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1.
Nature ; 615(7950): 134-142, 2023 03.
Article in English | MEDLINE | ID: mdl-36470304

ABSTRACT

Preventing SARS-CoV-2 infection by modulating viral host receptors, such as angiotensin-converting enzyme 2 (ACE2)1, could represent a new chemoprophylactic approach for COVID-19 that complements vaccination2,3. However, the mechanisms that control the expression of ACE2 remain unclear. Here we show that the farnesoid X receptor (FXR) is a direct regulator of ACE2 transcription in several tissues affected by COVID-19, including the gastrointestinal and respiratory systems. We then use the over-the-counter compound z-guggulsterone and the off-patent drug ursodeoxycholic acid (UDCA) to reduce FXR signalling and downregulate ACE2 in human lung, cholangiocyte and intestinal organoids and in the corresponding tissues in mice and hamsters. We show that the UDCA-mediated downregulation of ACE2 reduces susceptibility to SARS-CoV-2 infection in vitro, in vivo and in human lungs and livers perfused ex situ. Furthermore, we reveal that UDCA reduces the expression of ACE2 in the nasal epithelium in humans. Finally, we identify a correlation between UDCA treatment and positive clinical outcomes after SARS-CoV-2 infection using retrospective registry data, and confirm these findings in an independent validation cohort of recipients of liver transplants. In conclusion, we show that FXR has a role in controlling ACE2 expression and provide evidence that modulation of this pathway could be beneficial for reducing SARS-CoV-2 infection, paving the way for future clinical trials.


Subject(s)
Angiotensin-Converting Enzyme 2 , COVID-19 , Receptors, Virus , Ursodeoxycholic Acid , Animals , Humans , Mice , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/metabolism , COVID-19/metabolism , COVID-19/prevention & control , Receptors, Virus/genetics , Receptors, Virus/metabolism , Retrospective Studies , SARS-CoV-2/metabolism , COVID-19 Drug Treatment , Cricetinae , Transcription, Genetic , Ursodeoxycholic Acid/pharmacology , Lung/drug effects , Lung/metabolism , Organoids/drug effects , Organoids/metabolism , Liver/drug effects , Liver/metabolism , Nasal Mucosa/drug effects , Nasal Mucosa/metabolism , Registries , Reproducibility of Results , Liver Transplantation
2.
Circ Res ; 135(8): 822-837, 2024 Sep 27.
Article in English | MEDLINE | ID: mdl-39234692

ABSTRACT

BACKGROUND: Atherosclerotic plaques form unevenly due to disturbed blood flow, causing localized endothelial cell (EC) dysfunction. Obesity exacerbates this process, but the underlying molecular mechanisms are unclear. The transcription factor EPAS1 (HIF2A) has regulatory roles in endothelium, but its involvement in atherosclerosis remains unexplored. This study investigates the potential interplay between EPAS1, obesity, and atherosclerosis. METHODS: Responses to shear stress were analyzed using cultured porcine aortic EC exposed to flow in vitro coupled with metabolic and molecular analyses and by en face immunostaining of murine aortic EC exposed to disturbed flow in vivo. Obesity and dyslipidemia were induced in mice via exposure to a high-fat diet or through Leptin gene deletion. The role of Epas1 in atherosclerosis was evaluated by inducible endothelial Epas1 deletion, followed by hypercholesterolemia induction (adeno-associated virus-PCSK9 [proprotein convertase subtilisin/kexin type 9]; high-fat diet). RESULTS: En face staining revealed EPAS1 enrichment at sites of disturbed blood flow that are prone to atherosclerosis initiation. Obese mice exhibited substantial reduction in endothelial EPAS1 expression. Sulforaphane, a compound with known atheroprotective effects, restored EPAS1 expression and concurrently reduced plasma triglyceride levels in obese mice. Consistently, triglyceride derivatives (free fatty acids) suppressed EPAS1 in cultured EC by upregulating the negative regulator PHD2. Clinical observations revealed that reduced serum EPAS1 correlated with increased endothelial PHD2 and PHD3 in obese individuals. Functionally, endothelial EPAS1 deletion increased lesion formation in hypercholesterolemic mice, indicating an atheroprotective function. Mechanistic insights revealed that EPAS1 protects arteries by maintaining endothelial proliferation by positively regulating the expression of the fatty acid-handling molecules CD36 (cluster of differentiation 36) and LIPG (endothelial type lipase G) to increase fatty acid beta-oxidation. CONCLUSIONS: Endothelial EPAS1 attenuates atherosclerosis at sites of disturbed flow by maintaining EC proliferation via fatty acid uptake and metabolism. This endothelial repair pathway is inhibited in obesity, suggesting a novel triglyceride-PHD2 modulation pathway suppressing EPAS1 expression. These findings have implications for therapeutic strategies addressing vascular dysfunction in obesity.


