Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function.

Kidney disease is highly heritable; however, the causal genetic variants, the cell types in which these variants function, and the molecular mechanisms underlying kidney disease remain largely unknown. To identify genetic loci affecting kidney function, we performed a GWAS using multiple kidney function biomarkers and identified 462 loci. To begin to investigate how these loci affect kidney function, we generated single-cell chromatin accessibility (scATAC-seq) maps of the human kidney and identified candidate cis -regulatory elements (cCREs) for kidney podocytes, tubule epithelial cells, and kidney endothelial, stromal, and immune cells. Kidney tubule epithelial cCREs explained 58% of kidney function SNP-heritability and kidney podocyte cCREs explained an additional 6.5% of SNP-heritability. In contrast, little kidney function heritability was explained by kidney endothelial, stromal, or immune cell-specific cCREs. Through functionally informed fine-mapping, we identified putative causal kidney function variants and their corresponding cCREs. Using kidney scATAC-seq data, we created a deep learning model (which we named ChromKid) to predict kidney cell type-specific chromatin accessibility from sequence. ChromKid and allele specific kidney scATAC-seq revealed that many fine-mapped kidney function variants locally change chromatin accessibility in tubule epithelial cells. Enhancer assays confirmed that fine-mapped kidney function variants alter tubule epithelial regulatory element function. To map the genes which these regulatory elements control, we used CRISPR interference (CRISPRi) to target these regulatory elements in tubule epithelial cells and assessed changes in gene expression. CRISPRi of enhancers harboring kidney function variants regulated NDRG1 and RBPMS expression. Thus, inherited differences in tubule epithelial NDRG1 and RBPMS expression may predispose to kidney disease in humans. We conclude that genetic variants affecting tubule epithelial regulatory element function account for most SNP-heritability of human kidney function. This work provides an experimental approach to identify the variants, regulatory elements, and genes involved in polygenic disease.

Discovery of RXFP2 genetic association in resistant hypertensive men and RXFP2 antagonists for the treatment of resistant hypertension.

Hypertension remains a leading cause of cardiovascular and kidney diseases. Failure to control blood pressure with ≥ 3 medications or control requiring ≥ 4 medications is classified as resistant hypertension (rHTN) and new therapies are needed to reduce the resulting increased risk of morbidity and mortality. Here, we report genetic evidence that relaxin family peptide receptor 2 (RXFP2) is associated with rHTN in men, but not in women. This study shows that adrenal gland gene expression of RXFP2 is increased in men with hypertension and the RXFP2 natural ligand, INSL3, increases adrenal steroidogenesis and corticosteroid secretion in human adrenal cells. To address the hypothesis that RXFP2 activation is an important mechanism in rHTN, we discovered and characterized small molecule and monoclonal antibody (mAb) blockers of RXFP2. The novel chemical entities and mAbs show potent, selective inhibition of RXFP2 and reduce aldosterone and cortisol synthesis and release. The RXFP2 mAbs have suitable rat pharmacokinetic profiles to evaluate the role of RXFP2 in the development and maintenance of rHTN. Overall, we identified RXFP2 activity as a potential new mechanism in rHTN and discovered RXFP2 antagonists for the future interrogation of RXFP2 in cardiovascular and renal diseases.

The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits.

Associations between human genetic variation and clinical phenotypes have become a foundation of biomedical research. Most repositories of these data seek to be disease-agnostic and therefore lack disease-focused views. The Type 2 Diabetes Knowledge Portal (T2DKP) is a public resource of genetic datasets and genomic annotations dedicated to type 2 diabetes (T2D) and related traits. Here, we seek to make the T2DKP more accessible to prospective users and more useful to existing users. First, we evaluate the T2DKP's comprehensiveness by comparing its datasets with those of other repositories. Second, we describe how researchers unfamiliar with human genetic data can begin using and correctly interpreting them via the T2DKP. Third, we describe how existing users can extend their current workflows to use the full suite of tools offered by the T2DKP. We finally discuss the lessons offered by the T2DKP toward the goal of democratizing access to complex disease genetic results.

