An eQTL landscape of kidney tissue in human nephrotic syndrome

Gillies, Christopher E.; Putler, Rosemary; Menon, Rajasree; Yasutake, Kalyn; Nair, Viji; Fermin, Damian; Eddy, Sean; Vega-Warner, Virginia; Hacohen, Nir; Wen, Xiaoquan; Kretzler, Matthias; Sampson, Matthew G.

doi:10.1101/281162

Cited by 26 publications

(47 citation statements)

References 55 publications

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“…Consensus findings from IPA and CMap profiles were then investigated for the potential underlying genetic components that might contributed to an alteration in disease-associated expression and activity. TI and glomerular-specific cis-eQTLs were generated across the NEPTUNE cohort (www.nephqtl.org) 11 ; cis-eQTLs were fine mapped using the Bayesian Deterministic Approximation of Posteriors 12 , which identifies clusters of variants predicted to drive eQTL associations. STAT1, CD44, SOX2, FOXA1, ATP2A1, ATP2A2, ATP2A3 (the ATP2A family members encode sarcoplasmic reticulum Ca 2+ ATPase and are targets of thapsigargin), IPMK, HNF4A, MAPK1, and NR3C1 (translated protein is the glucocorticoid receptor, a target of prednisone and dexamethasone) were assessed in TI-specific eQTL analyses, and TLR7, IL2, NR0B2, PLAUR, IFNGR1, FLT3 (the translated protein is a target of sunitinib) FOXA1, HNF4A, HNF1A, and NR3C1 were assessed in glomerularspecific multi-SNP eQTL analyses.…”

Section: Resultsmentioning

confidence: 99%

Inflammatory and JAK-STAT Pathways as Shared Molecular Targets for ANCA-Associated Vasculitis and Nephrotic Syndrome

Eddy

Nair

Mariani

et al. 2018

Preprint

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249 words ABSTRACT Background: Glomerular diseases of the kidney are presently differentiated, diagnosed and treated according to conventional clinical or structural features. While etiologically diverse, these diseases share common clinical features including but not limited to reduced glomerular filtration rate, increased serum creatinine and proteinuria suggesting shared pathogenic mechanisms across diseases. Renal biopsies from patients with nephrotic syndrome (NS) or ANCA-associated vasculitis (AAV) were evaluated for molecular signals cutting across conventional disease categories as candidates for therapeutic targets. Methods: Renal biopsies were obtained from patients with NS (minimal change disease, focal segmental glomerulosclerosis, or membranous nephropathy) (n=187) or AAV (granulomatosis with polyangiitis or microscopic polyangiitis) (n=80) from the Nephrotic Syndrome Study Network (NEPTUNE) and the European Renal cDNA Bank. Transcriptional profiles were assessed for shared disease mechanisms.Results: In the discovery cohort, 10-25% transcripts were differentially regulated versus healthy controls in both NS and AAV, >500 transcripts were shared across diseases. The majority of shared transcripts (60-77%) were validated in independent samples. Therapeutically targetable networks were identified, including inflammatory JAK-STAT signaling. STAT1 eQTLs were identified and STAT1 expression associated with GFRbased outcome. A transcriptional STAT1 activity score was generated from STAT1-regulated target genes which correlated with CXCL10 (p<0.001), a JAK-STAT biomarker, predictors of CKD progression, interstitial fibrosis (r=0.41, p<0.001), and urinary EGF (r=-0.51, p<0.001).Conclusion: AAV and NS caused from histopathologically distinct disease categories share common intra-renal molecular pathways cutting across conventional disease classifications. This approach provides a starting point for de novo drug development, and repurposing efforts in rare kidney diseases.