Subject(s)
Atherosclerosis , Basic Helix-Loop-Helix Transcription Factors , Endothelial Cells , Fatty Acids , Obesity , Animals , Basic Helix-Loop-Helix Transcription Factors/metabolism , Basic Helix-Loop-Helix Transcription Factors/genetics , Atherosclerosis/metabolism , Atherosclerosis/genetics , Atherosclerosis/pathology , Mice , Endothelial Cells/metabolism , Endothelial Cells/pathology , Obesity/metabolism , Obesity/genetics , Cells, Cultured , Fatty Acids/metabolism , Mice, Inbred C57BL , Swine , Male , Diet, High-Fat , Endothelium, Vascular/metabolism , Endothelium, Vascular/pathology
3.
Trends Genet ; 38(1): 8-11, 2022 01.
Article in English | MEDLINE | ID: mdl-34167831

ABSTRACT

Haldane's rule, which states that the heterogametic sex (XY or ZW females) fares more poorly in interspecific hybrids, is generally attributed to absence of one of the two species' X/Z chromosomes. However, Haldane's rule is also observed in mouse placentas despite paternal X silencing. This pattern could reflect Y chromosomes having evolved to promote growth due to maternal-paternal conflict. If so, balanced sex investment arises from a complex intra- and intergenomic duel.


Subject(s)
Hybridization, Genetic , Models, Genetic , Animals , Female , Mice , Sex Chromosomes/genetics , X Chromosome , Y Chromosome/genetics
4.
Mol Syst Biol ; 2024 Aug 12.
Article in English | MEDLINE | ID: mdl-39134886

ABSTRACT

Genome-scale metabolic models (GEMs) can facilitate metabolism-focused multi-omics integrative analysis. Since Yeast8, the yeast-GEM of Saccharomyces cerevisiae, published in 2019, has been continuously updated by the community. This has increased the quality and scope of the model, culminating now in Yeast9. To evaluate its predictive performance, we generated 163 condition-specific GEMs constrained by single-cell transcriptomics from osmotic pressure or reference conditions. Comparative flux analysis showed that yeast adapting to high osmotic pressure benefits from upregulating fluxes through central carbon metabolism. Furthermore, combining Yeast9 with proteomics revealed metabolic rewiring underlying its preference for nitrogen sources. Lastly, we created strain-specific GEMs (ssGEMs) constrained by transcriptomics for 1229 mutant strains. Well able to predict the strains' growth rates, fluxomics from those large-scale ssGEMs outperformed transcriptomics in predicting functional categories for all studied genes in machine learning models. Based on those findings we anticipate that Yeast9 will continue to empower systems biology studies of yeast metabolism.

5.
Bioessays ; 45(12): e2100164, 2023 12.
Article in English | MEDLINE | ID: mdl-37941456

ABSTRACT

The creeping vole Microtus oregoni exhibits remarkably transformed sex chromosome biology, with complete chromosome drive/drag, X-Y fusions, sex reversed X complements, biased X inactivation, and X chromosome degradation. Beginning with a selfish X chromosome, I propose a series of adaptations leading to this system, each compensating for deleterious consequences of the preceding adaptation: (1) YY embryonic inviability favored evolution of a selfish feminizing X chromosome; (2) the consequent Y chromosome transmission disadvantage favored X-Y fusion ("XP "); (3) Xist-based silencing of Y-derived XP genes favored a second X-Y fusion ("XM "); (4) X chromosome dosage-related costs in XP XM males favored the evolution of XM loss during spermatogenesis; (5) X chromosomal dosage-related costs in XM 0 females favored the evolution of XM drive during oogenesis; and (6) degradation of the non-recombining XP favored the evolution of biased X chromosome inactivation. I discuss recurrent rodent sex chromosome transformation, and selfish genes as a constructive force in evolution.