Genetically proxied therapeutic prolyl-hydroxylase inhibition and cardiovascular risk.

Prolyl hydroxylase (PHD) inhibitors are in clinical development for anaemia in chronic kidney disease. Epidemiological studies have reported conflicting results regarding safety of long-term therapeutic haemoglobin (Hgb) rises through PHD inhibition on risk of cardiovascular disease. Genetic variation in genes encoding PHDs can be used as partial proxies to investigate the potential effects of long-term Hgb rises. We used Mendelian randomization to investigate the effect of long-term Hgb level rises through genetically proxied PHD inhibition on coronary artery disease (CAD: 60 801 cases; 123 504 controls), myocardial infarction (MI: 42 561 cases; 123 504 controls) or stroke (40 585 cases; 406 111 controls). To further characterize long-term effects of Hgb level rises, we performed a phenome-wide association study (PheWAS) in up to 451 099 UK Biobank individuals. Genetically proxied therapeutic PHD inhibition, equivalent to a 1.00 g/dl increase in Hgb levels, was not associated (at P < 0.05) with increased odds of CAD; odd ratio (OR) [95% confidence intervals (CI)] = 1.06 (0.84, 1.35), MI [OR (95% CI) = 1.02 (0.79, 1.33)] or stroke [OR (95% CI) = 0.91 (0.66, 1.24)]. PheWAS revealed associations with blood related phenotypes consistent with EGLN's role, relevant kidney- and liver-related biomarkers like estimated glomerular filtration rate and microalbuminuria, and non-alcoholic fatty liver disease (Bonferroni-adjusted P < 5.42E-05) but these were not clinically meaningful. These findings suggest that long-term alterations in Hgb through PHD inhibition are unlikely to substantially increase cardiovascular disease risk; using large disease genome-wide association study data, we could exclude ORs of 1.35 for cardiovascular risk with a 1.00 g/dl increase in Hgb.

Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention.

Although physical activity and sedentary behavior are moderately heritable, little is known about the mechanisms that influence these traits. Combining data for up to 703,901 individuals from 51 studies in a multi-ancestry meta-analysis of genome-wide association studies yields 99 loci that associate with self-reported moderate-to-vigorous intensity physical activity during leisure time (MVPA), leisure screen time (LST) and/or sedentary behavior at work. Loci associated with LST are enriched for genes whose expression in skeletal muscle is altered by resistance training. A missense variant in ACTN3 makes the alpha-actinin-3 filaments more flexible, resulting in lower maximal force in isolated type IIA muscle fibers, and possibly protection from exercise-induced muscle damage. Finally, Mendelian randomization analyses show that beneficial effects of lower LST and higher MVPA on several risk factors and diseases are mediated or confounded by body mass index (BMI). Our results provide insights into physical activity mechanisms and its role in disease prevention.

Identification and single-base gene-editing functional validation of a cis-EPO variant as a genetic predictor for EPO-increasing therapies.

Hypoxia-inducible factor prolyl hydroxylase inhibitors (HIF-PHIs) are currently under clinical development for treating anemia in chronic kidney disease (CKD), but it is important to monitor their cardiovascular safety. Genetic variants can be used as predictors to help inform the potential risk of adverse effects associated with drug treatments. We therefore aimed to use human genetics to help assess the risk of adverse cardiovascular events associated with therapeutically altered EPO levels to help inform clinical trials studying the safety of HIF-PHIs. By performing a genome-wide association meta-analysis of EPO (n = 6,127), we identified a cis-EPO variant (rs1617640) lying in the EPO promoter region. We validated this variant as most likely causal in controlling EPO levels by using genetic and functional approaches, including single-base gene editing. Using this variant as a partial predictor for therapeutic modulation of EPO and large genome-wide association data in Mendelian randomization tests, we found no evidence (at p < 0.05) that genetically predicted long-term rises in endogenous EPO, equivalent to a 2.2-unit increase, increased risk of coronary artery disease (CAD, OR [95% CI] = 1.01 [0.93, 1.07]), myocardial infarction (MI, OR [95% CI] = 0.99 [0.87, 1.15]), or stroke (OR [95% CI] = 0.97 [0.87, 1.07]). We could exclude increased odds of 1.15 for cardiovascular disease for a 2.2-unit EPO increase. A combination of genetic and functional studies provides a powerful approach to investigate the potential therapeutic profile of EPO-increasing therapies for treating anemia in CKD.

Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals.

Reduced glomerular filtration rate (GFR) can progress to kidney failure. Risk factors include genetics and diabetes mellitus (DM), but little is known about their interaction. We conducted genome-wide association meta-analyses for estimated GFR based on serum creatinine (eGFR), separately for individuals with or without DM (nDM = 178,691, nnoDM = 1,296,113). Our genome-wide searches identified (i) seven eGFR loci with significant DM/noDM-difference, (ii) four additional novel loci with suggestive difference and (iii) 28 further novel loci (including CUBN) by allowing for potential difference. GWAS on eGFR among DM individuals identified 2 known and 27 potentially responsible loci for diabetic kidney disease. Gene prioritization highlighted 18 genes that may inform reno-protective drug development. We highlight the existence of DM-only and noDM-only effects, which can inform about the target group, if respective genes are advanced as drug targets. Largely shared effects suggest that most drug interventions to alter eGFR should be effective in DM and noDM.

Genetic loci and prioritization of genes for kidney function decline derived from a meta-analysis of 62 longitudinal genome-wide association studies.

Estimated glomerular filtration rate (eGFR) reflects kidney function. Progressive eGFR-decline can lead to kidney failure, necessitating dialysis or transplantation. Hundreds of loci from genome-wide association studies (GWAS) for eGFR help explain population cross section variability. Since the contribution of these or other loci to eGFR-decline remains largely unknown, we derived GWAS for annual eGFR-decline and meta-analyzed 62 longitudinal studies with eGFR assessed twice over time in all 343,339 individuals and in high-risk groups. We also explored different covariate adjustment. Twelve genome-wide significant independent variants for eGFR-decline unadjusted or adjusted for eGFR-baseline (11 novel, one known for this phenotype), including nine variants robustly associated across models were identified. All loci for eGFR-decline were known for cross-sectional eGFR and thus distinguished a subgroup of eGFR loci. Seven of the nine variants showed variant-by-age interaction on eGFR cross section (further about 350,000 individuals), which linked genetic associations for eGFR-decline with age-dependency of genetic cross-section associations. Clinically important were two to four-fold greater genetic effects on eGFR-decline in high-risk subgroups. Five variants associated also with chronic kidney disease progression mapped to genes with functional in-silico evidence (UMOD, SPATA7, GALNTL5, TPPP). An unfavorable versus favorable nine-variant genetic profile showed increased risk odds ratios of 1.35 for kidney failure (95% confidence intervals 1.03-1.77) and 1.27 for acute kidney injury (95% confidence intervals 1.08-1.50) in over 2000 cases each, with matched controls). Thus, we provide a large data resource, genetic loci, and prioritized genes for kidney function decline, which help inform drug development pipelines revealing important insights into the age-dependency of kidney function genetics.

The complex optical index of PbS nanocrystal thin films and their use for short wave infrared sensor design.

As nanocrystals (NCs) gain maturity, they become central building blocks for optoelectronics in devices such as solar cells and, more recently, infrared focal plane arrays. Now that the proof of concept of these devices has been established, their optimization requires a deeper understanding of their electronic and optical features to engineer their optoelectronic properties accurately. Though PbS NCs have been extensively investigated, the complex optical index of PbS NC thin films remains mostly unknown. Some previous works have unveiled the optical index for this type of material optimized for solar cells (excitonic peak at 940 nm), but longer wavelengths remain scarce and surface chemistry effects, which are known to be of central importance for layer doping, are simply unexplored. Here, we conduct a systematic investigation of the complex optical index of PbS NC thin films using broadband spectrally resolved ellipsometry. The obtained results are then compared with simulations combining tight-binding (TB) modeling at the NC level and the Bruggeman model to expand the results to the film scale. While TB calculation gives the NC optical indices, we extract the key NC film parameters such as the NC volume fraction and ligand indices by fitting the Bruggeman formula to ellipsometry measurements. We also bring evidence that this joint modeling method can be conducted without the need for ellipsometry data while preserving the main feature of the experimental results. Finally, the unveiled optical indices are used to model the absorption of short-wave infrared diode stacks based on PbS NCs and are relevant for state-of-the-art devices. Our electromagnetic modeling shows that the absorption within the contact is now a major limitation of the current device operated at the telecom wavelength.

