bluuebunny/crossref_metadata_2025 huggingface dataset:
Druggable causal genes of bipolar disorder identified through Mendelian Randomization analysis offer a route to intervention in integrated stress response
Authors: Ting Zhai
Published: December 2023

Bipolar disorder (BD) is known to be comorbid with many medical and psychiatric conditions and they may share inflammatory and stress-related aetiologies, which could give rise to this association. Psychosomatic illnesses are characterized by widespread immune signaling in the central nervous system, oxidative stress, and increased immune trafficking into the brain. The integrated stress response (ISR) responds to a variety of different stress conditions that lead to alterations in cellular homeostasis. However, as a causative mechanism underlying the cognitive deficits and neurodegeneration in a broad range of brain disorders, the impact of ISR on BD is understudied, particularly for the ISR’s central regulatory switch lies in eIF2 ternary complex formation. We aimed to prioritize eIF2-associated genes for follow-up studies using the summary data-based Mendelian Randomization (SMR) and Bayesian colocalization (COLOC) methods to integrate the summary-level data of the GWAS on BD and the expression quantitative trait locus (eQTL) study in blood. We utilized the GWAS data including 41917 BD cases and 371549 controls from the Psychiatric Genomics Consortium and the eQTL data from 31,684 participants of predominantly European ancestry from the eQTLGen consortium. Plus, we use Graph DB to alt drug targets. The SMR analysis identified EIF2B5 gene that were associated with BD due to no linkage but pleiotropy or causality. The COLOC analysis strongly suggested that EIF2B5 and the trait of BD were affected by shared causal variants, and thus were colocalized. Utilizing data in EpiGraphDB we find other putative causal BD genes (EIF2AK4 and GSK3B) to prioritise potential alternative drug targets.
An Endogenous Aryl Hydrocarbon Receptor Ligand Induces Preeclampsia-like Phenotypes: Transcriptome, Phosphoproteome, and Cell Functions
Authors: Zhao Ying-jie , Zhou Chi , Wei Ying-ying , Zhang Si-yan , Mishra Jay S. , Li Hui-hui , Lei Wei , Wang Kai , Kumar Sathish , Zheng Jing
Published: December 2023

Background

Preeclampsia (PE) is one hypertensive disorder and a leading cause of maternal and fetal mortality and morbidity during human pregnancy. Aryl hydrocarbon receptor (AhR) is a transcription factor, which regulates vascular functions. Exogenous and endogenous AhR ligands can induce hypertension in animals. However, if dysregulation of endogenous AhR ligands contributes to the pathophysiology of PE remains elusive.

Methods

We measured AhR activities in human maternal and umbilical vein sera. We also applied physiological, cellular, and molecular approaches to dissect the role of endogenous AhR ligands in vascular functions during pregnancy using pregnant rats and primary human umbilical vein endothelial cells (HUVECs) as models.

Results

PE elevated AhR activities in human umbilical vein sera. Exposure of pregnant rats to an endogenous AhR ligand, 2-(1’H-indole-3’-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE) increased blood pressure and proteinuria, while decreased uteroplacental blood flow and reduced fetal and placental weights, all of which are hallmarks of PE. ITE dampened vascular growth and fetal sex-specifically altered immune cell infiltration in rat placentas. ITE also decreased cell proliferation and cell monolayer integrity in HUVECsin vitro. RNA sequencing analysis revealed that ITE dysregulated transcriptome in rat placentas and HUVECs in a fetal sex-specific manner. Bottom-up phosphoproteomics showed that ITE disrupted phosphoproteome in HUVECs. These ITE-dysregulated genes and phosphoproteins were enriched in biological functions and pathways which are highly relevant to diseases of heart, liver, and kidney, vascular functions, inflammation responses, cell death, and kinase inhibition.

Conclusions

Dysregulation of endogenous AhR ligands during pregnancy may lead to the development of PE with underlying impaired vascular functions, fetal sex-specific immune cell infiltration and transcriptome, and phosphoproteome. Thus, this study has provided a novel mechanism for the development of PE and potentially other forms of hypertensive pregnancies. These AhR ligand-activated genes and phosphoproteins might represent promising therapeutic and fetal sex-specific targets for PE-impaired vascular functions.
Olfactory ensheathing cells from adult female rats are hybrid glia that promote neural repair
Authors: Phelps Patricia E. , Ha Sung Min , Khankan Rana R. , Mekonnen Mahlet A. , Juarez Giovanni , Ingraham Dixie Kaitlin L. , Chen Yen-Wei , Yang Xia
Published: December 2023