Subject(s)
Sex Chromosomes , X Chromosome , Male , Female , Animals , Sex Chromosomes/genetics , X Chromosome/genetics , Y Chromosome/genetics , X Chromosome Inactivation/genetics , Arvicolinae/genetics
6.
Proc Natl Acad Sci U S A ; 119(23): e2122580119, 2022 06 07.
Article in English | MEDLINE | ID: mdl-35653559

ABSTRACT

Haplodiploidy and paternal genome elimination (HD/PGE) are common in invertebrates, having evolved at least two dozen times, all from male heterogamety (i.e., systems with X chromosomes). However, why X chromosomes are important for the evolution of HD/PGE remains debated. The Haploid Viability Hypothesis posits that X-linked genes promote the evolution of male haploidy by facilitating purging recessive deleterious mutations. The Intragenomic Conflict Hypothesis holds that conflict between genes drives genetic system turnover; under this model, X-linked genes could promote the evolution of male haploidy due to conflicts with autosomes over sex ratios and genetic transmission. We studied lineages where we can distinguish these hypotheses: species with germline PGE that retain an XX/X0 sex determination system (gPGE+X). Because evolving PGE in these cases involves changes in transmission without increases in male hemizygosity, a high degree of X linkage in these systems is predicted by the Intragenomic Conflict Hypothesis but not the Haploid Viability Hypothesis. To quantify the degree of X linkage, we sequenced and compared 7 gPGE+X species' genomes with 11 related species with typical XX/XY or XX/X0 genetic systems, representing three transitions to gPGE. We find highly increased X linkage in both modern and ancestral genomes of gPGE+X species compared to non-gPGE relatives and recover a significant positive correlation between percent X linkage and the evolution of gPGE. These empirical results substantiate longstanding proposals for a role for intragenomic conflict in the evolution of genetic systems such as HD/PGE.


Subject(s)
Genome , Sex Determination Processes , X Chromosome , Animals , Diploidy , Evolution, Molecular , Genome/genetics , Haploidy , Male , X Chromosome/genetics
7.
Trends Genet ; 37(2): 102-104, 2021 02.
Article in English | MEDLINE | ID: mdl-33243450

ABSTRACT

The sex-determining gene SRY has undergone rapid evolution in rodents. Curiously, a new study by Miyawaki et al. reveals that a recently evolved SRY gene sequence antagonizes SRY protein stability, necessitating splicing of a novel intron. Other data suggest that this troublesome gene region has noncoding RNA functions, possibly related to conflict between sex chromosomes.


Subject(s)
Genes, sry/genetics , Genome/genetics , RNA, Untranslated/genetics , Rodentia/genetics , Sex Determination Processes/genetics , Amino Acid Sequence , Animals , Evolution, Molecular , Introns/genetics , Phylogeny , Sex Chromosomes/genetics
8.
J Cell Sci ; 135(18)2022 09 15.
Article in English | MEDLINE | ID: mdl-36148799

ABSTRACT

Tropomyosins are structurally conserved α-helical coiled-coil proteins that bind along the length of filamentous actin (F-actin) in fungi and animals. Tropomyosins play essential roles in the stability of actin filaments and in regulating myosin II contractility. Despite the crucial role of tropomyosin in actin cytoskeletal regulation, in vivo investigations of tropomyosin are limited, mainly due to the suboptimal live-cell imaging tools currently available. Here, we report on an mNeonGreen (mNG)-tagged tropomyosin, with native promoter and linker length configuration, that clearly reports tropomyosin dynamics in Schizosaccharomyces pombe (Cdc8), Schizosaccharomyces japonicus (Cdc8) and Saccharomyces cerevisiae (Tpm1 and Tpm2). We also describe a fluorescent probe to visualize mammalian tropomyosin (TPM2 isoform). Finally, we generated a camelid nanobody against S. pombe Cdc8, which mimics the localization of mNG-Cdc8 in vivo. Using these tools, we report the presence of tropomyosin in previously unappreciated patch-like structures in fission and budding yeasts, show flow of tropomyosin (F-actin) cables to the cytokinetic actomyosin ring and identify rearrangements of the actin cytoskeleton during mating. These powerful tools and strategies will aid better analyses of tropomyosin and F-actin cables in vivo.


