functional relevance of the kidney organoid model to human kidney disease.
American Journal of Human Genetics, Dec 7, 2017
exome resequencing distinguishes cystic kidney
Background: Congenital nephrotic syndrome (CNS) is defined as nephrotic syndrome that manifests w... more Background: Congenital nephrotic syndrome (CNS) is defined as nephrotic syndrome that manifests within the first 3 months of life. Mutations in the NPHS1 gene encoding nephrin, are a major cause for CNS. Currently, more than 173 different mutations of NPHS1 have been published as causing CNS, affecting most exons. Methods: We performed mutation analysis of NPHS1 in a worldwide cohort of 20 families (23 children) with CNS. All 29 exons of the NPHS1 gene were examined using direct sequencing. New mutations were confirmed by demonstrating their absence in 96 healthy control individuals. Results: We detected disease-causing mutations in 9 of 20 families (45%). Seven of the families showed a homozygous mutation, while two were compound heterozygous. In another 2 families, single heterozygous NPHS1 mutations were detected. Out of 10 different mutations discovered, 3 were novel, consisting of 1 splice site mutation and 2 missense mutations. Conclusion: Our data demonstrate that the spectru...
BackgroundClassification of nephrotic syndrome relies on clinical presentation and descriptive pa... more BackgroundClassification of nephrotic syndrome relies on clinical presentation and descriptive patterns of injury on kidney biopsies. This approach does not reflect underlying disease biology, limiting the ability to predict progression or treatment response.MethodsSystems biology approaches were used to categorize patients with minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS) based on kidney biopsy tissue transcriptomics across three cohorts and assessed association with clinical outcomes. Patient-level tissue pathway activation scores were generated using differential gene expression. Then, functional enrichment and non-invasive urine biomarker candidates were identified. Biomarkers were validated in kidney organoid models and single nucleus RNA-seq (snRNAseq) from kidney biopsies.ResultsTranscriptome-based categorization identified three subgroups of patients with shared molecular signatures across independent North American, European and African cohorts...
Kidney International Reports, 2018
Introduction: In South Africa (SA), steroid-resistant nephrotic syndrome (SRNS) is more frequent ... more Introduction: In South Africa (SA), steroid-resistant nephrotic syndrome (SRNS) is more frequent in black than in Indian children. Methods: Seeking a genetic basis for this disparity, we enrolled 33 Indian and 31 black children with steroid-sensitive nephrotic syndrome (SSNS) and SRNS from KwaZulu-Natal, SA; SRNS children underwent kidney biopsy. We sequenced NPHS2 and genotyped APOL1 in 15 SSNS and 64 SRNS unrelated patients and 104 controls and replicated results in 18 black patients with steroid-resistant focal segmental glomerulosclerosis (SR-FSGS). Known FSGS genes (n ¼ 21) were sequenced in a subset of patients. Results: Homozygosity for NPHS2 V260E was found in 8 of 30 black children with SRNS (27%); all 260E/E carriers had SR-FSGS. Combining SR-FSGS patients from the 2 groups, 14 of 42 (33%) were homozygous for V260E. One black control was heterozygous for V260E; no Indian patients or controls were carriers. Haplotype analysis indicated that homozygosity for V260E was not explained by cryptic consanguinity. Children with NPHS2 260E/E developed SRNS at earlier age than noncarriers (34 vs. 78 months, P ¼ 0.01), and none achieved partial or complete remission (0% vs. 47%, P ¼ 0.002). APOL1 variants did not associate with NS. Sequencing FSGS genes identified a CD2AP predicted pathogenic variant in the heterozygous state in 1 Indian case with SR-FSGS. Conclusion: NPHS2 260E/E was present in one-third of black FSGS patients, was absent in black controls and Indian patients, and affected patients were unresponsive to therapy. Genotyping V260E in black children from South Africa with NS will identify a substantial group with SR-FSGS, potentially sparing these children biopsy and ineffective steroid treatment.