Genetic analysis of dietary intake identifies new loci and functional links with metabolic traits.

Dietary intake is a major contributor to the global obesity epidemic and represents a complex behavioural phenotype that is partially affected by innate biological differences. Here, we present a multivariate genome-wide association analysis of overall variation in dietary intake to account for the correlation between dietary carbohydrate, fat and protein in 282,271 participants of European ancestry from the UK Biobank (n = 191,157) and Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (n = 91,114), and identify 26 distinct genome-wide significant loci. Dietary intake signals map exclusively to specific brain regions and are enriched for genes expressed in specialized subtypes of GABAergic, dopaminergic and glutamatergic neurons. We identified two main clusters of genetic variants for overall variation in dietary intake that were differently associated with obesity and coronary artery disease. These results enhance the biological understanding of interindividual differences in dietary intake by highlighting neural mechanisms, supporting functional follow-up experiments and possibly providing new avenues for the prevention and treatment of prevalent complex metabolic diseases.

Bias Tunable Spectral Response of Nanocrystal Array in a Plasmonic Cavity.

Nanocrystals (NCs) have gained considerable attention for their broadly tunable absorption from the UV to the THz range. Nevertheless, their optical features suffer from a lack of tunability once integrated into optoelectronic devices. Here, we show that bias tunable aspectral response is obtained by coupling a HgTe NC array with a plasmonic resonator. Up to 15 meV blueshift can be achieved from a 3 µm absorbing wavelength structure under a 3 V bias voltage when the NC exciton is coupled with a mode of the resonator. We demonstrate that the blueshift arises from the interplay between hopping transport and inhomogeneous absorption due to the presence of the photonic structure. The observed tunable spectral response is qualitatively reproduced in simulation by introducing a bias-dependent diffusion length in the charge transport. This work expands the realm of existing NC-based devices and paves the way toward light modulators.

The trans-ancestral genomic architecture of glycemic traits.

Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 × 10-8), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution.

Correlating Structure and Detection Properties in HgTe Nanocrystal Films.

HgTe nanocrystals (NCs) enable broadly tunable infrared absorption, now commonly used to design light sensors. This material tends to grow under multipodic shapes and does not present well-defined size distributions. Such point generates traps and reduces the particle packing, leading to a reduced mobility. It is thus highly desirable to comprehensively explore the effect of the shape on their performance. Here, we show, using a combination of electron tomography and tight binding simulations, that the charge dissociation is strong within HgTe NCs, but poorly shape dependent. Then, we design a dual-gate field-effect-transistor made of tripod HgTe NCs and use it to generate a planar p-n junction, offering more tunability than its vertical geometry counterpart. Interestingly, the performance of the tripods is higher than sphere ones, and this can be correlated with a stronger Te excess in the case of sphere shapes which is responsible for a higher hole trap density.

Mercury Chalcogenide Quantum Dots: Material Perspective for Device Integration.

Nanocrystals (NCs) are one of the few nanotechnologies to have attained mass market applications with their use as light sources for displays. This success relies on Cd- and In-based wide bandgap materials. NCs are likely to be employed in more applications as they provide a versatile platform for optoelectronics, specifically, infrared optoelectronics. The existing material technologies in this range of wavelengths are generally not cost-effective, which limits the spread of technologies beyond a few niche domains, such as defense and astronomy. Among the potential candidates to address the infrared window, mercury chalcogenide (HgX) NCs exhibit the highest potential in terms of performance. In this review, we discuss how material developments have facilitated device enhancements. Because these materials are mainly used for their infrared optical features, we first review the strategies for their colloidal growth and their specific electronic structure. The review is organized considering three main device-related applications: light emission, electronic transport, and infrared photodetection.