Subject(s)
Schizosaccharomyces pombe Proteins , Schizosaccharomyces , Single-Domain Antibodies , Actin Cytoskeleton/metabolism , Actins/metabolism , Actomyosin/metabolism , Animals , Cell Cycle Proteins/metabolism , Cytokinesis , Fluorescent Dyes/metabolism , Mammals/metabolism , Protein Isoforms/metabolism , Saccharomyces cerevisiae/metabolism , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Single-Domain Antibodies/metabolism , Tropomyosin/genetics , Tropomyosin/metabolism
9.
PLoS Pathog ; 18(1): e1009718, 2022 01.
Article in English | MEDLINE | ID: mdl-35073381

ABSTRACT

Salmonella enterica serovar Typhimurium is a Gram-negative pathogen that uses two distinct type III secretion systems (T3SSs), termed Salmonella pathogenicity island (SPI)-1 and SPI-2, to deliver virulence factors into the host cell. The SPI-1 T3SS enables Salmonella to invade host cells, while the SPI-2 T3SS facilitates Salmonella's intracellular survival. In mice, a family of cytosolic immune sensors, including NAIP1, NAIP2, and NAIP5/6, recognizes the SPI-1 T3SS needle, inner rod, and flagellin proteins, respectively. Ligand recognition triggers assembly of the NAIP/NLRC4 inflammasome, which mediates caspase-1 activation, IL-1 family cytokine secretion, and pyroptosis of infected cells. In contrast to mice, humans encode a single NAIP that broadly recognizes all three ligands. The role of NAIP/NLRC4 or other inflammasomes during Salmonella infection of human macrophages is unclear. We find that although the NAIP/NLRC4 inflammasome is essential for detecting T3SS ligands in human macrophages, it is partially required for responses to infection, as Salmonella also activated the NLRP3 and CASP4/5 inflammasomes. Importantly, we demonstrate that combinatorial NAIP/NLRC4 and NLRP3 inflammasome activation restricts Salmonella replication in human macrophages. In contrast to SPI-1, the SPI-2 T3SS inner rod is not sensed by human or murine NAIPs, which is thought to allow Salmonella to evade host recognition and replicate intracellularly. Intriguingly, we find that human NAIP detects the SPI-2 T3SS needle protein. Critically, in the absence of both flagellin and the SPI-1 T3SS, the NAIP/NLRC4 inflammasome still controlled intracellular Salmonella burden. These findings reveal that recognition of Salmonella SPI-1 and SPI-2 T3SSs and engagement of both the NAIP/NLRC4 and NLRP3 inflammasomes control Salmonella infection in human macrophages.


Subject(s)
Inflammasomes/immunology , Macrophages/immunology , Macrophages/microbiology , Salmonella Infections/immunology , Type III Secretion Systems/immunology , CARD Signaling Adaptor Proteins/immunology , Calcium-Binding Proteins/immunology , Humans , NLR Family, Pyrin Domain-Containing 3 Protein/immunology , Neuronal Apoptosis-Inhibitory Protein/immunology , Salmonella typhimurium/immunology , Salmonella typhimurium/pathogenicity , Virulence
10.
J Pediatr ; 264: 113773, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37839508