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Section: Resultsmentioning

confidence: 99%

Inflammatory and JAK-STAT Pathways as Shared Molecular Targets for ANCA-Associated Vasculitis and Nephrotic Syndrome

Eddy

Nair

Mariani

et al. 2018

Preprint

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“…( Supplementary Table S4). Additionally, among nearly 900 recently identified eQTLs for human nephrotic syndrome 29 assembly requires the conserved action of many actin binding and regulatory proteins, many of which are WT1 target genes. For a large number of these genes, WT1 binding and their expression levels were increased at D9.…”

Section: Discussionmentioning

confidence: 99%

“…5a) and ChIP-seq ( Supplementary Fig. 6a) data sets were largely consistent with each other in neuron projection extension involved in neuron projection guidance (11) nuclear import (34) protein targeting to nucleus (34) single−organism nuclear import (34) protein import into nucleus (34) protein localization to nucleus (41) positive regulation of cell morphogenesis involved in differentiation (27) regulation of cytoskeleton organization (49) actin filament organization (42) cell−cell adhesion via plasma−membrane adhesion molecules (34) homophilic cell adhesion via plasma membrane adhesion molecules (28) regulation of cell morphogenesis involved in differentiation (47) nucleoside monophosphate metabolic process (42) ribose phosphate metabolic process (63) purine nucleoside monophosphate metabolic process (41) purine ribonucleoside monophosphate metabolic process (41) ribonucleoside triphosphate metabolic process (42) purine ribonucleoside metabolic process (48) ATP metabolic process (40) purine ribonucleoside triphosphate metabolic process (42) purine nucleoside triphosphate metabolic process (43) purine nucleoside metabolic process (49) ribonucleoside metabolic process (51) small molecule catabolic process (48) nucleoside triphosphate metabolic process (47) nucleoside metabolic process (55) glycosyl compound metabolic process (59) response to oxidative stress (14) intrinsic apoptotic signaling pathway (12) signal transduction by p53 class mediator (13) regulation of actin cytoskeleton organization (55) cell−substrate adhesion (54) regulation of actin filament−based process (61) positive regulation of cell−cell adhesion (22) leukocyte aggregation (34) lymphocyte aggregation (34) vascular process in circulatory system (21) regulation of body fluid levels (29) tissue migration (24) renal system development (59) epithelium migration (24) peptidyl−tyrosine modification (26) epithelial cell migration (24) peptidyl−tyrosine phosphorylation (26) ameboidal−type cell migration (64) positive regulation of cell adhesion (32) endothelial cell migration (21) angiogenesis (42) 0.03 0.01…”

Section: Functional Implications Of Wt1 Dynamic Bindingmentioning

confidence: 99%

Epigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury

Ettou

Jung

Miyoshi

et al. 2020

Preprint

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In the context of human disease, the mechanisms whereby transcription factors reprogram gene expression in response to injury are not well understood. This is particularly true in kidney podocytes, injury to which is the common and initial event in many processes that lead End Stage Kidney Disease. WT1 is a master regulator of gene expression in podocytes, binding nearly all genes known to be crucial for maintenance of the glomerular filtration barrier. Here, using purified populations of podocytes and glomeruli, we investigated WT1-mediated transcriptional reprogramming during the course of podocyte injury. Using the Adriamycin murine model of Focal Segmental Glomerulosclerosis, we discovered that podocyte injury led to increased intensity of WT1 binding and to the acquisition of new WT1 binding sites, both at previously identified target genes and at newly bound target genes, providing mechanistic insight on the transcriptional response to injury. We also observed a previously unrecognized transient increase in expression of WT1 target genes in both mice and human kidney organoids.Together, these features appear to constitute an attempt to repair the glomerular filtration barrier after podocyte injury. At later stages of injury, when proteinuria became severe, there was greatly decreased WT1 binding to most target genes.Furthermore, WT1 appeared to be required to maintain active chromatin marks at its target genes. These active marks were converted to repressive marks after loss of WT1 or Adriamycin-induced injury. This response to injury suggests that there may be a potential window of opportunity for repairing podocyte injury as a treatment for glomerular disease in humans. RESULTS Epigenetic regulation of podocyte gene expression by WT1WT1 has been identified as a key regulator of podocyte gene expression 3,4 and WT1 target genes are crucial for maintaining glomerular filtration barrier 4,11 . Two WT1 target genes were studied to elucidate the transcriptional response to injury.Nphs2 encodes Podocin, an essential component of the slit diaphragm and Synpo encodes Synaptopodin, an actin-associated protein important for maintaining the cytoskeleton integrity. To directly demonstrate WT1-dependent gene expression, Wt1 was conditionally inactivated in podocytes 12 of adult Nphs2-CreERT2, WT1fl/fl mice, leading to massive proteinuria (Fig. 1a). Kidneys appeared pale (Fig. 1b) with H&E and PAS staining showing protein casts, mesangial expansion and dilated tubules (Fig. 1c). WT1, Podocin and Synaptopodin transcript and protein levels were greatly reduced ( Fig. 1d, e). Tissue specific TFs activate gene expression in part by promoting histonemodifications that maintain open chromatin, such as H3K4me3 and H4K8ac. We used FACS-isolated podocytes to analyze the effect of WT1 inactivation on histone modifications during the course of injury at previously defined WT1 binding sites at the Nphs2 and Synpo genes 4 , here identified as Nphs2-1, Nphs2-2, Nphs2-3, Synpo-1, Synpo-2 and Synpo-3. Nphs2-1 and Nphs2-2 are located...