Olfactory ensheathing cells (OECs) are unique glial cells found in both central and peripheral nervous systems where they support continuous axonal outgrowth of olfactory sensory neurons to their targets. Previously we reported that following severe spinal cord injury, OECs transplanted near the injury site modify the inhibitory glial scar and facilitate axon regeneration past the scar border and into the lesion. To better understand the mechanisms underlying the reparative properties of OECs, we used single-cell RNA-sequencing of OECs from adult rats to study their gene expression programs. Our analyses revealed five diverse OEC subtypes, each expressing novel marker genes and pathways indicative of progenitor, axonal regeneration, secreted molecules, or microglia-like functions. We found substantial overlap of OEC genes with those of Schwann cells, but also with microglia, astrocytes, and oligodendrocytes. We confirmed established markers on cultured OECs, and localized select top genes of OEC subtypes in olfactory bulb tissue. We also show that OECs secrete Reelin and Connective tissue growth factor, extracellular matrix molecules which are important for neural repair and axonal outgrowth. Our results support that OECs are a unique hybrid glia, some with progenitor characteristics, and that their gene expression patterns indicate functions related to wound healing, injury repair and axonal regeneration.
Comprehensive Assessment of Ischemic Stroke in Nonhuman Primates: Neuroimaging, Behavioral, and Serum Proteomic Analysis
Authors: Li Ge , Lan Lan , He Tingting , Tang Zheng , Liu Shuhua , Li Yunfeng , Huang Zhongqiang , Guan Yalun , Li Xuejiao , Zhang Yu , Lai Hsin-Yi
Published: December 2023

Ischemic strokes, prevalence and impactful, underscore the necessity of advanced research models closely resembling human physiology. O integrating n ur study in nonhuman primates (NHPs) offers a comprehensive exploration of ischemic stroke, integrating neuroimaging data, behavioral outcomes, and serum proteomics to elucidate the complex interplay of factors involved in stroke pathophysiology. We observed a consistent pattern in infarct volume, peaking at 1-month post-middle cerebral artery occlusion (MCAO) and stabilizing thereafter. This trend was closely correlated with notable changes in motor function and working memory performance. Using diffusion tensor imaging (DTI), we detected significant alterations in fractional anisotropy (FA) and mean diffusivity (MD) values, indicative of microstructural changes in the brain. These findings were strongly correlated with the observed neurological and cognitive deficits, highlighting the sensitivity of DTI metrics in stroke assessment. Behaviorally, the monkeys exhibited a reliance on their unaffected limb for compensatory movements, a response commonly observed in stroke impairment. This adaptation, alongside the consistent findings in DTI metrics, suggests a substantial impact of stroke on motor function and spatial perception. Proteomic analysis through MS/MS functional enrichment revealed two distinct groups of proteins with significant changes post-MCAO. Notably, MMP9, THBS1, MB, PFN1, and YWHAZ emerged as potential biomarkers and therapeutic targets in ischemic stroke. Our findings underscore the complex nature of stroke and the potential of an integrated approach, combining neuroimaging, behavioral studies, and proteomics, for advancing our understanding and treatment of this condition.
Cryptic female choice in response to male pheromones inDrosophila melanogaster
Authors: Doubovetzky Nicolas , Kohlmeier Philip , Bal Sanne , Billeter Jean-Christophe
Published: December 2023

Females control the paternity of their offspring by selectively mating with males they perceive to be of high quality. In species where females mate with multiple males in succession, females may bias offspring paternity by favoring the sperm of one male over another, a process known as cryptic female choice (CFC). While evidence of CFC exists in multiple taxa, the mechanisms underlying this process have remained difficult to unravel. Understanding CFC requires demonstration of a female-driven post mating bias in sperm use and paternity, and a causal link between this bias and male cues. Here, we show that in the vinegar flyDrosophila melanogaster,mated females eject the ejaculate of their first mate faster when exposed to the pheromones of an attractive male than in the presence of an unattractive one. Using transgenic males expressing fluorescent sperm, we show that exposure to attractive males between mating causes twice-mated females to bias sperm storage towards the second male, affecting paternity. Using pheromonal bioassays in combination with genetic manipulation of sensory systems, we show that females modulate ejaculate ejection latency in response to male pheromones heptanal and 11-cis-Vaccenyl acetate (cVA) sensed via olfactory receptor neurons OR35a, Or22a, Or65a and OR67d, demonstrating that polyandrous females use male pheromonal cues to modulate ejaculate ejection timing. We provide the first demonstration to our knowledge of a CFC mechanism allowing a female to increase or decrease the share of paternity of her first mate depending on the sensing of the quality of potential mates in her environment. These findings showcase that paternity can be influenced by events that go beyond copulation and highlights the importance of post-copulatory sexual selection.