ABSTRACT

OBJECTIVE: To determine how bronchopulmonary dysplasia (BPD) affects health-related quality of life (HRQL) among infants from NICU hospitalization through 1-year postdischarge. STUDY DESIGN: This was a prospective cohort study of infants with BPD and their parents. Parent HRQL was measured with the PedsQL Family Impact Module before NICU discharge and 3- and 12-months post-discharge. At 12 months, parent-reported child health outcomes included questions from the Test of Respiratory and Asthma Control in Kids, Warner Initial Developmental Evaluation of Adaptive and Functional Skills, and National Survey of Children with Special Health Care Needs. HRQL change over time was assessed by multivariable linear regression. RESULTS: Of 145 dyads, 129 (89%) completed 3-month follow-up, and 113 (78%) completed 12-month follow-up. In the NICU, lower HRQL was associated with earlier gestational age, postnatal corticosteroids, outborn status, and gastrostomy tubes. At 3 months, lower HRQL was associated with readmissions and home oxygen use. At 12 months, lower HRQL was associated with parent-reported difficulty breathing, lower developmental scores, and not playing with other children. At 3 and 12 months, 81% of parents reported similar or improved HRQL compared with the NICU period. Parents reporting infant respiratory symptoms experienced less improvement. CONCLUSIONS: BPD affects parent HRQL over the first year. Most parents report similar or better HRQL after discharge compared with the NICU stay. Less improvement is reported by parents of infants experiencing respiratory symptoms at 12 months. Efforts to improve parent HRQL should target respiratory symptoms and social isolation.


Subject(s)
Bronchopulmonary Dysplasia , Infant, Premature , Infant, Newborn , Infant , Child , Humans , Quality of Life , Aftercare , Prospective Studies , Patient Discharge , Intensive Care Units, Neonatal , Parents
11.
Am J Med Genet A ; 194(4): e63489, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38058249

ABSTRACT

Chronic diarrhea presents a significant challenge for managing nutritional and electrolyte deficiencies, especially in children, given the higher stakes of impacting growth and developmental consequence. Congenital secretory diarrhea (CSD) compounds this further, particularly in the case of the activating variants of the guanylate-cyclase 2C (GUCY2C) gene. GUCY2C encodes for the guanylate-cyclase 2C (GC-C) receptor that activates the downstream cystic fibrosis transmembrane receptor (CFTR) that primarily drives the severity of diarrhea with an unclear extent of influence on other intestinal channels. Thus far, management for CSD primarily consists of mitigating nutritional, electrolyte, and volume deficiencies with no known pathophysiology-driven treatments. For activating variants of GUCY2C, experimental compounds have shown efficacy in vitro for direct inhibition of GC-C but are not currently available for clinical use. However, Crofelemer, a CFTR inhibitory modulator with negligible systemic absorption, can theoretically help to treat this type of CSD. Herein, we describe and characterize the clinical course of a premature male infant with a de novo missense variant of GUCY2C not previously reported and highly consistent with CSD. With multi-disciplinary family-directed decision-making, a treatment for CSD was evaluated for the first time to our knowledge with Crofelemer.


Subject(s)
Cystic Fibrosis Transmembrane Conductance Regulator , Cystic Fibrosis , Child , Humans , Male , Cystic Fibrosis Transmembrane Conductance Regulator/genetics , Diarrhea/genetics , Diarrhea/therapy , Diarrhea/congenital , Intestines , Electrolytes/therapeutic use , Disease Progression , Receptors, Enterotoxin
12.
PLoS Comput Biol ; 19(8): e1011363, 2023 08.
Article in English | MEDLINE | ID: mdl-37578975

ABSTRACT

Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize this potential, it is critical to understand the mechanisms behind the interactions that structure microbial consortia and determine their functions. Constraint-based reconstruction and analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as the state-of-the-art tool to simulate the behavior of microbial communities from their constituent genomes. In the last decade, many tools have been developed that use COBRA approaches to simulate multi-species consortia, under either steady-state, dynamic, or spatiotemporally varying scenarios. Yet, these tools have not been systematically evaluated regarding their software quality, most suitable application, and predictive power. Hence, it is uncertain which tools users should apply to their system and what are the most urgent directions that developers should take in the future to improve existing capacities. This study conducted a systematic evaluation of COBRA-based tools for microbial communities using datasets from two-member communities as test cases. First, we performed a qualitative assessment in which we evaluated 24 published tools based on a list of FAIR (Findability, Accessibility, Interoperability, and Reusability) features essential for software quality. Next, we quantitatively tested the predictions in a subset of 14 of these tools against experimental data from three different case studies: a) syngas fermentation by C. autoethanogenum and C. kluyveri for the static tools, b) glucose/xylose fermentation with engineered E. coli and S. cerevisiae for the dynamic tools, and c) a Petri dish of E. coli and S. enterica for tools incorporating spatiotemporal variation. Our results show varying performance levels of the best qualitatively assessed tools when examining the different categories of tools. The differences in the mathematical formulation of the approaches and their relation to the results were also discussed. Ultimately, we provide recommendations for refining future GEM microbial modeling tools.