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“…The importance of the ratio of PDZK1 to uric acid transport proteins (such as URAT1, encoded by SLC22A12) that it interacts with in the kidney is unknown, but it is established that PDZK1 stabilizes transporter localization in the membrane and increases transporter activity (12,15). It was interesting to note that only tissues with very strong evidence for an eQTL were the colon and small intestine, with no evidence for an eQTL in the kidney (23-25). It is possible that other regulatory mechanisms exist in the kidney instead of the rs1967017 -mediated regulatory mechanism of PDZK1 expression observed in the gut.…”

Section: Discussionmentioning

confidence: 99%

“…Increased HNF4A binding leads to increased PDZK1 protein, which is predicted to stabilise the transportosome and increase the activity of uric acid transporters, such as ABCG2 (14,36). In human kidney samples there is no association between rs1967017 and PDZK1 expression (23-25). Therefore we propose that HNF1A-dependent regulation of PDZK1 expression independent of rs1967017 is the dominant mechanism in the kidney.…”

Section: Discussionmentioning

confidence: 99%

A non-coding genetic variant maximally associated with serum urate levels is functionally linked to HNF4A-dependent PDZK1 expression

Ketharnathan

Leask

Boocock

et al. 2018

Preprint

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Several dozen genetic variants associate with serum urate levels, but the precise molecular mechanisms by which they affect serum urate are unknown. Here we tested for functional linkage of the maximally-associated genetic variant rs1967017 at the PDZK1 locus to elevated PDZK1 expression.We performed expression quantitative trait locus (eQTL) and likelihood analyses followed by gene expression assays. Zebrafish were used to determine the ability of rs1967017 to direct tissue-specific gene expression. Luciferase assays in HEK293 and HepG2 cells measured the effect of rs1967017 on transcription amplitude. PAINTOR analysis revealed rs1967017 as most likely to be causal and rs1967017 was an eQTL for PDZK1 in the intestine. The region harboring rs1967017 was capable of directly driving green fluorescent protein expression in the kidney, liver and intestine of zebrafish embryos, consistent with a conserved ability to confer tissue-specific expression. The urate-increasing T-allele of rs1967017 strengthens a binding site for the transcription factor HNF4A. siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells. Luciferase assays showed that the T-allele of rs1967017 gains enhancer activity relative to the urate-decreasing C-allele, with T-allele enhancer activity abrogated by HNF4A depletion. HNF4A physically binds the rs1967017 region, suggesting direct transcriptional regulation of PDZK1 by HNF4A.With other reports our data predict that the urate-raising T-allele of rs1967017 enhances HNF4A binding to the PDZK1 promoter, thereby increasing PDZK1 expression. As PDZK1 is a scaffold protein for many ion channel transporters, increased expression can be predicted to increase activity of urate transporters and alter excretion of urate.

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An eQTL landscape of kidney tissue in human nephrotic syndrome

Abstract: Abstract:Expression quantitative trait loci (eQTL)

Cited by 26 publications

References 55 publications

Inflammatory and JAK-STAT Pathways as Shared Molecular Targets for ANCA-Associated Vasculitis and Nephrotic Syndrome

Inflammatory and JAK-STAT Pathways as Shared Molecular Targets for ANCA-Associated Vasculitis and Nephrotic Syndrome

Epigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury

A non-coding genetic variant maximally associated with serum urate levels is functionally linked to HNF4A-dependent PDZK1 expression

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