A scalable approach to characterize pleiotropy across thousands of human diseases and complex traits using GWAS summary statistics.

Genome-wide association studies (GWASs) across thousands of traits have revealed the pervasive pleiotropy of trait-associated genetic variants. While methods have been proposed to characterize pleiotropic components across groups of phenotypes, scaling these approaches to ultra-large-scale biobanks has been challenging. Here, we propose FactorGo, a scalable variational factor analysis model to identify and characterize pleiotropic components using biobank GWAS summary data. In extensive simulations, we observe that FactorGo outperforms the state-of-the-art (model-free) approach tSVD in capturing latent pleiotropic factors across phenotypes while maintaining a similar computational cost. We apply FactorGo to estimate 100 latent pleiotropic factors from GWAS summary data of 2,483 phenotypes measured in European-ancestry Pan-UK BioBank individuals (N = 420,531). Next, we find that factors from FactorGo are more enriched with relevant tissue-specific annotations than those identified by tSVD (p = 2.58E-10) and validate our approach by recapitulating brain-specific enrichment for BMI and the height-related connection between reproductive system and muscular-skeletal growth. Finally, our analyses suggest shared etiologies between rheumatoid arthritis and periodontal condition in addition to alkaline phosphatase as a candidate prognostic biomarker for prostate cancer. Overall, FactorGo improves our biological understanding of shared etiologies across thousands of GWASs.

DISP1 deficiency: Monoallelic and biallelic variants cause a spectrum of midline craniofacial malformations.

PURPOSE: DISP1 encodes a transmembrane protein that regulates the secretion of the morphogen, Sonic hedgehog, a deficiency of which is a major cause of holoprosencephaly (HPE). This disorder covers a spectrum of brain and midline craniofacial malformations. The objective of the present study was to better delineate the clinical phenotypes associated with division transporter dispatched-1 (DISP1) variants. METHODS: This study was based on the identification of at least 1 pathogenic variant of the DISP1 gene in individuals for whom detailed clinical data were available. RESULTS: A total of 23 DISP1 variants were identified in heterozygous, compound heterozygous or homozygous states in 25 individuals with midline craniofacial defects. Most cases were minor forms of HPE, with craniofacial features such as orofacial cleft, solitary median maxillary central incisor, and congenital nasal pyriform aperture stenosis. These individuals had either monoallelic loss-of-function variants or biallelic missense variants in DISP1. In individuals with severe HPE, the DISP1 variants were commonly found associated with a variant in another HPE-linked gene (ie, oligogenic inheritance). CONCLUSION: The genetic findings we have acquired demonstrate a significant involvement of DISP1 variants in the phenotypic spectrum of midline defects. This underlines its importance as a crucial element in the efficient secretion of Sonic hedgehog. We also demonstrated that the very rare solitary median maxillary central incisor and congenital nasal pyriform aperture stenosis combination is part of the DISP1-related phenotype. The present study highlights the clinical risks to be flagged up during genetic counseling after the discovery of a pathogenic DISP1 variant.

Synonymous variants in holoprosencephaly alter codon usage and impact the Sonic Hedgehog protein.

Synonymous single nucleotide variants (sSNVs) have been implicated in various genetic disorders through alterations of pre-mRNA splicing, mRNA structure and miRNA regulation. However, their impact on synonymous codon usage and protein translation remains to be elucidated in clinical context. Here, we explore the functional impact of sSNVs in the Sonic Hedgehog (SHH) gene, identified in patients affected by holoprosencephaly, a congenital brain defect resulting from incomplete forebrain cleavage. We identified eight sSNVs in SHH, selectively enriched in holoprosencephaly patients as compared to healthy individuals, and systematically assessed their effect at both transcriptional and translational levels using a series of in silico and in vitro approaches. Although no evidence of impact of these sSNVs on splicing, mRNA structure or miRNA regulation was found, five sSNVs introduced significant changes in codon usage and were predicted to impact protein translation. Cell assays demonstrated that these five sSNVs are associated with a significantly reduced amount of the resulting protein, ranging from 5% to 23%. Inhibition of the proteasome rescued the protein levels for four out of five sSNVs, confirming their impact on protein stability and folding. Remarkably, we found a significant correlation between experimental values of protein reduction and computational measures of codon usage, indicating the relevance of in silico models in predicting the impact of sSNVs on translation. Considering the critical role of SHH in brain development, our findings highlight the clinical relevance of sSNVs in holoprosencephaly and underline the importance of investigating their impact on translation in human pathologies.

