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Genetic variation in the genomic regulatory landscape likely plays a crucial role in the pathology of disease. Non-coding variants associated with disease can influence the expression of long intergenic non-coding RNAs (lincRNAs), which in turn function in the control of protein-coding gene expression. Here, we investigate the function of two indep...
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... used COLOC ( Giambartolomei et al., 2014) and expression data from The Genotype Tissue Expression (GTEx) project (Carithers and Moore, 2015) to identify cis-eQTL that colocalize with SUA1 and SUA2. eQTL for the genes MAFTRR and LINC01229 (Figure 2, gene body depicted in black) colocalize with the SUA1 urate signal (Table 2) although the lead eQTL variants are not the lead urate variants at SUA1 (Supplementary Figure S2). SUA1 urate-raising alleles associate with increased expression of MAFTRR but with lowered expression of LINC01229 (e.g., rs7188445_G Supplementary Figure S3 and Supplementary Table S1). ...
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... urate-raising alleles associate with increased expression of MAFTRR but with lowered expression of LINC01229 (e.g., rs7188445_G Supplementary Figure S3 and Supplementary Table S1). An eQTL for LINC01229 in the GTEx tissue Skin -Exposed (Lower leg) (Supplementary Figure S2) colocalises with the SUA2 urate signal ( Table 2). Urate- raising variants within SUA2 increase LINC01229 expression (Supplementary Table S2). ...
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... eQTL for LINC01229 in the GTEx tissue Skin -Exposed (Lower leg) (Supplementary Figure S2) colocalises with the SUA2 urate signal ( Table 2). Urate- raising variants within SUA2 increase LINC01229 expression (Supplementary Table S2). Colocalization of the SUA1 and SUA2 urate signals with MAFTRR and LINC01229 eQTL suggests that Kanai et al. (2018). ...
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... SUA1 urate-raising variants associate with increased expression of MAFTRR in kidney tubule (Supplementary Table S1). No SUA2 variants were eQTL for MAFTRR in the kidney tubules within the NepheQTL database ( Gillies et al., 2018) ( Supplementary Table S2). Furthermore, there were no significant gene eQTL signals for MAF or LINC01229 within NepheQTL. ...
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... SUA2 the lead PAINTOR SNP rs192158533 (Table 3 Table 2 and Supplementary Table S2). ...
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... urate excretion is predominantly carried out in the kidney tubules with the remainder managed by the intestine (Merriman, 2015). We observed a colocalization of the SUA1 urate signal and the MAFTRR colon cis-eQTL (Table 2 and Supplementary Figure S2) and the partial overlap with the MAFTRR kidney tubule eQTL signal (Supplementary Figure S2). This is consistent with our co-expression analyses which indicate that MAFTRR associates with the kidney-relevant human phenotype ontology term 'tubulointerstitial abnormality.' ...
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... data from renal cells supports this interaction, in addition to a further connection between SUA2 and the MAF promoter (SUA3) (Supplementary Figure S11). Our eQTL analyses indicate that the SUA2 genomic contacts with LINC01229 are functional (Fadason et al., 2017), colocalize with the SUA2 urate signal (Table 2) and that the serum urate-raising alleles of rs4077450 and rs4077451 increase the expression of LINC01229 but not of MAFTRR (Supplementary Figure S8). ...
Citations
... As only some lines of evidence support these two TF, further functional characterisation of these two loci is warranted. Interestingly, in the locus on chromosome 16, two of the other genes with some evidence for a retinolrelated function (MAFTRR and LINC01229) have been shown experimentally to regulate MAF expression and are also associated with other biochemical traits like urate, further supporting the role of the Maf family on retinol abundance in serum 36 . Finally, the remaining locus on chromosome 2 (2:122078406-122084285) had the least interpretable functional prioritisation results. ...
Retinol is a fat-soluble vitamin that plays an essential role in many biological processes throughout the human lifespan. Here, we perform the largest genome-wide association study (GWAS) of retinol to date in up to 22,274 participants. We identify eight common variant loci associated with retinol, as well as a rare-variant signal. An integrative gene prioritisation pipeline supports novel retinol-associated genes outside of the main retinol transport complex (RBP4:TTR) related to lipid biology, energy homoeostasis, and endocrine signalling. Genetic proxies of circulating retinol were then used to estimate causal relationships with almost 20,000 clinical phenotypes via a phenome-wide Mendelian randomisation study (MR-pheWAS). The MR-pheWAS suggests that retinol may exert causal effects on inflammation, adiposity, ocular measures, the microbiome, and MRI-derived brain phenotypes, amongst several others. Conversely, circulating retinol may be causally influenced by factors including lipids and serum creatinine. Finally, we demonstrate how a retinol polygenic score could identify individuals more likely to fall outside of the normative range of circulating retinol for a given age. In summary, this study provides a comprehensive evaluation of the genetics of circulating retinol, as well as revealing traits which should be prioritised for further investigation with respect to retinol related therapies or nutritional intervention.