One Sentence Summary

We show that females bias sperm use and paternity towards specific males in response to male pheromones.
Gap junction mediated bioelectric coordination is required for slow muscle development, organization, and function
Authors: Lukowicz-Bedford RM , Eisen JS , Miller AC
Published: December 2023

Bioelectrical signaling, intercellular communication facilitated by membrane potential and electrochemical coupling, is emerging as a key regulator of animal development. Gap junction (GJ) channels can mediate bioelectric signaling by creating a fast, direct pathway between cells for the movement of ions and other small molecules. In vertebrates, GJ channels are formed by a highly conserved transmembrane protein family called the Connexins. Theconnexingene family is large and complex, presenting a challenge in identifying the specific Connexins that create channels within developing and mature tissues. Using the embryonic zebrafish neuromuscular system as a model, we identify aconnexinconserved across vertebrate lineages,gjd4,which encodes the Cx46.8 protein, that mediates bioelectric signaling required for appropriate slow muscle development and function. Through a combination of mutant analysis andin vivoimaging we show thatgjd4/Cx46.8 creates GJ channels specifically in developing slow muscle cells. Using genetics, pharmacology, and calcium imaging we find that spinal cord generated neural activity is transmitted to developing slow muscle cells and synchronized activity spreads viagjd4/Cx46.8 GJ channels. Finally, we show that bioelectrical signal propagation within the developing neuromuscular system is required for appropriate myofiber organization, and that disruption leads to defects in behavior. Our work reveals the molecular basis for GJ communication among developing muscle cells and reveals how perturbations to bioelectric signaling in the neuromuscular system may contribute to developmental myopathies. Moreover, this work underscores a critical motif of signal propagation between organ systems and highlights the pivotal role played by GJ communication in coordinating bioelectric signaling during development.
Tryptophan Metabolites And Their Predicted Microbial Sources In Fecal Samples Of Healthy Individuals
Authors: Chappell Cynthia L. , Hoffman Kristi L. , Lorenzi Philip L. , Tan Lin , Petrosino Joseph F. , Gibbs Richard A. , Muzny Donna M. , Doddapaneni Harsha , Ross Matthew C. , Menon Vipin K. , Surathu Anil , Javornik Cregeen Sara J. , Reyes Anaid G. , Okhuysen Pablo C.
Published: December 2023

Gut microbiota produce tryptophan metabolites (TMs) important to homeostasis. However, measuring TM levels in stool and determining their microbial sources can be difficult. Here, we measured TMs from the indole pathway in fecal samples from 21 healthy adults with the goal to: 1) determine fecal TM concentrations in healthy individuals; 2) link TM levels to bacterial abundance using 16S and whole genome shotgun (WGS) sequencing data; and 3) predict likely bacterial sources of TM production. Within our samples, we identified 151 genera (16S) and 592 bacterial species (WGS). Eight TMs were found in ≥17 fecal samples, including four in all persons. To our knowledge, we are the first to report fecal levels for indole-3-lactate, indole-3-propionate, and 3-indoleacrylate levels in healthy persons. Overall, indole, indole-3-acetate (IAA), and skatole accounted for 86% of the eight TMs measured. Significant correlations were found between seven TMs and 29 bacterial species. Predicted multiple TM sources support the notion of a complex network of TM production and regulation. Further, the data suggest key roles forCollinsella aerofaciensand IAA, a metabolite reported to maintain intestinal homeostasis through enhanced barrier integrity and anti-inflammatory/antioxidant activities. These findings extend our understanding of TMs and their relationship to the microbial species that act as effectors and/or regulators in the healthy intestine and may lead to novel strategies designed to manipulate tryptophan metabolism to prevent disease and/or restore health to the dysbiotic gut.

IMPORTANCE

Tryptophan metabolites (TMs) of bacterial origin are increasingly recognized as important signaling molecules among gut microbiota and with the host. However, few reports exist for fecal TM levels in healthy humans, and reported levels vary widely. Further, the specific bacterial species producing TMs and the combinations of fecal TMs in healthy individuals are not well known. Our research combines 16S and whole genome shotgun sequencing of gut bacteria with a sensitive method (LC/MS) for measuring TMs and a reported method to predict which species are likely TM contributors. To our knowledge, this combination of analyses has not been reported elsewhere and will add significantly to the existing literature. Understanding TM levels and their sources in the healthy intestine are fundamental to elucidating how TMs contribute to maintaining homeostasis. Such knowledge of gut microbiota and their metabolic products will inform novel strategies to maintain intestinal health and prevent or treat dysbioses.
Intronic miR-6741-3p is involved in oral squamous cell carcinoma pathogenesis by targeting the oncogeneSRSF3
Authors: More Dhanashree Anil , Singh Nivedita , Mishra Radha , Muralidharan Harsha Pulakkat , Gopinath Kodaganur Srinivas , Gopal Champaka , Kumar Arun
Published: December 2023

Epigenetic silencing through methylation is one of the major mechanisms for downregulation of tumor suppressor miRNAs in various malignancies. The aim of this study was to identify novel tumor suppressor miRNAs which are silenced by DNA hypermethylation and investigate the role of at least one of these in oral squamous cell carcinoma (OSCC) pathogenesis.