Integrated clinical and omics approach to rare diseases: novel genes and oligogenic inheritance in holoprosencephaly.

Holoprosencephaly is a pathology of forebrain development characterized by high phenotypic heterogeneity. The disease presents with various clinical manifestations at the cerebral or facial levels. Several genes have been implicated in holoprosencephaly but its genetic basis remains unclear: different transmission patterns have been described including autosomal dominant, recessive and digenic inheritance. Conventional molecular testing approaches result in a very low diagnostic yield and most cases remain unsolved. In our study, we address the possibility that genetically unsolved cases of holoprosencephaly present an oligogenic origin and result from combined inherited mutations in several genes. Twenty-six unrelated families, for whom no genetic cause of holoprosencephaly could be identified in clinical settings [whole exome sequencing and comparative genomic hybridization (CGH)-array analyses], were reanalysed under the hypothesis of oligogenic inheritance. Standard variant analysis was improved with a gene prioritization strategy based on clinical ontologies and gene co-expression networks. Clinical phenotyping and exploration of cross-species similarities were further performed on a family-by-family basis. Statistical validation was performed on 248 ancestrally similar control trios provided by the Genome of the Netherlands project and on 574 ancestrally matched controls provided by the French Exome Project. Variants of clinical interest were identified in 180 genes significantly associated with key pathways of forebrain development including sonic hedgehog (SHH) and primary cilia. Oligogenic events were observed in 10 families and involved both known and novel holoprosencephaly genes including recurrently mutated FAT1, NDST1, COL2A1 and SCUBE2. The incidence of oligogenic combinations was significantly higher in holoprosencephaly patients compared to two control populations (P < 10-9). We also show that depending on the affected genes, patients present with particular clinical features. This study reports novel disease genes and supports oligogenicity as clinically relevant model in holoprosencephaly. It also highlights key roles of SHH signalling and primary cilia in forebrain development. We hypothesize that distinction between different clinical manifestations of holoprosencephaly lies in the degree of overall functional impact on SHH signalling. Finally, we underline that integrating clinical phenotyping in genetic studies is a powerful tool to specify the clinical relevance of certain mutations.

Recent advances in understanding inheritance of holoprosencephaly.

Holoprosencephaly (HPE) is a complex genetic disorder of the developing forebrain characterized by high phenotypic and genetic heterogeneity. HPE was initially defined as an autosomal dominant disease, but recent research has shown that its mode of transmission is more complex. The past decade has witnessed rapid development of novel genetic technologies and significant progresses in clinical studies of HPE. In this review, we recapitulate genetic epidemiological studies of the largest European HPE cohort and summarize the novel genetic discoveries of HPE based on recently developed diagnostic methods. Our main purpose is to present different inheritance patterns that exist for HPE with a particular emphasis on oligogenic inheritance and its implications in genetic counseling.

Improved multi-ancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk.

Multi-ancestry statistical fine-mapping of cis-molecular quantitative trait loci (cis-molQTL) aims to improve the precision of distinguishing causal cis-molQTLs from tagging variants. However, existing approaches fail to reflect shared genetic architectures. To solve this limitation, we present the Sum of Shared Single Effects (SuShiE) model, which leverages LD heterogeneity to improve fine-mapping precision, infer cross-ancestry effect size correlations, and estimate ancestry-specific expression prediction weights. We apply SuShiE to mRNA expression measured in PBMCs (n=956) and LCLs (n=814) together with plasma protein levels (n=854) from individuals of diverse ancestries in the TOPMed MESA and GENOA studies. We find SuShiE fine-maps cis-molQTLs for 16% more genes compared with baselines while prioritizing fewer variants with greater functional enrichment. SuShiE infers highly consistent cis-molQTL architectures across ancestries on average; however, we also find evidence of heterogeneity at genes with predicted loss-of-function intolerance, suggesting that environmental interactions may partially explain differences in cis-molQTL effect sizes across ancestries. Lastly, we leverage estimated cis-molQTL effect-sizes to perform individual-level TWAS and PWAS on six white blood cell-related traits in AOU Biobank individuals (n=86k), and identify 44 more genes compared with baselines, further highlighting its benefits in identifying genes relevant for complex disease risk. Overall, SuShiE provides new insights into the cis-genetic architecture of molecular traits.