... The ligand binding domain of HNF4α responds to cell-specific cues to drive HNF4α transcriptional regulation [34]. Therefore, zebrafish HNF4α maintains the ability to recognize human HNF4α motifs encoded by human DNA sequence [35,36]. While a large proportion of the protein-coding genome is conserved, the zebrafish genome lacks many enhancers identifiable by sequence conservation in other species, including humans [37,38]. ...
... For example, layering imaging of regulatory element expression with fluorescently-labeled cell markers allows for the assessment of tissue-specific enhancer activity over developmental time. Additionally, by comparing tissues where the enhancer drives expression to those where a gene is expressed (e.g., in situ hybridisation), one can approximate the target gene of an enhancer if the enhancer and gene expression colocalizes [36,43]. Zebrafish are also a cost-effective and relatively low-maintenance model system, particularly when compared with mice (for which reporter assays exist), which makes them suitable for the longer-term rearing and maintenance [18]. ...
... Now, with data made available by the ENCODE consortium [6] and GTEx, it is possible to overlay genetic variants with regulatory data and gene expression data (eQTL) to prioritize putative causal variants before testing in zebrafish assays. The success of this approach is highlighted by two studies [35,36] that investigated loci with genetic associations of serum urate, a key metabolite involved in the development of the inflammatory arthritis, gout [114]. In these studies, transcription factor binding sites were overlaid with urate-associated genetic variants at the PDZK1 and MAFTRR genes. ...
Enhancers are genetically encoded elements that are critical for controlling gene expression. Despite the importance of enhancers in development, normal biological function, and disease, they have been historically overlooked and remain understudied. To understand how enhancers function, appropriate molecular tools are required that can capture the temporal and spatial function of enhancers within appropriate biological contexts. Zebrafish are an excellent in vivo model for the study of enhancer elements and the genetic variants that alter their function. Because zebrafish larvae are transparent, transgenes encoding enhancers tagged by fluorescent reporters can be visualized in the tissues and developmental stages where the enhancers function. Transgenesis of enhancers can be achieved using various plasmid technologies and transgene integration methods. Here, we describe the history and most recent developments in the zebrafish enhancer assay, from vector designs to various transgene integration techniques. We go on to describe how the application of these assays have been integral for our understanding of genetic variants found in humans and within enhancers that can contribute to both human Mendelian and complex polygenic disease.
... Beyond the urate transporter loci like ABCG2 and SLC2A9, little is known about other loci discovered in the past GWAS. Given that most of the urate-related SNPs residing in the non-coding regions of the genome [38], understanding their mechanisms is particularly challenging yet imperative, and using a study design analogous to ours could offer additional insights. ...
Studies have shown that genetic variations can influence metabolic response to nutrient intake, and that diets rich in fructose contribute to hyperuricemia. In this pilot study, our aim was to determine the variability of serum urate in response to an acute fructose challenge and to investigate if genetic variants would affect this response in young to middle-aged adults who self-reported as Black or White. Fifty-seven participants consumed a fructose-rich beverage after an overnight fast. Blood was drawn at five time points (baseline, 30, 60, 120, and 180 min after consumption). Thirty urate-related single nucleotide polymorphisms (SNPs) were analyzed for their associations with baseline serum urate and its percent changes, using a two-step modeling approach followed by meta-analysis. At baseline, serum urate (mg/dL, mean ± SD) was higher in Whites (5.60 ± 1.01 vs. 5.37 ± 0.96), men (6.17 ± 1.14 vs. 5.24 ± 0.79), and those with obesity (5.69 ± 1.08 vs. 5.42 ± 1.06 vs. 5.34 ± 0.80). Three SNPs were significantly associated with baseline serum urate or its percent changes, and six SNPs were nominally associated with percent changes in serum urate. In summary, our results showed that genetic variants could play a role in short-term urate metabolism.
... MAF is a transcription factor [102] involved in the regulation of SUA, which is highly expressed in human and mouse kidneys [103]. MAF gene expression is regulated by two independent upstream genetic signals, of which lncRNA is the most prominent [41]. ...
Gout is a chronic metabolic disease that seriously affects human health. It is also a major challenge facing the world, which has brought a heavy burden to patients and society. Hyperuricemia (HUA) is the most important risk factor for gout. In recent years, with the improvement of living standards and the change of dietary habits, the incidence of gout in the world has increased dramatically, and gradually tends to be younger. An increasing number of studies have shown that gene mutations may play an important role in the development of HUA and gout. Therefore, we reviewed the existing literature and summarized the susceptibility genes and research status of HUA and gout, in order to provide reference for the early diagnosis, individualized treatment and the development of new targeted drugs of HUA and gout.
