Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import.

Organisms maintain metabolic homeostasis through the combined functions of small-molecule transporters and enzymes. While many metabolic components have been well established, a substantial number remains without identified physiological substrates. To bridge this gap, we have leveraged large-scale plasma metabolome genome-wide association studies (GWAS) to develop a multiomic Gene-Metabolite Association Prediction (GeneMAP) discovery platform. GeneMAP can generate accurate predictions and even pinpoint genes that are distant from the variants implicated by GWAS. In particular, our analysis identified solute carrier family 25 member 48 (SLC25A48) as a genetic determinant of plasma choline levels. Mechanistically, SLC25A48 loss strongly impairs mitochondrial choline import and synthesis of its downstream metabolite betaine. Integrative rare variant and polygenic score analyses in UK Biobank provide strong evidence that the SLC25A48 causal effects on human disease may in part be mediated by the effects of choline. Altogether, our study provides a discovery platform for metabolic gene function and proposes SLC25A48 as a mitochondrial choline transporter.

The broad impact of cell death genes on the human disease phenome.

Cell death mediated by genetically defined signaling pathways influences the health and dynamics of all tissues, however the tissue specificity of cell death pathways and the relationships between these pathways and human disease are not well understood. We analyzed the expression profiles of an array of 44 cell death genes involved in apoptosis, necroptosis, and pyroptosis cell death pathways across 49 human tissues from GTEx, to elucidate the landscape of cell death gene expression across human tissues, and the relationship between tissue-specific genetically determined expression and the human phenome. We uncovered unique cell death gene expression profiles across tissue types, suggesting there are physiologically distinct cell death programs in different tissues. Using summary statistics-based transcriptome wide association studies (TWAS) on human traits in the UK Biobank (n ~ 500,000), we evaluated 513 traits encompassing ICD-10 defined diagnoses and laboratory-derived traits. Our analysis revealed hundreds of significant (FDR < 0.05) associations between genetically regulated cell death gene expression and an array of human phenotypes encompassing both clinical diagnoses and hematologic parameters, which were independently validated in another large-scale DNA biobank (BioVU) at Vanderbilt University Medical Center (n = 94,474) with matching phenotypes. Cell death genes were highly enriched for significant associations with blood traits versus non-cell-death genes, with apoptosis-associated genes enriched for leukocyte and platelet traits. Our findings are also concordant with independently published studies (e.g. associations between BCL2L11/BIM expression and platelet & lymphocyte counts). Overall, these results suggest that cell death genes play distinct roles in their contribution to human phenotypes, and that cell death genes influence a diverse array of human traits.

Relative leg-to-arm skeletal strength proportions in orangutans by species and sex.

Among extant great apes, orangutans climb most frequently. However, Bornean orangutans (Pongo pygmaeus) exhibit higher frequencies of terrestrial locomotion than do Sumatran orangutans (Pongo abelii). Variation in long bone cross-sectional geometry is known to reflect differential loading of the limbs. Thus, Bornean orangutans should show greater relative leg-to-arm strength than their Sumatran counterparts. Using skeletal specimens from museum collections, we measured two cross-sectional geometric measures of bone strength: the polar section modulus (Zpol) and the ratio of maximum to minimum area moments of inertia (Imax/Imin), at the midshaft of long bones in Bornean (n = 19) and Sumatran adult orangutans (n = 12) using medical CT and peripheral quantitative CT scans, and compared results to published data of other great apes. Relative leg-to-arm strength was quantified using ratios of femur and tibia over humerus, radius, and ulna, respectively. Differences between orangutan species and between sexes in median ratios were assessed using Wilcoxon rank sum tests. The tibia of Bornean orangutans was stronger relative to the humerus and the ulna than in Sumatran orangutans (p = 0.008 and 0.025, respectively), consistent with behavioral studies that indicate higher frequencies of terrestrial locomotion in the former. In three Zpol ratios, adult female orangutans showed greater leg-to-arm bone strength compared to flanged males, which may relate to females using their legs more during arboreal locomotion than in adult flanged males. A greater amount of habitat discontinuity on Borneo compared to Sumatra has been posited as a possible explanation for observed interspecific differences in locomotor behaviors, but recent camera trap studies has called this into question. Alternatively, greater frequencies of terrestriality in Pongo pygmaeus may be due to the absence of tigers on Borneo. The results of this study are consistent with the latter explanation given that habitat continuity was greater a century ago when our study sample was collected.