Inferring causal cell types of human diseases and risk variants from candidate regulatory elements.

The heritability of human diseases is extremely enriched in candidate regulatory elements (cRE) from disease-relevant cell types. Critical next steps are to infer which and how many cell types are truly causal for a disease (after accounting for co-regulation across cell types), and to understand how individual variants impact disease risk through single or multiple causal cell types. Here, we propose CT-FM and CT-FM-SNP, two methods that leverage cell-type-specific cREs to fine-map causal cell types for a trait and for its candidate causal variants, respectively. We applied CT-FM to 63 GWAS summary statistics (average N = 417K) using nearly one thousand cRE annotations, primarily coming from ENCODE4. CT-FM inferred 81 causal cell types with corresponding SNP-annotations explaining a high fraction of trait SNP-heritability (~2/3 of the SNP-heritability explained by existing cREs), identified 16 traits with multiple causal cell types, highlighted cell-disease relationships consistent with known biology, and uncovered previously unexplored cellular mechanisms in psychiatric and immune-related diseases. Finally, we applied CT-FM-SNP to 39 UK Biobank traits and predicted high confidence causal cell types for 2,798 candidate causal non-coding SNPs. Our results suggest that most SNPs impact a phenotype through a single cell type, and that pleiotropic SNPs target different cell types depending on the phenotype context. Altogether, CT-FM and CT-FM-SNP shed light on how genetic variants act collectively and individually at the cellular level to impact disease risk.

Structure and Properties of High-Entropy Boride Ceramics Synthesized by Mechanical Alloying and Spark Plasma Sintering.

This manuscript shows the study of the structure, mechanical, and chemical properties of high-entropy borides MeB2 (Me = Ti, Ta, Nb, Hf, Zr). High-entropy borides were synthesized by mechanical alloying and spark plasma sintering. A chemically homogeneous powder with a low iron content (0.12%) was obtained in a planetary mill by rotating the planetary disk/pots at 200-400 rpm and a processing time of 7.5 h. The structure, mechanical, and chemical properties of the resulting high-entropy borides have been studied. A single-phase hexagonal structure is formed during spark plasma sintering of mechanically alloyed powders at 2000 °C. The microhardness of the samples ranged from 1763 to 1959 HV. Gas-dynamic tests of the synthesized materials showed that an increase in the content of Zr and Hf in the composition increases the thermal-oxidative resistance of the material.

A scalable variational approach to characterize pleiotropic components across thousands of human diseases and complex traits using GWAS summary statistics.

Genome-wide association studies (GWAS) across thousands of traits have revealed the pervasive pleiotropy of trait-associated genetic variants. While methods have been proposed to characterize pleiotropic components across groups of phenotypes, scaling these approaches to ultra large-scale biobanks has been challenging. Here, we propose FactorGo, a scalable variational factor analysis model to identify and characterize pleiotropic components using biobank GWAS summary data. In extensive simulations, we observe that FactorGo outperforms the state-of-the-art (model-free) approach tSVD in capturing latent pleiotropic factors across phenotypes, while maintaining a similar computational cost. We apply FactorGo to estimate 100 latent pleiotropic factors from GWAS summary data of 2,483 phenotypes measured in European-ancestry Pan-UK BioBank individuals (N=420,531). Next, we find that factors from FactorGo are more enriched with relevant tissue-specific annotations than those identified by tSVD (P=2.58E-10), and validate our approach by recapitulating brain-specific enrichment for BMI and the height-related connection between reproductive system and muscular-skeletal growth. Finally, our analyses suggest novel shared etiologies between rheumatoid arthritis and periodontal condition, in addition to alkaline phosphatase as a candidate prognostic biomarker for prostate cancer. Overall, FactorGo improves our biological understanding of shared etiologies across thousands of GWAS.