We treated cells from an OSCC cell line SCC131 with 5-Azacytidine, a DNA methyltransferase inhibitor, to reactivate tumor suppressor miRNA genes silenced/downregulated due to DNA methylation. At 5-day post-treatment, total RNA was isolated from the 5-Azacytidine and vehicle control-treated cells. The expression of 2,459 mature miRNAs was analysed between 5-Azacytidine and control-treated OSCC cells by the microRNA microarray analysis.

Of the 50 miRNAs which were found to be upregulated following 5-Azacytidine treatment, we decided to work with miR-6741-3p in details for further analysis, as it showed a mean fold expression of >4.0. The results of qRT-PCR, Western blotting, and dual-luciferase reporter assay indicated that miR-6741-3p directly targets the oncogeneSRSF3at the translational level only. The tumor-suppressive role of miR-6741-3p was established by variousin vitroandin vivoassays.

Our results revealed that miR-6741-3p plays a tumor-suppressive role in OSCC pathogenesis, in part, by directly regulatingSRSF3. Based on our observations, we propose that miR-6741-3p may serve as a potential biological target in tumor diagnostics, prognostic evaluation, and treatment of OSCC and perhaps other malignancies.
Development of KASP markers for the potato virus Y resistance geneRychcusing whole-genome resequencing data
Authors: Asano Kenji , Endelman Jeffrey B.
Published: December 2023

Potato virus Y is the most important potato virus worldwide, affecting tuber yield and quality. The resistance geneRychc, derived from the potato wild relativeSolanum chacoense, provides broad spectrum and durable resistance to the virus and has been used to develop resistant cultivars. Several DNA markers have been developed and have contributed to the efficient selection of resistant individuals. In this study, we developed Kompetitive Allele Specific PCR markers forRychcusing whole-genome resequencing data for a diverse set of 25 PVY susceptible cultivars and aRychc-positive clone. Marker Ry_4099 targets two variants in the 3’-UTR and was able to discriminate all five allele dosages in a tetraploid test population. Marker Ry_3331 targets two variants in Exon 4 and, although it only provides presence/absence information, it discriminates between the two known resistant alleles ofRychc. These markers will greatly contribute to efficient development of resistant cultivars.
Identifying functional multi-host shuttle plasmids to advance synthetic biology applications inMesorhizobiumandBradyrhizobium
Authors: Meaney Jordyn S. , Panchal Aakanx K. , Wilcox Aiden J. , diCenzo George C. , Karas Bogumil J.
Published: December 2023

Ammonia availability has a crucial role in agriculture as it ensures healthy plant growth and increased crop yields. Since diazotrophs are the only organisms capable of reducing dinitrogen to ammonium, they have a great ecological importance and potential to mitigate the environmental and economic costs of synthetic fertilizer use. Rhizobia are especially valuable being that they can engage in nitrogen-fixing symbiotic relationships with legumes, and they demonstrate great diversity and plasticity in genomic and phenotypic traits. However, few rhizobial species have improved genetic tractability for synthetic biology applications. This study established a basic genetic toolbox with antibiotic resistance markers, multi-host shuttle plasmids and a streamlined protocol for biparental conjugation withMesorhizobiumandBradyrhizobiumspecies. We identified tworepABCorigins of replication fromSinorhizobium meliloti(pSymB) andRhizobium etli(p42d) that were stable across all three strains of interest. Furthermore, the NZP2235 genome was sequenced and phylogenetic analysis determined its reclassification toMesorhizobium huakuii. These tools will enable the use of plasmid-based strategies for more advanced genetic engineering projects and ultimately contribute towards the development of more sustainable agriculture practices by means of novel nitrogen-fixing organelles, elite bioinoculants or symbiotic association with non-legumes.