Infrared photoconduction at the diffusion length limit in HgTe nanocrystal arrays.

Narrow band gap nanocrystals offer an interesting platform for alternative design of low-cost infrared sensors. It has been demonstrated that transport in HgTe nanocrystal arrays occurs between strongly-coupled islands of nanocrystals in which charges are partly delocalized. This, combined with the scaling of the noise with the active volume of the film, make case for device size reduction. Here, with two steps of optical lithography we design a nanotrench which effective channel length corresponds to 5-10 nanocrystals, matching the carrier diffusion length. We demonstrate responsivity as high as 1 kA W-1, which is 105 times higher than for conventional µm-scale channel length. In this work the associated specific detectivity exceeds 1012 Jones for 2.5 µm peak detection under 1 V at 200 K and 1 kHz, while the time response is as short as 20 µs, making this performance the highest reported for HgTe NC-based extended short-wave infrared detection.

Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline.

Rapid decline of glomerular filtration rate estimated from creatinine (eGFRcrea) is associated with severe clinical endpoints. In contrast to cross-sectionally assessed eGFRcrea, the genetic basis for rapid eGFRcrea decline is largely unknown. To help define this, we meta-analyzed 42 genome-wide association studies from the Chronic Kidney Diseases Genetics Consortium and United Kingdom Biobank to identify genetic loci for rapid eGFRcrea decline. Two definitions of eGFRcrea decline were used: 3 mL/min/1.73m2/year or more ("Rapid3"; encompassing 34,874 cases, 107,090 controls) and eGFRcrea decline 25% or more and eGFRcrea under 60 mL/min/1.73m2 at follow-up among those with eGFRcrea 60 mL/min/1.73m2 or more at baseline ("CKDi25"; encompassing 19,901 cases, 175,244 controls). Seven independent variants were identified across six loci for Rapid3 and/or CKDi25: consisting of five variants at four loci with genome-wide significance (near UMOD-PDILT (2), PRKAG2, WDR72, OR2S2) and two variants among 265 known eGFRcrea variants (near GATM, LARP4B). All these loci were novel for Rapid3 and/or CKDi25 and our bioinformatic follow-up prioritized variants and genes underneath these loci. The OR2S2 locus is novel for any eGFRcrea trait including interesting candidates. For the five genome-wide significant lead variants, we found supporting effects for annual change in blood urea nitrogen or cystatin-based eGFR, but not for GATM or LARP4B. Individuals at high compared to those at low genetic risk (8-14 vs. 0-5 adverse alleles) had a 1.20-fold increased risk of acute kidney injury (95% confidence interval 1.08-1.33). Thus, our identified loci for rapid kidney function decline may help prioritize therapeutic targets and identify mechanisms and individuals at risk for sustained deterioration of kidney function.

Electroluminescence from HgTe Nanocrystals and Its Use for Active Imaging.

Mercury telluride (HgTe) nanocrystals are among the most versatile infrared (IR) materials with the absorption of lowest energy optical absorption which can be tuned from the visible to the terahertz range. Therefore, they have been extensively considered as near IR emitters and as absorbers for low-cost IR detectors. However, the electroluminescence of HgTe remains poorly investigated despite its ability to go toward longer wavelengths compared to traditional lead sulfide (PbS). Here, we demonstrate a light-emitting diode (LED) based on an indium tin oxide (ITO)/zinc oxide (ZnO)/ZnO-HgTe/PbS/gold-stacked structure, where the emitting layer consists of a ZnO/HgTe bulk heterojunction which drives the charge balance in the system. This LED has low turn-on voltage, long lifetime, and high brightness. Finally, we conduct short wavelength infrared (SWIR) active imaging, where illumination is obtained from a HgTe NC-based LED, and demonstrate moisture detection.