Structural, Electrical, and Mechanical Properties Investigation of Open-Cell Aluminum Foams Obtained by Spark Plasma Sintering and Replication on Polyurethane Template.

The present paper illustrates a comparison of open-cell aluminum foams. The foams were fabricated by two different methods: spark plasma sintering and replication on a polyurethane template. The influence of pressure, temperature, and diameter of space holding material on foam obtained by the spark plasma sintering method was investigated. Additionally, the aluminum powder content in slurry and atmosphere during thermal processing of foam prepared by the replication technique were studied. The morphology and structure of obtained samples were analyzed by scanning electron microscopy and X-ray diffraction analysis. Supplementarily, mechanical properties and electrical conductivity were studied. The porosity of obtained samples was 83% for the SPS sample and 85% for the replication sample. The results of the studies carried out gave us an understanding that the SPS method is more promising for using the obtained foams as cathode current collectors in lithium-ion batteries due to excessive aluminum oxidation during sintering in the furnace.

Refractory CrMoNbWV High-Entropy Alloy Manufactured by Mechanical Alloying and Spark Plasma Sintering: Evolution of Microstructure and Properties.

In this study, bulk samples of a CrMoNbWV high-entropy alloy (HEA) were obtained for the first time by spark plasma sintering (SPS) of mechanically alloyed (MA) powders at 1200 °C, 1300 °C, and 1400 °C. Microstructure evolution, phase formation as well as wear and corrosion behavior were investigated. The MA powders' phase composition was found to be represented by body-centered-cubic (BCC) solid solution. The solid solution partially decomposed to Laves phases under the sintering, such as Cr2Nb and (Fe, Cr)Nb, and NbVO4-VO oxides mixture. The temperature increase to 1400 °C led to a grain coarsening of the BCC phase and decreased the Laves phase content accompanied by precipitation at the grain boundaries. The sintered samples showed high hardness and compressive strength (2700-2800 MPa) at room temperature. The wear tests demonstrated excellent results in comparison to conventional wear-resistant composites. The obtained samples also exhibited high corrosion resistance under electrochemical tests in H2SO4 solution. The CrMoNbWV HEA has comparable mechanical and corrosive properties with the WNbMoTaV type HEA, but at the same time has a reduced density: CrMoNbWV-10.55 g/cm3, WNbMoTaV-12.42 g/cm3.

Atomic Layer Deposition of Ni-Co-O Thin-Film Electrodes for Solid-State LIBs and the Influence of Chemical Composition on Overcapacity.

Nanostructured metal oxides (MOs) demonstrate good electrochemical properties and are regarded as promising anode materials for high-performance lithium-ion batteries (LIBs). The capacity of nickel-cobalt oxides-based materials is among the highest for binary transition metals oxide (TMOs). In the present paper, we report the investigation of Ni-Co-O (NCO) thin films obtained by atomic layer deposition (ALD) using nickel and cobalt metallocenes in a combination with oxygen plasma. The formation of NCO films with different ratios of Ni and Co was provided by ALD cycles leading to the formation of nickel oxide (a) and cobalt oxide (b) in one supercycle (linear combination of a and b cycles). The film thickness was set by the number of supercycles. The synthesized films had a uniform chemical composition over the depth with an admixture of metallic nickel and carbon up to 4 at.%. All samples were characterized by a single NixCo1-xO phase with a cubic face-centered lattice and a uniform density. The surface of the NCO films was uniform, with rare inclusions of nanoparticles 15-30 nm in diameter. The growth rates of all films on steel were higher than those on silicon substrates, and this difference increased with increasing cobalt concentration in the films. In this paper, we propose a method for processing cyclic voltammetry curves for revealing the influence of individual components (nickel oxide, cobalt oxide and solid electrolyte interface-SEI) on the electrochemical capacity. The initial capacity of NCO films was augmented with an increase of nickel oxide content.

Influence of Alloying Elements on the Mechanical Properties of Anodized Aluminum and on the Adhesion of Copper Metallization.