GRAPHICAL ABSTRACT
Deciphering Abnormal Platelet Subpopulations in Inflammatory Diseases through Machine Learning and Single-Cell Transcriptomics
Authors: Qiu Xinru , Nair Meera G. , Jaroszewski Lukasz , Godzik Adam
Published: December 2023

Introduction: The transcriptional heterogeneity of activated platelets, play a significant role in contributing to negative outcomes in sepsis, COVID-19, and autoimmune diseases such as systemic lupus erythematosus (SLE). Despite this, our understanding of these heterogeneous platelet responses remains limited. In this study, we aim to investigate the diverse transcriptional profiles of activated platelets in these diseases, with the goal of deciphering this platelet heterogeneity for new therapeutic strategies to target abnormal and pathogenic platelet subtypes. Materials and methods: We obtained the single cell transcriptional profiles of blood platelets from patients with COVID-19, sepsis, and SLE. Utilizing machine learning algorithms, Deep Neural Network (DNN) and eXtreme Gradient Boosting (XGB), we discerned the distinct transcriptomic signatures indicative of fatal versus survival clinical outcomes. Our methodological framework incorporated source data annotations and platelet markers and used SingleR and Seurat for detailed profiling. Additionally, we implemented Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction and visualization, aiding in the detection of various platelet subtypes and their correlation with disease status and patient outcomes. Results: Our study identified distinct platelet subpopulations that are associated with disease severity. We demonstrated that alterations in platelet transcription patterns can exacerbate endotheliopathy, potentially heightening the risk of coagulation in fatal patients. Moreover, these changes can also influence lymphocyte function, indicating a more extensive role for platelets in inflammatory and immune responses. Conclusions: Enhanced transcriptional heterogeneity in activated platelets is linked to adverse outcomes in conditions such as sepsis, COVID-19, and autoimmune diseases. The discovery of these unique platelet subpopulations paves the way for innovative therapeutic strategies targeting platelet activation, which could potentially improve patient outcomes.
Fluorescent Chiral Quantum Dots to Unveil Origin-Dependent Exosome Uptake and Cargo Release
Authors: Kim Gaeun , Zhu Runyao , Zhang Youwen , Jeon Hyunsu , Wang Yichun
Published: December 2023

Exosomes are promising nanocarriers for drug delivery. Yet, it is challenging to apply exosomes in clinical use due to the limited understanding of their physiological functions. While cellular uptake of exosomes is generally known through endocytosis and/or membrane fusion, the mechanisms of origin-dependent cellular uptake and subsequent cargo release of exosomes into recipient cells are still unclear. Herein, we investigated the intricate mechanisms of exosome entry into recipient cells and the intracellular cargo release. In this study, we utilized chiral graphene quantum dots (GQDs) as representatives of exosomal cargo, taking advantage of the superior permeability of chiral GQDs into lipid membranes, as well as their excellent optical properties for tracking analysis. We observed a higher uptake rate of exosomes in their parental recipient cells. However, these exosomes were predominantly entrapped in lysosomes through endocytosis (intraspecies endocytic uptake). On the other hand, in non-parental recipient cells, exosomes exhibited a greater inclination for cellular uptake through membrane fusion, followed by direct cargo release into the cytosol (cross-species direct fusion uptake). We revealed the underlying mechanisms involved in the cellular uptake and the subsequent cargo release of exosomes depending on their cell-of-origin and recipient cell types. This study envisions valuable insights into further advancements in the effective drug delivery using exosomes, as well as a comprehensive understanding of cellular communication, including disease pathogenesis.
Neurotrophin NT-4/5 Promotes Structural Changes in Neurons of the Developing Visual Cortex
Authors: Antonini Antonella , Harris Sheri L. , Stryker Michael P.
Published: December 2023

Current hypotheses on the mechanisms underlying the development and plasticity of the ocular dominance system through competitive interactions between pathways serving the two eyes strongly suggest the involvement of neurotrophins and their high affinity receptors. In the cat, infusion of the tyrosine kinase B ligand (trkB), neurotrophin-4/5 (NT-4/5), abolishes ocular dominance plasticity that follows monocular deprivation (Gillespie et al., 2000), while tyrosine kinase A and C ligands (trkA and trkC) do not have this effect. One interpretation of this finding is that NT-4/5 causes overgrowth and sprouting of thalamocortical and/or corticocortical terminals, leading to promiscuous neuronal connections which override the experience-dependent fine tuning of connections based on correlated activity. The present study tested whether neurons in cortical regions infused with NT-4/5 showed anatomical changes compatible with this hypothesis. Cats at the peak of the critical period received chronic infusion NT-4/5 into visual cortical areas 17/18 via an osmotic minipump. Visual cortical neurons were labeled in fixed slices using the DiOlistics methods (Gan et al., 2000) and analyzed in confocal microsco-py. Infusion of NT-4/5 induced a significant increase of spine-like processes on primary dendrites and a distinctive sprouting of protuberances from neuronal somata in all layers. The increase of neuronal membrane was paralleled by an increase in density of the presynaptic marker synaptophysin in infused areas, suggesting an increase in the numbers of synapses. A contingent of these newly formed synapses may feed into inhibitory circuits, as suggested by an increase of GAD-65 immunostaining in NT-4/5 affected areas. These anatomical changes are consistent with the physiological changes in such animals, suggesting that excess trkB neurotrophin can stimulate the formation of promiscuous connections during the critical period.
Nucleosome wrapping state encodes principles of 3D genome organization
Authors: Wen Zengqi , Yu Xinqian , Fang Ruixin , Long Haizhen
Published: December 2023

