Failure of the glomerular filtration barrier, primarily by loss of slit diaphragm architecture, underlies nephrotic syndrome in minimal change disease. The etiology remains unknown. The efficacy of B ...cell-targeted therapies in some patients, together with the known proteinuric effect of anti-nephrin antibodies in rodent models, prompted us to hypothesize that nephrin autoantibodies may be present in patients with minimal change disease.
We evaluated sera from patients with minimal change disease, enrolled in the Nephrotic Syndrome Study Network (NEPTUNE) cohort and from our own institutions, for circulating nephrin autoantibodies by indirect ELISA and by immunoprecipitation of full-length nephrin from human glomerular extract or a recombinant purified extracellular domain of human nephrin. We also evaluated renal biopsies from our institutions for podocyte-associated punctate IgG colocalizing with nephrin by immunofluorescence.
In two independent patient cohorts, we identified circulating nephrin autoantibodies during active disease that were significantly reduced or absent during treatment response in a subset of patients with minimal change disease. We correlated the presence of these autoantibodies with podocyte-associated punctate IgG in renal biopsies from our institutions. We also identified a patient with steroid-dependent childhood minimal change disease that progressed to end stage kidney disease; she developed a massive post-transplant recurrence of proteinuria that was associated with high pretransplant circulating nephrin autoantibodies.
Our discovery of nephrin autoantibodies in a subset of adults and children with minimal change disease aligns with published animal studies and provides further support for an autoimmune etiology. We propose a new molecular classification of nephrin autoantibody minimal change disease to serve as a framework for instigation of precision therapeutics for these patients.
Ensuring reproducibility of results in high-throughput experiments is crucial for biomedical research. Here, we propose a set of computational methods, INTRIGUE, to evaluate and control ...reproducibility in high-throughput settings. Our approaches are built on a new definition of reproducibility that emphasizes directional consistency when experimental units are assessed with signed effect size estimates. The proposed methods are designed to (1) assess the overall reproducible quality of multiple studies and (2) evaluate reproducibility at the individual experimental unit levels. We demonstrate the proposed methods in detecting unobserved batch effects via simulations. We further illustrate the versatility of the proposed methods in transcriptome-wide association studies: in addition to reproducible quality control, they are also suited to investigating genuine biological heterogeneity. Finally, we discuss the potential extensions of the proposed methods in other vital areas of reproducible research (for example, publication bias and conceptual replications).
Transcriptome-wide association studies and colocalization analysis are popular computational approaches for integrating genetic-association data from molecular and complex traits. They show the ...unique ability to go beyond variant-level genetic-association evidence and implicate critical functional units, e.g., genes, in disease etiology. However, in practice, when the two approaches are applied to the same molecular and complex-trait data, the inference results can be markedly different. This paper systematically investigates the inferential reproducibility between the two approaches through theoretical derivation, numerical experiments, and analyses of four complex trait GWAS and GTEx eQTL data. We identify two classes of inconsistent inference results. We find that the first class of inconsistent results (i.e., genes with strong colocalization but weak transcriptome-wide association study TWAS signals) might suggest an interesting biological phenomenon, i.e., horizontal pleiotropy; thus, the two approaches are truly complementary. The inconsistency in the second class (i.e., genes with weak colocalization but strong TWAS signals) can be understood and effectively reconciled. To this end, we propose a computational approach for locus-level colocalization analysis. We demonstrate that the joint TWAS and locus-level colocalization analysis improves specificity and sensitivity for implicating biologically relevant genes.
Chronic kidney disease (CKD) is a growing health burden currently affecting 10-15% of adults worldwide. Estimated glomerular filtration rate (eGFR) as a marker of kidney function is commonly used to ...diagnose CKD. We analyze eGFR data from the Nord-Trøndelag Health Study and Michigan Genomics Initiative and perform a GWAS meta-analysis with public summary statistics, more than doubling the sample size of previous meta-analyses. We identify 147 loci (53 novel) associated with eGFR, including genes involved in transcriptional regulation, kidney development, cellular signaling, metabolism, and solute transport. Additionally, sex-stratified analysis identifies one locus with more significant effects in women than men. Using genetic risk scores constructed from these eGFR meta-analysis results, we show that associated variants are generally predictive of CKD with only modest improvements in detection compared with other known clinical risk factors. Collectively, these results yield additional insight into the genetic factors underlying kidney function and progression to CKD.