The active development of the power electronics market and a constant increase in the prices of components require new materials and approaches, including a power module packaging technology. The use of aluminum instead of copper in the power module baseplate is an interesting and promising solution. The insulated metal baseplate is one of the most extensively developed technologies nowadays. The object of this study is an insulated metal substrate based on anodized aluminum. The main goal of the article is the comparison of copper topology adhesion to an anodized aluminum oxide layer formed on different aluminum alloys with aluminum content of at least 99.3 wt %. Peel test and pull-off adhesions showed a twofold difference for both aluminum alloys. The high ordered defect-free anodized alumina formed on alloys with copper content of 0.06 wt % had a mean pull-off adhesion of 27 N/mm2 and hardness of 489 HV. In the case of the alloy with copper content of around 0.15 wt %, it had hardness of 295 HV and a mean pull-off adhesion of 12 N/mm2. The results of our microstructure investigation showed that anodized alumina based on alloys with copper content of around 0.15 wt % is fragile due to spherical holes. Summing up the results, it can be concluded that not all initial impurities are critical for anodized alumina, but some, specifically copper, dramatically decreased the mechanical properties of anodized alumina.

Disrupted Hypothalamo-Pituitary Axis in Association With Reduced SHH Underlies the Pathogenesis of NOTCH-Deficiency.

CONTEXT: In human, Sonic hedgehog (SHH) haploinsufficiency is the predominant cause of holoprosencephaly, a structural malformation of the forebrain midline characterized by phenotypic heterogeneity and incomplete penetrance. The NOTCH signaling pathway has recently been associated with holoprosencephaly in humans, but the precise mechanism involving NOTCH signaling during early brain development remains unknown. OBJECTIVE: The aim of this study was to evaluate the relationship between SHH and NOTCH signaling to determine the mechanism by which NOTCH dysfunction could cause midline malformations of the forebrain. DESIGN: In this study, we have used a chemical inhibition approach in the chick model and a genetic approach in the mouse model. We also reported results obtained from the clinical diagnosis of a cohort composed of 141 holoprosencephaly patients. RESULTS: We demonstrated that inhibition of NOTCH signaling in chick embryos as well as in mouse embryos induced a specific downregulation of SHH in the anterior hypothalamus. Our data in the mouse also revealed that the pituitary gland was the most sensitive tissue to Shh insufficiency and that haploinsufficiency of the SHH and NOTCH signaling pathways synergized to produce a malformed pituitary gland. Analysis of a large holoprosencephaly cohort revealed that some patients possessed multiple heterozygous mutations in several regulators of both pathways. CONCLUSIONS: These results provided new insights into molecular mechanisms underlying the extreme phenotypic variability observed in human holoprosencephaly. They showed how haploinsufficiency of the SHH and NOTCH activity could contribute to specific congenital hypopituitarism that was associated with a sella turcica defect.

Depicting the genetic architecture of pediatric cancers through an integrative gene network approach.

The genetic etiology of childhood cancers still remains largely unknown. It is therefore essential to develop novel strategies to unravel the spectrum of pediatric cancer genes. Statistical network modeling techniques have emerged as powerful methodologies for enabling the inference of gene-disease relationship and have been performed on adult but not pediatric cancers. We performed a deep multi-layer understanding of pan-cancer transcriptome data selected from the Treehouse Childhood Cancer Initiative through a co-expression network analysis. We identified six modules strongly associated with pediatric tumor histotypes that were functionally linked to developmental processes. Topological analyses highlighted that pediatric cancer predisposition genes and potential therapeutic targets were central regulators of cancer-histotype specific modules. A module was related to multiple pediatric malignancies with functions involved in DNA repair and cell cycle regulation. This canonical oncogenic module gathered most of the childhood cancer predisposition genes and clinically actionable genes. In pediatric acute leukemias, the driver genes were co-expressed in a module related to epigenetic and post-transcriptional processes, suggesting a critical role of these pathways in the progression of hematologic malignancies. This integrative pan-cancer study provides a thorough characterization of pediatric tumor-associated modules and paves the way for investigating novel candidate genes involved in childhood tumorigenesis.