GeneMAP: A discovery platform for metabolic gene function.

Organisms maintain metabolic homeostasis through the combined functions of small molecule transporters and enzymes. While many of the metabolic components have been well-established, a substantial number remains without identified physiological substrates. To bridge this gap, we have leveraged large-scale plasma metabolome genome-wide association studies (GWAS) to develop a multiomic Gene-Metabolite Associations Prediction (GeneMAP) discovery platform. GeneMAP can generate accurate predictions, even pinpointing genes that are distant from the variants implicated by GWAS. In particular, our work identified SLC25A48 as a genetic determinant of plasma choline levels. Mechanistically, SLC25A48 loss strongly impairs mitochondrial choline import and synthesis of its downstream metabolite, betaine. Rare variant testing and polygenic risk score analyses have elucidated choline-relevant phenomic consequences of SLC25A48 dysfunction. Altogether, our study proposes SLC25A48 as a mitochondrial choline transporter and provides a discovery platform for metabolic gene function.

Mapping the landscape of lineage-specific dynamic regulation of gene expression using single-cell transcriptomics and application to genetics of complex disease.

Single-cell transcriptome data can provide insights into how genetic variation influences biological processes involved in human biology and disease. However, the identification of gene-level associations in distinct cell types faces several challenges, including the limited reference resource from population scale studies, data sparsity in single-cell RNA sequencing, and the complex cell-state pattern of expression within individual cell types. Here we develop genetic models of cell type specific and cell state adjusted gene expression in mid-brain neurons in the process of specializing from induced pluripotent stem cells. The resulting framework quantifies the dynamics of the genetic regulation of gene expression and estimates its cell type specificity. As an application, we show that the approach detects known and new genes associated with schizophrenia and enables insights into context-dependent disease mechanisms. We provide a genomic resource from a phenome-wide application of our models to more than 1500 phenotypes from the UK Biobank. Using longitudinal genetically determined expression, we implement a predictive causality framework, evaluating the prediction of future values of a target gene expression using prior values of a putative regulatory gene. Collectively, this work demonstrates the insights that can be gained into the molecular underpinnings of diseases by quantifying the genetic control of gene expression at single-cell resolution.

Hypergraph factorization for multi-tissue gene expression imputation.

Integrating gene expression across tissues and cell types is crucial for understanding the coordinated biological mechanisms that drive disease and characterise homeostasis. However, traditional multitissue integration methods cannot handle uncollected tissues or rely on genotype information, which is often unavailable and subject to privacy concerns. Here we present HYFA (Hypergraph Factorisation), a parameter-efficient graph representation learning approach for joint imputation of multi-tissue and cell-type gene expression. HYFA is genotype-agnostic, supports a variable number of collected tissues per individual, and imposes strong inductive biases to leverage the shared regulatory architecture of tissues and genes. In performance comparison on Genotype-Tissue Expression project data, HYFA achieves superior performance over existing methods, especially when multiple reference tissues are available. The HYFA-imputed dataset can be used to identify replicable regulatory genetic variations (eQTLs), with substantial gains over the original incomplete dataset. HYFA can accelerate the effective and scalable integration of tissue and cell-type transcriptome biorepositories.

The broad impact of cell death genes on the human disease phenome.