Nucleosome is the basic structural unit of the genome. During processes like DNA replication and gene transcription, the conformation of nucleosomes undergoes dynamic changes, including DNA unwrapping and rewrapping, as well as histone disassembly and assembly. However, the wrapping characteristics of nucleosomes across the entire genome, including region-specificity and their correlation with higher-order chromatin organization, remain to be studied. In this study, we investigated the wrapping length of DNA on nucleosomes across the whole genome using wrapping-seq. We discovered that the chromatin of mouse ES cells formsNucleosome WrappingDomains (NRDs), which is conserved in yeast and fly. We found that the degree of nucleosome wrapping decreases after DNA replication and is promoted by transcription. Furthermore, we observed that nucleosome wrapping states delineate 3D genome organization and DNA replication timing. In conclusion, we have revealed a novel principle of higher-order chromatin organization.
BulkLMM: Real-time genome scans for multiple quantitative traits using linear mixed models
Authors: Yu Zifan , Farage Gregory , Williams Robert W. , Broman Karl W. , Sen Śaunak
Published: December 2023

Genetic studies often collect data using high-throughput phenotyping. That has led to the need for fast genomewide scans for large number of traits using linear mixed models (LMMs). Computing the scans one by one on each trait is time consuming. We have developed new algorithms for performing genome scans on a large number of quantitative traits using LMMs, BulkLMM, that speeds up the computation by orders of magnitude compared to one trait at a time scans. On a mouse BXD Liver Proteome data with more than 35,000 traits and 7,000 markers, BulkLMM completed in a few seconds. We use vectorized, multi-threaded operations and regularization to improve optimization, and numerical approximations to speed up the computations. Our soft-ware implementation in the Julia programming language also provides permutation testing for LMMs and is available athttps://github.com/senresearch/BulkLMM.jl.
Dueling Endogenous Viral-Like Sequences Control Synaptic Plasticity
Authors: M’Angale P. Githure , Lemieux Adrienne , Liu Yumeng , Graslie Jasmine , Wang Shuhao , Simkin Alfred , Budnik Vivian , Kelch Brian A. , Thomson Travis
Published: December 2023

The function of a large part of most genomes, generally called “junk DNA”, remains largely unknown. Much of this enigmatic DNA corresponds to transposons, which are considered genomic parasites. Here, we show the protein of the Ty1 retrotransposonCopiais enriched at theDrosophilaneuromuscular junction and is transported across synapses. Unexpectedly, disruptingCopiaexpression results in increases in both synapse development and structural synaptic plasticity. Plasticity is kept in balance asCopiaantagonizes theDrosophila Arc(activity-regulated cytoskeleton-associated protein) homolog, which is a transposon-derived gene. Our cryo-EM structure of theCopiacapsid shows a shell with large cargo capacity and leads to a hypothesis for mutual antagonism of Arc andCopiacapsid assembly. Our findings provide evidence that a fully functional transposon plays a role at synapses, suggesting that transposons and other types of ‘junk DNA’ are essential to developmental and cellular processes.
Fabry Cardiomyopathy: Myocardial Fibrosis, Inflammation and Down-Regulation of Mannose6Phosphate Receptors cause Low accessibility to Enzyme Replacement Therapy
Authors: Frustaci Andrea , Verardo Romina , Magnocavallo Michele , Frustaci Emanuela , Russo Matteo Antonio , Chimenti Cristina
Published: December 2023

Background

Clinical impact of enzyme replacement therapy (ERT) on advanced Fabry disease cardiomyopathy (FDCM) appears limited. The pathologic mechanisms involved are still unclear.

Methods

Ten male patients with advanced FDCM (echocardiographic maximal wall thickness 19.3 ± 2.1 mm) underwent left ventricular endomyocardial biopsy before and 4 hours after beta-agalsidase infusion (1 mg/Kg). Comparative studies between pre and post infusion samples included: histology and electron microscopy; assessment of myocardial alpha-galactosidase A activity; immunohistochemistry for alpha-galactosidase A and semiquantitative evaluation (from 0 to 3) of its cardiomyocyte content; Ultrastructural immunogold analysis with anti-alpha-galactosidase A ab. Western Blot (WB) quantification of mannose-6-phosphate receptors (M6Pr). Controls were surgical left ventricular biopsies from patients with mitral stenosis.