Subject(s)
Escherichia coli , Microbial Consortia , Microbial Consortia/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Saccharomyces cerevisiae , Genome , Software
13.
Org Biomol Chem ; 22(3): 590-605, 2024 Jan 17.
Article in English | MEDLINE | ID: mdl-38131271

ABSTRACT

Biphenyl-fused-dioxacyclodecynes are a promising class of strained alkyne for use in Cu-free 'click' reactions. In this paper, a series of functionalised derivatives of this class of reagent, containing fluorescent groups, are described. Studies aimed at understanding and increasing the reactivity of the alkynes are also presented, together with an investigation of the bioconjugation of the reagents with an azide-labelled protein.

14.
Dig Dis Sci ; 69(8): 2961-2969, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38902460

ABSTRACT

BACKGROUND: Extraintestinal Manifestations (EIMs) are a common and potentially debilitating complication of Inflammatory Bowel Diseases (IBD), sometimes requiring additional treatment beyond those used to control intestinal disease. IBD-associated arthritis (IAA), a form of spondyloarthritis, is associated with several factors including disease location, sex, and IBD type. However, much remains unknown about other clinical factors predicting development of EIMs. Our goal was to identify additional factors associated with IAA. METHODS: Participants in the LOCATION-IBD cohort were included in this analysis. We performed univariate and multivariate analysis of demographics, clinical data, and patient-reported outcomes data. RESULTS: The LOCATION-IBD cohort included 182 participants with (n = 53) and without (n = 110) joint EIMs and with joint pain of unclear etiology (n = 19). In a multivariate analysis comparing those with and without joint EIMs, female sex (OR = 2.5, p = 0.014), the presence of concomitant autoimmune and inflammatory disorders (OR = 2.5, p = 0.038), and Crohn's disease (OR = 2.9, p = 0.026) were associated with the presence of joint EIMs. CONCLUSION: This analysis reveals patients with IAA are more likely to have concomitant autoimmune disorders. Further studies are needed to confirm this association, understand the mechanisms underlying the common pathogenesis of these concurrent disorders, and evaluate their impact on the treatment of IAA.


Subject(s)
Inflammatory Bowel Diseases , Humans , Female , Male , Adult , Middle Aged , Inflammatory Bowel Diseases/complications , Inflammatory Bowel Diseases/epidemiology , Autoimmune Diseases/complications , Autoimmune Diseases/epidemiology , Crohn Disease/complications , Crohn Disease/epidemiology , Risk Factors , Sex Factors , Multivariate Analysis , Arthritis/epidemiology
15.
PLoS Genet ; 17(11): e1009909, 2021 11.
Article in English | MEDLINE | ID: mdl-34780483

ABSTRACT

The ATRX ATP-dependent chromatin remodelling/helicase protein associates with the DAXX histone chaperone to deposit histone H3.3 over repetitive DNA regions. Because ATRX-protein interactions impart functions, such as histone deposition, we used proximity-dependent biotinylation (BioID) to identify proximal associations for ATRX. The proteomic screen captured known interactors, such as DAXX, NBS1, and PML, but also identified a range of new associating proteins. To gauge the scope of their roles, we examined three novel ATRX-associating proteins that likely differed in function, and for which little data were available. We found CCDC71 to associate with ATRX, but also HP1 and NAP1, suggesting a role in chromatin maintenance. Contrastingly, FAM207A associated with proteins involved in ribosome biosynthesis and localized to the nucleolus. ATRX proximal associations with the SLF2 DNA damage response factor help inhibit telomere exchanges. We further screened for the proteomic changes at telomeres when ATRX, SLF2, or both proteins were deleted. The loss caused important changes in the abundance of chromatin remodelling, DNA replication, and DNA repair factors at telomeres. Interestingly, several of these have previously been implicated in alternative lengthening of telomeres. Altogether, this study expands the repertoire of ATRX-associating proteins and functions.