... Our histone landscape predicted 57,345 active enhancers with H3K27ac but lacking H3K4me3, representing 19.6% of the genome (Fig. 1c). Previously reported enhancer SUA2 [27] and enhancer in DAB2 loci [28] were confirmed by the histone landscape we derived ( Fig. 1e and Additional file 1: Fig. S3). The majority of the enhancers we discovered have never been annotated before. ...
Background
Cell type-specific transcriptional programming results from the combinatorial interplay between the repertoire of active regulatory elements. Disease-associated variants disrupt such programming, leading to altered expression of downstream regulated genes and the onset of pathological states. However, due to the non-linear regulatory properties of non-coding elements such as enhancers, which can activate transcription at long distances and in a non-directional way, the identification of causal variants and their target genes remains challenging. Here, we provide a multi-omics analysis to identify regulatory elements associated with functional kidney disease variants, and downstream regulated genes.
Results
In order to understand the genetic risk of kidney diseases, we generated a comprehensive dataset of the chromatin landscape of human kidney tubule cells, including transcription-centered 3D chromatin organization, histone modifications distribution and transcriptome with HiChIP, ChIP-seq and RNA-seq. We identified genome-wide functional elements and thousands of interactions between the distal elements and target genes. The results revealed that risk variants for renal tumor and chronic kidney disease were enriched in kidney tubule cells. We further pinpointed the target genes for the variants and validated two target genes by CRISPR/Cas9 genome editing techniques in zebrafish, demonstrating that SLC34A1 and MTX1 were indispensable genes to maintain kidney function.
Conclusions
Our results provide a valuable multi-omics resource on the chromatin landscape of human kidney tubule cells and establish a bioinformatic pipeline in dissecting functions of kidney disease-associated variants based on cell type-specific epigenome.
... Among the other top hits, five are close to transcription factors involved in kidney and liver development (HNF4G, HNF1A, HNF4A, HLF, and MAF). These are not part of a globally enriched gene set, but recent functional work has shown that the associated missense variant in HNF4A results in differential regulation of the urate solute carrier ABCG2 (Tin et al., 2019), while the MAF association has been shown to regulate SLC5A8 (Leask et al., 2018). Finally, two other loci show large signals: a missense variant in INHBC, a TGF-family hormone, and a variant in/near GCKR, a glucose-enzyme regulator. ...
Genome-wide association studies (GWAS) have been used to study the genetic basis of a wide variety of complex diseases and other traits. We describe UK Biobank GWAS results for three molecular traits—urate, IGF-1, and testosterone—with better-understood biology than most other complex traits. We find that many of the most significant hits are readily interpretable. We observe huge enrichment of associations near genes involved in the relevant biosynthesis, transport, or signaling pathways. We show how GWAS data illuminate the biology of each trait, including differences in testosterone regulation between females and males. At the same time, even these molecular traits are highly polygenic, with many thousands of variants spread across the genome contributing to trait variance. In summary, for these three molecular traits we identify strong enrichment of signal in putative core gene sets, even while most of the SNP-based heritability is driven by a massively polygenic background.
... 22 It is interesting because the lead, and likely causal, variant for serum urate is a missense variant (rs1800961; p. Thr139Ile), with the urate-lowering isoleucine allele better able to activate ABCG2 transcription. 5 HNF4A also is implicated in the regulation of expression of SLC2A9 isoform 1, the serum urate−associated transporter regulatory gene PDZK1, and serum urate−associated transcription factor MAF. [23][24][25] This variant is genetically independent of the signal associated with kidney function. Although it is not known how the eGFR-associated genetic signals at HNF4A ultimately influence kidney function, the genetic data do suggest that hepatocyte nuclear factor-4 alpha (HNF4A) has differing effects on urate levels and kidney function in the kidney tubule, mediated by different pathways that depend on what alleles are inherited and expressed. ...
Increased urate levels and gout correlate with chronic kidney disease with consensus that the primary driver of this relationship is reduced kidney function. However, a comparison of results of genome-wide association studies in serum urate levels and kidney function indicate a more complex situation. Approximately 20% of loci are shared—comprised of those in which the urate-raising allele associates with reduced kidney function, the vice versa situation, and those in which the signals/alleles are different. Although there is very little known regarding the molecular basis of the shared genetic relationship, it is clear that there is no major role for urate transporters and associated transportasome machinery. Some loci, however, do provide clues. The ATXN2 locus, with a shared signal, is one of only a small number of master regulators of expression by chromatin interaction, regulating expression of genes relevant for cholesterol and blood pressure. This suggests a role for systemic metabolic alteration. At HNF4A there is genetic heterogeneity with different genetic variants conferring risk to hyperuricemia and chronic kidney disease, suggesting different pathways. Interestingly, the shared loci congregate in the olfactory receptor pathway. The genome-wide association studies have generated a range of experimentally testable hypotheses that should provide insights into the shared pathogenesis of hyperuricemia/gout and chronic kidney disease.