JAMA Network Open
IMPORTANCE Focal segmental glomerulosclerosis (FSGS) is a common cause of end-stage kidney diseas... more IMPORTANCE Focal segmental glomerulosclerosis (FSGS) is a common cause of end-stage kidney disease (ESKD) across the lifespan. While 10% to 15% of children and 3% of adults who develop ESKD have FSGS, it remains uncertain whether the natural history differs in pediatric vs adult patients, and this uncertainty contributes to the exclusion of children and adolescents in clinical trials. OBJECTIVE To examine whether there are differences in the kidney health outcomes among children, adolescents, and adults with FSGS. DESIGN, SETTING, AND PARTICIPANTS This cohort study used pooled and parallel analyses, completed July 5, 2022, from 3 complimentary data sources: (1) Nephrotic Syndrome Rare Disease Clinical Research Network (NEPTUNE); (2) FSGS clinical trial (FSGS-CT); and (3) Kidney Research Network (KRN). NEPTUNE is a multicenter US/Canada cohort study; FSGS-CT is a multicenter US/Canada clinical trial; and KRN is a multicenter US electronic health record-based registry from academic and community nephrology practices. NEPTUNE included 166 patients with incident FSGS enrolled at first kidney biopsy; FSGS-CT included 132 patients with steroid-resistant FSGS
Allele frequency of variants with ACâ =â 1 in Exome Chip. The log10 allele frequency from the ExA... more Allele frequency of variants with ACâ =â 1 in Exome Chip. The log10 allele frequency from the ExAC r0.3 database of variants from the Exome Chip with an allele count of one in our cohort is shown. 69Â % of the variants have an allele frequency less than 10^-3. (PPTX 66 kb)
Kidney International Reports, 2016
ABSTRACTBackgroundMore than 30 genes can harbor rare exonic variants sufficient to cause nephroti... more ABSTRACTBackgroundMore than 30 genes can harbor rare exonic variants sufficient to cause nephrotic syndrome (NS), and the number of genes implicated in monogenic NS continues to grow. However, outside the first year of life, the majority of affected patients, particularly in ancestrally mixed populations, do not have a known monogenic form of NS. Even in those children classified with a monogenic form of NS, there is phenotypic heterogeneity. Thus, we have only discovered a fraction of the heritability of NS – the underlying genetic factors contributing to phenotypic variation. Part of the “missing heritability” for NS has been posited to be explained by patients harboring coding variants across one or more previously implicated NS genes, insufficient to cause NS in a classical Mendelian manner, but that nonetheless impact protein function enough to cause disease. However, systematic evaluation in patients with NS for rare or low-frequency risk alleles within single genes, or in com...
BMC bioinformatics, Jan 10, 2016
Targeted sequencing of discrete gene sets is a cost effective strategy to screen subjects for mon... more Targeted sequencing of discrete gene sets is a cost effective strategy to screen subjects for monogenic forms of disease. One method to achieve this pairs microfluidic PCR with next generation sequencing. The PCR step of this pipeline creates challenges in accurate variant calling. This includes that most reads targeting a specific exon are duplicates that have been amplified from the PCR step. To reduce false positive variant calls from these experiments, previous studies have used threshold-based filtering of alternative allele depth ratio and manual inspection of the alignments. However even after manual inspection and filtering, many variants fail to be validated via Sanger sequencing. To improve the accuracy of variant calling from these experiments, we are challenged to design a variant filtering strategy that sufficiently models microfluidic PCR-specific issues. We developed an open source variant filtering pipeline, targeted sequencing support vector machine ("tarSVM&qu...
Nature communications, Jan 24, 2016
Steroid-resistant nephrotic syndrome (SRNS) causes 15% of chronic kidney disease (CKD). Here we s... more Steroid-resistant nephrotic syndrome (SRNS) causes 15% of chronic kidney disease (CKD). Here we show that recessive mutations in FAT1 cause a distinct renal disease entity in four families with a combination of SRNS, tubular ectasia, haematuria and facultative neurological involvement. Loss of FAT1 results in decreased cell adhesion and migration in fibroblasts and podocytes and the decreased migration is partially reversed by a RAC1/CDC42 activator. Podocyte-specific deletion of Fat1 in mice induces abnormal glomerular filtration barrier development, leading to podocyte foot process effacement. Knockdown of Fat1 in renal tubular cells reduces migration, decreases active RAC1 and CDC42, and induces defects in lumen formation. Knockdown of fat1 in zebrafish causes pronephric cysts, which is partially rescued by RAC1/CDC42 activators, confirming a role of the two small GTPases in the pathogenesis. These findings provide new insights into the pathogenesis of SRNS and tubulopathy, linki...
Pediatric Nephrology, 2012
Background The most frequently mutated gene of steroidresistant nephrotic syndrome (SRNS) is NPHS... more Background The most frequently mutated gene of steroidresistant nephrotic syndrome (SRNS) is NPHS2. Current guidelines propose the sequencing of all NPHS2 exons only in childhood-onset SRNS. Methods A cohort of 38 Hungarian patients with childhoodonset nephrotic-range proteinuria was screened for NPHS2 mutations. The frequency of the p.V290M mutation in lateonset SRNS was examined in the French and PodoNet cohorts. Results Of the 38 Hungarian patients screened, seven carried NPHS2 mutations on both alleles, of whom twodiagnosed with proteinuria through school screening programs at the age of 9.7 and 14 years, respectively-did not develop nephrotic syndrome in childhood. The first, an 18year-old boy, homozygous for p.V290M, has never developed edema. The second, a 31-year-old woman-compound heterozygous for p.V290M and p.R138Q-was first detected with hypoalbuminemia (<30 g/l) and edema at the age of 24.3 and 27.5 years, respectively. Both patients currently have a normal glomerular filtration rate. The mutation p.V290M was carried by three of the 38 patients in the Hungarian cohort, by two of the 95 patients with late-onset SRNS in the PodoNet cohort and by none of the 83 patients in the French cohort. Conclusions We propose that not only the p.R229Q variant, but also the p.V290M mutation should be screened in Central and Eastern European patients with late-onset SRNS.