Subject(s)
Co-Repressor Proteins/genetics , DNA-Binding Proteins/genetics , Intracellular Signaling Peptides and Proteins/genetics , Nuclear Proteins/genetics , X-linked Nuclear Protein/genetics , Biotinylation/genetics , Cell Cycle Proteins/genetics , Cell Line , Chromatin/genetics , Chromobox Protein Homolog 5/genetics , DNA Damage/genetics , DNA Repair/genetics , Histone Chaperones/genetics , Histones/genetics , Humans , Molecular Chaperones/genetics , Promyelocytic Leukemia Protein/genetics , Telomere/genetics , tRNA Methyltransferases
16.
Biotechnol Bioeng ; 120(7): 1998-2012, 2023 07.
Article in English | MEDLINE | ID: mdl-37159408

ABSTRACT

Fermentation employing Saccharomyces cerevisiae has produced alcoholic beverages and bread for millennia. More recently, S. cerevisiae has been used to manufacture specific metabolites for the food, pharmaceutical, and cosmetic industries. Among the most important of these metabolites are compounds associated with desirable aromas and flavors, including higher alcohols and esters. Although the physiology of yeast has been well-studied, its metabolic modulation leading to aroma production in relevant industrial scenarios such as winemaking is still unclear. Here we ask what are the underlying metabolic mechanisms that explain the conserved and varying behavior of different yeasts regarding aroma formation under enological conditions? We employed dynamic flux balance analysis (dFBA) to answer this key question using the latest genome-scale metabolic model (GEM) of S. cerevisiae. The model revealed several conserved mechanisms among wine yeasts, for example, acetate ester formation is dependent on intracellular metabolic acetyl-CoA/CoA levels, and the formation of ethyl esters facilitates the removal of toxic fatty acids from cells using CoA. Species-specific mechanisms were also found, such as a preference for the shikimate pathway leading to more 2-phenylethanol production in the Opale strain as well as strain behavior varying notably during the carbohydrate accumulation phase and carbohydrate accumulation inducing redox restrictions during a later cell growth phase for strain Uvaferm. In conclusion, our new metabolic model of yeast under enological conditions revealed key metabolic mechanisms in wine yeasts, which will aid future research strategies to optimize their behavior in industrial settings.


Subject(s)
Saccharomyces cerevisiae , Wine , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Wine/analysis , Fermentation , Esters/metabolism , Carbohydrates/analysis
17.
Pediatr Res ; 93(4): 1085-1095, 2023 03.
Article in English | MEDLINE | ID: mdl-35835848

ABSTRACT

BACKGROUND: Late-Onset Neonatal Sepsis (LOS) is a rare condition, involving widespread infection, immune disruption, organ dysfunction, and often death. Because exposure to pathogens is not completely preventable, identifying susceptibility factors is critical to characterizing the pathophysiology and developing interventions. Prior studies demonstrated both genetics and infant sex influence susceptibility. Our study was designed to identify LOS associated genetic variants. METHODS: We performed an exploratory genome wide association study (GWAS) with 224 LOS cases and 273 controls from six European countries. LOS was defined as sepsis presenting from 3 to 90 days of age; diagnosis was established by clinical criteria consensus guidelines. We tested for association with both autosomal and X-chromosome variants in the total sample and in sex-stratified analyses. RESULTS: In total, 71 SNPs associated with neonatal sepsis at p < 1 × 10-4 in at least one analysis. Most importantly, sex-stratified analyses revealed associations with multiple SNPs (28 in males and 16 in females), but no variants from single-sex analyses associated with sepsis in the other sex. Pathway analyses showed NOTCH signaling is over-represented among genes linked to these SNPS. CONCLUSION: Our results indicate genetic susceptibility to LOS is sexually dimorphic and corroborate that NOTCH signaling plays a role in determining risk. IMPACT: Genes associate with late onset neonatal sepsis. Notch pathway genes are overrepresented in associations with sepsis. Genes associating with sepsis do not overlap between males and females. Sexual dimorphism can lead to sex specific treatment of sepsis.