... In a GWAS meta-analysis of Japanese subjects, Nakatochi et al. (9) identified eight novel loci associated with SUA: rs738409 of PNPLA3 and rs74896528 of SESN2 that were predicted to impair the function of the encoded proteins; TMEM18 rs10188118, TM4SF4 rs6774054, MXD3-LMAN2 rs11952102, PSORS1C1-PSORS1C2 rs16898823 and HNF4A rs6031598 that were related to cell metabolism or oxidative stress; and the unknown LINC01578 rs8024067. PNPLA3 risk allele (rs738409) was also reported inversely associated with gout in a phenome-wide association study (PheWAS) on non-alcoholic fatty liver disease (NAFLD) (10) Leask and colleagues provided evidence that two prominent urate-association signals (SUA1 and SUA2) and MAF constitute a functional genomic regulatory domain that contributes to serum urate regulation (11). SUA1 and SUA2 are conserved between GWAS in European and Japanese sample sets and can be modulated by serum urate-associated variants. ...
Gout is the most prevalent form of inflammatory arthritis, with a strong impact on individual health and healthcare systems. This article reviews clinical and experimental evidences about gout emerged throughout the 2019. Starting with an epidemiological analysis, the review explores new insights on genetic factors influencing the development of gout flare, pathogenetic mechanisms, risk factors for the disease and comorbidities. An overview on pharmacological therapies and recent knowledge on the impact of lifestyle and dietary habits are also included. Finally, the review contains a novel section on animal models, which reflects the renewed interest of researchers in the acute process triggered by monosodium urate crystals.
... However, demonstrating causality of hyperuricemia in the pathophysiology of hypertension or metabolic diseases has been complicated by the reciprocal relationship between target organs for these disorders, the kidney and liver respectively, and the function of these organs in urate production and excretion. Further, we lack mechanistic understanding in how urate excretion is mediated and how urate homeostasis is regulated, even as important pieces to these puzzles have been recently identified 7,8 . ...
The pathophysiological nature of the common ABCG2 gout and hyperuricemia associated variant Q141K (rs2231142) remains undefined. Here, we use a human interventional cohort study (ACTRN12615001302549) to understand the physiological role of ABCG2 and find that participants with the Q141K ABCG2 variant display elevated serum urate, unaltered FEUA, and significant evidence of reduced extra-renal urate excretion. We explore mechanisms by generating a mouse model of the orthologous Q140K Abcg2 variant and find male mice have significant hyperuricemia and metabolic alterations, but only subtle alterations of renal urate excretion and ABCG2 abundance. By contrast, these mice display a severe defect in ABCG2 abundance and function in the intestinal tract. These results suggest a tissue specific pathobiology of the Q141K variant, support an important role for ABCG2 in urate excretion in both the human kidney and intestinal tract, and provide insight into the importance of intestinal urate excretion for serum urate homeostasis. The common ABCG2 variant Q141K contributes to hyperuricemia and gout risk. Here, using a human interventional study and a new orthologous mouse model, the authors report a tissue specific pathobiology of the Q141K variant, and support a significant role for ABCG2 in urate excretion in both the kidney and intestine.
... Among the other top hits, five are close to transcription factors involved in kidney and liver development (HNF4G, HNF1A, HNF4A, HLF and MAF). These are not part of a globally enriched gene set, but recent functional work has shown that the associated missense variant in HNF4A results in differential regulation of the urate solute carrier ABCG2 [17], while the MAF association has been shown to regulate SLC5A8 [20]. Finally, two other loci show large signals: a missense variant in INHBC, a TGF-family hormone, and a variant in/near GCKR, a glucose-enzyme regulator. ...
Genome-wide association studies (GWAS) have been used to study the genetic basis of a wide variety of complex diseases and other traits. However, for most traits it remains difficult to interpret what genes and biological processes are impacted by the top hits. Here, as a contrast, we describe UK Biobank GWAS results for three molecular traits--urate, IGF-1, and testosterone--that are biologically simpler than most diseases, and for which we know a great deal in advance about the core genes and pathways. Unlike most GWAS of complex traits, for all three traits we find that most top hits are readily interpretable. We observe huge enrichment of significant signals near genes involved in the relevant biosynthesis, transport, or signaling pathways. We show how GWAS data illuminate the biology of variation in each trait, including insights into differences in testosterone regulation between females and males. Meanwhile, in other respects the results are reminiscent of GWAS for more-complex traits. In particular, even these molecular traits are highly polygenic, with most of the variance coming not from core genes, but from thousands to tens of thousands of variants spread across most of the genome. Given that diseases are often impacted by many distinct biological processes, including these three, our results help to illustrate why so many variants can affect risk for any given disease.