Nanoplatelet-Based Light-Emitting Diode and Its Use in All-Nanocrystal LiFi-like Communication.

Now that colloidal nanocrystals (NCs) have been integrated as green and red sources for liquid crystal displays, the next challenge for quantum dots is their use in electrically driven light-emitting diodes (LEDs). Among various colloidal NCs, nanoplatelets (NPLs) have appeared as promising candidates for light-emitting devices because their two-dimensional shape allows a narrow luminescence spectrum, directional emission, and high light extraction. To reach high quantum efficiency, it is critical to grow core/shell structures. High temperature growth of the shells seems to be a better strategy than previously reported low-temperature approaches to obtain bright NPLs. Here, we synthesize CdSe/CdZnS core/shell NPLs whose shell alloy content is tuned to optimize the charge injection in the LED structure. The obtained LED has exceptionally low turn-on voltage, long-term stability (>3100 h at 100 cd m-2), external quantum efficiency above 5%, and luminance up to 35,000 cd m-2. We study the low-temperature performance of the LED and find that there is a delay of droop in terms of current density as temperature decreases. In the last part of the paper, we design a large LED (56 mm2 emitting area) and test its potential for LiFi-like communication. In such an approach, the LED is not only a lightning source but also used to transmit a communication signal to a PbS quantum dot solar cell used as a broadband photodetector. Operating conditions compatible with both lighting and information transfer have been identified. This work paves the way toward an all NC-based communication setup.

Pushing Absorption of Perovskite Nanocrystals into the Infrared.

To date, defect-tolerance electronic structure of lead halide perovskite nanocrystals is limited to an optical feature in the visible range. Here, we demonstrate that IR sensitization of formamidinium lead iodine (FAPI) nanocrystal array can be obtained by its doping with PbS nanocrystals. In this hybrid array, absorption comes from the PbS nanocrystals while transport is driven by the perovskite which reduces the dark current compared to pristine PbS. In addition, we fabricate a field-effect transistor using a high capacitance ionic glass made of hybrid FAPI/PbS nanocrystal arrays. We show that the hybrid material has an n-type nature with an electron mobility of 2 × 10-3 cm2 V-1 s-1. However, the dark current reduction is mostly balanced by a loss of absorption. To overcome this limitation, we couple the FAPI/PbS hybrid to a guided mode resonator that can enhance the infrared light absorption.

Reconfigurable 2D/0D p-n Graphene/HgTe Nanocrystal Heterostructure for Infrared Detection.

Nanocrystals are promising building blocks for the development of low-cost infrared optoelectronics. Gating a nanocrystal film in a phototransistor geometry is commonly proposed as a strategy to tune the signal-to-noise ratio by carefully controlling the carrier density within the semiconductor. However, the performance improvement has so far been quite marginal. With metallic electrodes, the gate dependence of the photocurrent follows the gate-induced change of the dark current. Graphene presents key advantages: (i) infrared transparency that allows back-side illumination, (ii) vertical electric field transparency, and (iii) carrier selectivity under gate bias. Here, we investigate a configuration of 2D/0D infrared photodetectors taking advantage of a high capacitance ionic glass gate, large-scale graphene electrodes, and a HgTe nanocrystals layer of high carrier mobility. The introduction of graphene electrodes combined with ionic glass enables one to reconfigure selectively the HgTe nanocrystals and the graphene electrodes between electron-doped (n) and hole-doped (p) states. We unveil that this functionality enables the design a 2D/0D p-n junction that expands throughout the device, with a built-in electric field that assists charge dissociation. We demonstrate that, in this specific configuration, the signal-to-noise ratio for infrared photodetection can be enhanced by 2 orders of magnitude, and that photovoltaic operation can be achieved. The detectivity now reaches 109 Jones, whereas the device only absorbs 8% of the incident light. Additionally, the time response of the device is fast (<10 µs), which strongly contrasts with the slow response commonly observed for 2D/0D mixed-dimensional heterostructures, where larger photoconduction gains come at the cost of slower response.