Steroid-sensitive nephrotic syndrome (SSNS) is a childhood disease with unclear pathophysiology and genetic architecture. We investigated the genomic basis of SSNS in children recruited in Europe and ...the biopsy-based North American NEPTUNE cohort.
We performed three ancestry-matched, genome-wide association studies (GWAS) in 273 children with NS (Children Cohort Nephrosis and Virus NEPHROVIR cohort: 132 European, 56 African, and 85 Maghrebian) followed by independent replication in 112 European children, transethnic meta-analysis, and conditional analysis. GWAS alleles were used to perform glomerular
-expression quantitative trait loci studies in 39 children in the NEPTUNE cohort and epidemiologic studies in GWAS and NEPTUNE (97 children) cohorts.
Transethnic meta-analysis identified one SSNS-associated single-nucleotide polymorphism (SNP) rs1063348 in the 3' untranslated region of
(
=9.3×10
). Conditional analysis identified two additional independent risk alleles upstream of
(rs28366266,
=3.7×10
) and in the 3' untranslated region of
(rs9348883,
=9.4×10
) within introns of
and
These three risk alleles were independent of the risk haplotype
identified in European patients. Increased burden of risk alleles across independent loci was associated with higher odds of SSNS. Increased burden of risk alleles across independent loci was associated with higher odds of SSNS, with younger age of onset across all cohorts, and with increased odds of complete remission across histologies in NEPTUNE children. rs1063348 associated with decreased glomerular expression of HLA-DRB1, HLA-DRB5, and HLA-DQB1.
Transethnic GWAS empowered discovery of three independent risk SNPs for pediatric SSNS. Characterization of these SNPs provide an entry for understanding immune dysregulation in NS and introducing a genomically defined classification.
Expression quantitative trait locus (eQTL) studies illuminate genomic variants that regulate specific genes and contribute to fine-mapped loci discovered via genome-wide association studies (GWAS). ...Efforts to maximize their accuracy are ongoing. Using 240 glomerular (GLOM) and 311 tubulointerstitial (TUBE) micro-dissected samples from human kidney biopsies, we discovered 5371 GLOM and 9787 TUBE genes with at least one variant significantly associated with expression (eGene) by incorporating kidney single-nucleus open chromatin data and transcription start site distance as an "integrative prior" for Bayesian statistical fine-mapping. The use of an integrative prior resulted in higher resolution eQTLs illustrated by (1) smaller numbers of variants in credible sets with greater confidence, (2) increased enrichment of partitioned heritability for GWAS of two kidney traits, (3) an increased number of variants colocalized with the GWAS loci, and (4) enrichment of computationally predicted functional regulatory variants. A subset of variants and genes were validated experimentally in vitro and using a Drosophila nephrocyte model. More broadly, this study demonstrates that tissue-specific eQTL maps informed by single-nucleus open chromatin data have enhanced utility for diverse downstream analyses.
Nephrotic syndrome (NS) is one of the most challenging conditions to manage and treat, partly because we lack a specific molecular understanding of its pathogenesis and progression. This limits our ...ability to provide targeted therapy or precise prognostications. Fortunately, genomic discovery in NS and its translation to genomic-informed medicine is allowing us to improve our understanding of the molecular anatomy of NS and our ability to care for patients with NS. In this Core Curriculum, we review the specific genes and loci discovered in childhood NS, specifically NS of Mendelian origin, APOL1-associated NS in black patients, HLA region variants associated with steroid-sensitive NS, their biological impacts, prevalence across populations, and clinical correlates. We also review the fundamentals of genetic architecture of human disease, technologies, and analytic strategies that currently exist to discover disease-related genetic variations. A facility with the concepts and vocabulary of modern genomics and ability to interpret results of genetic studies are essential skills for nephrologists caring for children with NS. As such, we hope to empower them to understand the literature in this area, appropriately order genetic tests and accurately interpret the results, and consider how they may participate in or drive the next wave of genomic discoveries in NS.
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