Results

Histologic and Ultrastructural evaluation showed no removal of storage material while myocardial fibrosis was 9.8 ± 6.8 vs 3.8 ± 2.0 of controls and virus-negative lymphocytic inflammation was observed in 7 out of 10 patients. At Ultrastructural immunogold analysis, Myocardial alpha-galactosidase A activity increased in post infusion samples by overall 1.89-fold. Alpha-galactosidase A immunostaining in cardiomyocytes was absent at baseline in all patients and did not significantly improve in post-infusion samples. Immunogold particles increased by 1.33-fold(17.6 ± 3.6 pre infusion vs 21.5 ± 5.9 post)remaining far from normal controls (86.9 ± 6.6). Protein analysis showed M6Pr in advanced FDCM to be 81% lower than in normal heart.

Conclusions

Our study shows a low accessibility to ERT of cardiomyocytes affected by advanced FDCM. It is sustained by myocardial fibrosis, inflammation and severe down-regulation of M6Pr.
Trends in antimicrobial resistance amongstSalmonellaTyphi in Bangladesh: a 24-year retrospective observational study (1999–2022)
Authors: Tanmoy Arif M , Hooda Yogesh , Sajib Mohammad S I , Rahman Hafizur , Sarkar Anik , Das Dipu , Islam Nazrul , Kanon Naito , Rahman Md. Asadur , Garrett Denise O , Endtz Hubert P , Luby Stephen P , Shahidullah Mohammod , Amin Md. Ruhul , Alam Jahangir , Hanif Mohammed , Saha Samir K , Saha Senjuti
Published: December 2023

Background

Rising antimicrobial resistance (AMR) inSalmonellaTyphi restricts typhoid treatment options, heightening concerns for pan-oral drug-resistant outbreaks. Bangladesh contemplates introducing typhoid conjugate vaccine (TCV) to address the typhoid burden and AMR. However, large-scale surveillance data on typhoid AMR in Bangladesh is scarce.

Objective

This study explores the AMR trends inSalmonellaTyphi isolates from Bangladesh, drawing comparisons with antibiotic consumption to optimize antibiotic stewardship strategies for the country.

Methods

Our typhoid fever surveillance included two pediatric hospitals and three private clinics in Dhaka, Bangladesh, spanning 1999 to 2022. Blood cultures were performed at physicians’ discretion; cases were confirmed by microbiological culture, serological, and biochemical tests. Antimicrobial susceptibility was determined following CLSI guidelines. National antibiotic consumption data for cotrimoxazole, ciprofloxacin, and azithromycin was obtained from IQVIA-MIDAS database for comparison.

Results

Our 24-year surveillance, encompassing 12,435SalmonellaTyphi cases, revealed declining trends in first-line drugs (amoxicillin, chloramphenicol, cotrimoxazole) and multidrug resistance (MDR; 38% to 17%, 1999–2022). Cotrimoxazole consumption dropped, 0.8 to 0.1 DDD/1000/day (1999–2020). Ciprofloxacin non-susceptibility persisted (>90%) with unchanged consumption (1.1-1.3 DDD/1000/day, 2002–2020). Low ceftriaxone resistance (<1%) was observed, with rising MIC (0.03 to 0.12 mg/L, 1999–2019). Azithromycin consumption increased (0.1 to 3.8 DDD/1000/day, 1999–2020), but resistance remained ≤4%.

Conclusion

Our study highlights declining MDR amongstSalmonellaTyphi in Bangladesh, thus reintroducing first-line antimicrobials could work as an empirical treatment option for typhoid fever. Our analysis provides a baseline for monitoring the impact of future interventions, including the TCV, on typhoid burden and associated AMR.
Insights into the complex formation of a trimeric autotransporter adhesin with a peptidoglycan-binding periplasmic protein
Authors: Yoshimoto Shogo , Suzuki Atsuo , Kanie Junichi , Koiwai Kotaro , Lupas Andrei N. , Hori Katsutoshi
Published: December 2023

Trimeric autotransporter adhesin (TAA) is an outer membrane (OM) protein that is widely distributed in gram-negative bacteria and is involved primarily in adhesion to biotic and abiotic surfaces, cell agglutination, and biofilm formation. TAAs are secreted onto the OM by the type Vc secretion system (SS). Because the interactions between TAAs and chaperones or special assistant proteins during secretion are short-lived, it is thought that TAAs reside on the OM without forming complexes with other proteins after secretion. In this study, we aimed to clarify the interactions between anAcinetobacterTAA, AtaA, and a peptidoglycan (PG)-binding periplasmic protein, TpgA, and to identify additional roles of TpgA based on these interactions. Pull-down assays using recombinant proteins identified the interacting domains. X-ray crystallography revealed the A3B3 heterohexameric complex structure of the N-terminal domain of TpgA with the transmembrane domain of AtaA and showed that both electrostatic and hydrophobic interactions contribute to stable complex formation. Bioinformatic analysis suggested that the TAA-TpgA complex is formed in a wide range of species that harbor thetaa-tpgAgene cassette in their genome. Furthermore, the absence of TpgA increased the release of AtaA from the cell surface, suggesting that TpgA prevents the release of TAA from the cell surface via its anchoring to the PG. We propose that the TAAs that form a complex with TpgA be assigned to type Vc2SS, a new subtype of type Vc SS.