Apoptotic, necroptotic, and pyroptotic cell death pathways are attractive and druggable targets for many human diseases, however the tissue specificity of these pathways and the relationship between these pathways and human disease is poorly characterized. Understanding the impact of modulating cell death gene expression on the human phenome could inform clinical investigation of cell death pathway-modulating therapeutics in human disorders by identifying novel trait associations and by detecting tissue-specific side effect profiles. We analyzed the expression profiles of an array of 44 cell death genes across somatic tissues in GTEx v8 and investigated the relationship between tissue-specific genetically determined expression of 44 cell death genes and the human phenome using summary statistics-based transcriptome wide association studies (TWAS) on human traits in the UK Biobank V3 (n ~500,000). We evaluated 513 traits encompassing ICD-10 defined diagnoses and hematologic traits (blood count labs). Our analysis revealed hundreds of significant (FDR<0.05) associations between cell death gene expression and diverse human phenotypes, which were independently validated in another large-scale biobank. Cell death genes were highly enriched for significant associations with blood traits versus non-cell-death genes, with apoptosis-associated genes enriched for leukocyte and platelet traits and necroptosis gene associations enriched for erythroid traits (e.g., Reticulocyte count, FDR=0.004). This suggests that immunogenic cell death pathways play an important role in regulating erythropoiesis and reinforces the paradigm that apoptosis pathway genes are critical for white blood cell and platelet development. Of functionally analogous genes, for instance pro-survival BCL2 family members, trait/direction-of-effect relationships were heterogeneous across blood traits. Overall, these results suggest that even functionally similar and/or orthologous cell death genes play distinct roles in their contribution to human phenotypes, and that cell death genes influence a diverse array of human traits.

Assessment of the ability of Aedes species mosquitoes to transmit feline Mycoplasma haemofelis and ' Candidatus Mycoplasma haemominutum'.

Objectives The objective of this study was to evaluate wild-caught mosquitoes for evidence of hemotropic Mycoplasma species DNA and to determine whether the feline hemoplasmas, Mycoplasma haemofelis (Mhf) and ' Candidatus Mycoplasma haemominutum' (Mhm), can be transmitted by Aedes aegypti mosquitoes in a laboratory setting. Methods Wild-caught mosquito pools (50 mosquitoes per pool, 84 pools) utilized in routine public health department disease surveillance programs were tested for hemotropic Mycoplasma species DNA using PCR with primers designed to amplify all known hemoplasmas. Additionally, mosquitoes were trapped in the vicinity of known feral cat colonies, pooled (50 mosquitoes per pool) and tested (84 pools). Purpose-bred cats housed in a research facility were infected with Mhf or Mhm and then colonized laboratory A aegypti were fed upon the bacteremic cats. After a 7 day incubation period, mosquitoes previously fed on infected cats were allowed to feed again on naive cats, which were monitored for bacteremia for 10 weeks. Results Mycoplasma wenyonii DNA was confirmed in one wild-caught mosquito pool by DNA sequencing. While 7% of cats tested in feral colonies were hemoplasma positive, none of the mosquitoes trapped near colonies were positive. Hemoplasma DNA was amplified from A aegypti by PCR immediately after the infectious blood meal, but DNA was not detected at 7 and 14 days after feeding. Although evidence for uptake of organisms existed, hemoplasma DNA was not amplified from the experimentally infested cats in the 10 week observation period. Conclusions and relevance While wild-caught mosquitoes contained hemoplasma DNA and laboratory reared A aegypti mosquitoes take up hemoplasmas during the blood meal, there was no evidence of biologic transmission in this model.

Biodegradable hydrogels composed of oxime crosslinked poly(ethylene glycol), hyaluronic acid and collagen: a tunable platform for soft tissue engineering.

In situ crosslinking hydrogels are attractive for application as injectable hydrogel-based tissue scaffolds that adapt to fill patient-specific cavities. Oxime click chemistry was used to crosslink hydrogels that were biodegradable, soft and supportive of cell adhesion. Linear poly(ethylene glycol)s (PEGs, Mn 2 or 4 kDa) terminated at both ends with aminooxy moieties and hyaluronic acid (HA, Mn 2 MDa) derivatives displaying aldehydes were non-toxic towards primary Schwann cells. The PEG and HA derivatives form oxime crosslinked hydrogels with mechanical and swelling properties that were tunable based on the composition of the hydrogels to values analogous to soft tissues such as those found in the central or peripheral nervous system. Gels incorporating collagen-1 supported the adhesion of human mesenchymal stem cells. Such chemistry has the potential to generate clinically relevant injectable hydrogels for minimally invasive personalized medical procedures in the central or peripheral nervous systems.