Subject(s)
Neonatal Sepsis , Sepsis , Infant, Newborn , Male , Infant , Female , Humans , Neonatal Sepsis/genetics , Genome-Wide Association Study , Sepsis/genetics , Sex Characteristics , Europe
18.
Alzheimer Dis Assoc Disord ; 37(3): 195-199, 2023.
Article in English | MEDLINE | ID: mdl-37561946

ABSTRACT

BACKGROUND: Verbal and visuospatial memory impairments are common to Alzheimer disease and Related Dementias (ADRD), but the patterns of decline in these domains may reflect genetic and lifestyle influences. The latter may be pertinent to populations such as the Amish who have unique lifestyle experiences. METHODS: Our data set included 420 Amish and 401 CERAD individuals. Sex-adjusted, age-adjusted, and education-adjusted Z-scores were calculated for the recall portions of the Constructional Praxis Delay (CPD) and Word List Delay (WLD). ANOVAs were then used to examine the main and interaction effects of cohort (Amish, CERAD), cognitive status (case, control), and sex on CPD and WLD Z-scores. RESULTS: The Amish performed better on the CPD than the CERAD cohort. In addition, the difference between cases and controls on the CPD and WLD were smaller in the Amish and Amish female cases performed better on the WLD than the CERAD female cases. DISCUSSION: The Amish performed better on the CPD task, and ADRD-related declines in CPD and WLD were less severe in the Amish. In addition, Amish females with ADRD may have preferential preservation of WLD. This study provides evidence that the Amish exhibit distinct patterns of verbal and visuospatial memory loss associated with aging and ADRD.


Subject(s)
Alzheimer Disease , Humans , Female , Alzheimer Disease/genetics , Amish , Neuropsychological Tests , Memory , Mental Recall , Memory Disorders
19.
Transpl Int ; 36: 11633, 2023.
Article in English | MEDLINE | ID: mdl-37822447

ABSTRACT

The field of transplantation has witnessed the emergence of Advanced Therapy Medicinal Products (ATMPs) as highly promising solutions to address the challenges associated with organ and tissue transplantation. ATMPs encompass gene therapy, cell therapy, and tissue-engineered products, hold immense potential for breakthroughs in overcoming the obstacles of rejection and the limited availability of donor organs. However, the development and academic research access to ATMPs face significant bottlenecks that hinder progress. This opinion paper emphasizes the importance of addressing bottlenecks in the development and academic research access to ATMPs by implementing several key strategies. These include the establishment of streamlined regulatory processes, securing increased funding for ATMP research, fostering collaborations and partnerships, setting up centralized ATMP facilities, and actively engaging with patient groups. Advocacy at the policy level is essential to provide support for the development and accessibility of ATMPs, thereby driving advancements in transplantation and enhancing patient outcomes. By adopting these strategies, the field of transplantation can pave the way for the introduction of innovative and efficacious ATMP therapies, while simultaneously fostering a nurturing environment for academic research.


Subject(s)
Cell- and Tissue-Based Therapy , Tissue Engineering , Humans , Genetic Therapy
20.
Transpl Int ; 36: 11374, 2023.
Article in English | MEDLINE | ID: mdl-37547751

ABSTRACT

The advent of Machine Perfusion (MP) as a superior form of preservation and assessment for cold storage of both high-risk kidney's and the liver presents opportunities in the field of beta-cell replacement. It is yet unknown whether such techniques, when applied to the pancreas, can increase the pool of suitable donor organs as well as ameliorating the effects of ischemia incurred during the retrieval process. Recent experimental models of pancreatic MP appear promising. Applications of MP to the pancreas, needs refinement regarding perfusion protocols and organ viability assessment criteria. To address the "Role of pancreas machine perfusion to increase the donor pool for beta cell replacement," the European Society for Organ Transplantation (ESOT) assembled a dedicated working group comprising of experts to review literature pertaining to the role of MP as a method of improving donor pancreas quality as well as quantity available for transplant, and to develop guidelines founded on evidence-based reviews in experimental and clinical settings. These were subsequently refined during the Consensus Conference when this took place in Prague.


Subject(s)
Organ Preservation , Organ Transplantation , Humans , Organ Preservation/methods , Pancreas , Perfusion/methods , Tissue Donors
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