Journal of Agricultural and Food Chemistry, 1996
... Anne B. Smyth, † Denise M. Smith,* Virginia Vega-Warner, and Eileen O&#x27;Neill †. Depar... more ... Anne B. Smyth, † Denise M. Smith,* Virginia Vega-Warner, and Eileen O&#x27;Neill †. Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan 48824-1224. J. Agric. Food Chem. , 1996 ...
Journal of the American Society of Nephrology : JASN, 2021
BACKGROUND Podocyte dysfunction is the main pathologic mechanism driving the development of FSGS ... more BACKGROUND Podocyte dysfunction is the main pathologic mechanism driving the development of FSGS and other morphologic types of steroid-resistant nephrotic syndrome (SRNS). Despite significant progress, the genetic causes of most cases of SRNS have yet to be identified. METHODS Whole-genome sequencing was performed on 320 individuals from 201 families with familial and sporadic NS/FSGS with no pathogenic mutations in any known NS/FSGS genes. RESULTS Two variants in the gene encoding regulator of calcineurin type 1 (RCAN1) segregate with disease in two families with autosomal dominant FSGS/SRNS. In vitro, loss of RCAN1 reduced human podocyte viability due to increased calcineurin activity. Cells expressing mutant RCAN1 displayed increased calcineurin activity and NFAT activation that resulted in increased susceptibility to apoptosis compared with wild-type RCAN1. Treatment with GSK-3 inhibitors ameliorated this elevated calcineurin activity, suggesting the mutation alters the balance...
American journal of human genetics, Jan 2, 2018
Expression quantitative trait loci (eQTL) studies illuminate the genetics of gene expression and,... more Expression quantitative trait loci (eQTL) studies illuminate the genetics of gene expression and, in disease research, can be particularly illuminating when using the tissues directly impacted by the condition. In nephrology, there is a paucity of eQTL studies of human kidney. Here, we used whole-genome sequencing (WGS) and microdissected glomerular (GLOM) and tubulointerstitial (TI) transcriptomes from 187 individuals with nephrotic syndrome (NS) to describe the eQTL landscape in these functionally distinct kidney structures. Using MatrixEQTL, we performed cis-eQTL analysis on GLOM (n = 136) and TI (n = 166). We used the Bayesian "Deterministic Approximation of Posteriors" (DAP) to fine-map these signals, eQTLBMA to discover GLOM- or TI-specific eQTLs, and single-cell RNA-seq data of control kidney tissue to identify the cell type specificity of significant eQTLs. We integrated eQTL data with an IgA Nephropathy (IgAN) GWAS to perform a transcriptome-wide association study...
European journal of human genetics : EJHG, Jan 11, 2018
A rare syndrome was first described in 1997 in a 17-year-old male patient presenting with Retinit... more A rare syndrome was first described in 1997 in a 17-year-old male patient presenting with Retinitis pigmentosa, HYpopituitarism, Nephronophthisis and Skeletal dysplasia (RHYNS). In the single reported familial case, two brothers were affected, arguing for X-linked or recessive mode of inheritance. Up to now, the underlying genetic basis of RHYNS syndrome remains unknown. Here we applied whole-exome sequencing in the originally described family with RHYNS to identify compound heterozygous variants in the ciliary gene TMEM67. Sanger sequencing confirmed a paternally inherited nonsense c.622A > T, p.(Arg208*) and a maternally inherited missense variant c.1289A > G, p.(Asp430Gly), which perturbs the correct splicing of exon 13. Overall, TMEM67 showed one of the widest clinical continuum observed in ciliopathies ranging from early lethality to adults with liver fibrosis. Our findings extend the spectrum of phenotypes/syndromes resulting from biallelic TMEM67 variants to now eight d...
American journal of human genetics, Jan 2, 2017
Renal agenesis and hypodysplasia (RHD) are major causes of pediatric chronic kidney disease and a... more 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(-5) for novel LOF, increased to p = 4.1 × 10(-6) for LOF and deleterious missense variants combined, and augmented further after accounting for segregation and de novo inhe...
Kidney International Reports
Pediatric nephrology (Berlin, Germany), 2017
was incorrectly rendered as BVega-Wagner^. In addition, Edgar A. Otto was wrongly listed as BEdga... more was incorrectly rendered as BVega-Wagner^. In addition, Edgar A. Otto was wrongly listed as BEdgar Otto^.
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Papers by Virginia Vega-warner