Significance

Gram-negative bacteria have specialized secretion systems (SSs) that translocate molecules from the cytoplasm to the extracellular space. This is the first report directly demonstrating that the transmembrane domain of a trimeric autotransporter adhesin (TAA), which is secreted by the type Vc SS, forms a stable complex with a peptidoglycan-binding periplasmic protein. This complex prevents the release of TAA from the cell surface. These results suggest that the secretion and architecture of some TAAs are more complex than was previously understood. Our work provides structural and functional insights into bacterial SSs that are important not only in microbiology but also for medical and bioengineering applications.
LLPS condensates of Fha initiate the inside-out assembly of the type VI secretion system
Authors: Pei Tong-Tong , An Ying , Wang Xing-Yu , Luo Han , Kan Yumin , Li Hao , Tang Ming-Xuan , Ye Zi-Yan , Liang Jia-Xin , Jian Tao , Zheng Hao-Yu , Wang Zeng-Hang , Liang Xiaoye , Zhang Mingjie , Liu Xiaotian , Dong Tao
Published: December 2023

The type VI secretion system (T6SS) is one of the most powerful nanomachines employed by Gram-negative pathogens for penetrating diverse cell envelopes, including bacteria and fungi, to deliver potent effectors into target cells. While the membrane-anchored contractile tubular structure of the T6SS is well characterized, the assembly process remains poorly understood. The prevailing model suggests that the assembly of T6SS initiates from its outer-membrane component. Here, we report a distinct model that the cytoplasmic protein Fha initiates T6SS assembly inAcidovorax citrulli, an important plant pathogen. Fha dictates the formation of the inner-membrane complex and the baseplate, and directly interacts with these key components. Importantly, imaging and biochemical assays reveal that Fha undergoes liquid-liquid phase separation (LLPS), forming condensates that selectively recruit essential T6SS proteins, which are otherwise dispersed in cells. Fha also exhibited conserved functions in human pathogensVibrio choleraeandPseudomonas aeruginosa. These findings unveil an inside-first LLPS-driven model for T6SS assembly and suggest LLPS might be broadly involved in mediating the assembly of bacterial macromolecular complexes and facilitating interspecies interactions and pathogenesis.

Significance statement

The T6SS plays a pivotal role in interspecies competition and host-microbe interactions by delivering toxins to various prokaryotes and eukaryotes. Its crucial function relies on a membrane-anchored macromolecular structure comprising at least 13 conserved components. However, the mechanisms governing the efficient assembly of its diverse cytosolic and membrane-bound components remain elusive. Here, we identify Fha, a conserved cytosolic protein, as a key initiator of T6SS assembly. Fha recruits multiple structural and effector components, forming LLPS condensates. Fha homologs of plant and human pathogens exhibit conserved functions. Our findings not only unveil an inside-first assembly model for the T6SS, initiating from inner-membrane and baseplate components, but also suggest LLPS may have a broader impact on bacterial physiology beyond intracellular activities.
Humoral immune responses to the monovalent XBB.1.5-adapted BNT162b2 mRNA booster
Authors: Marking Ulrika , Bladh Oscar , Aguilera Katherina , Yang Yiqiu , Norin Nina Greilert , Blom Kim , Hober Sophia , Klingström Jonas , Havervall Sebastian , Åberg Mikael , Sheward Daniel J. , Thålin Charlotte
Published: December 2023

Continued SARS-CoV-2 evolution and immune escape necessitated the development of updated vaccines, and a monovalent vaccine incorporating the XBB.1.5 variant spike protein is currently being rolled out. Amidst the emergence of the highly mutated BA.2.86 lineage and against the backdrop of pronounced immune imprinting, it is important to characterize the antibody responses following vaccination, particularly in the elderly.

Here, we show that the monovalent XBB.1.5-adapted booster vaccination substantially enhanced both binding and neutralising antibody responses against a panel of variants, including BA.2.86, in an older population with four or more previous vaccine doses. Furthermore, neutralizing antibody titers to XBB.1.5 and BA.2.86 were boosted more strongly than titers to historical variants were.

Our findings thereby suggest increased vaccine induced protection against both antigenically matched variants, as well as the more distant BA.2.86 variant, and support current vaccine policies recommending a monovalent XBB.1.5 booster dose to older individuals.
Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study
Authors: Durairaj Janani , Follonier Océane M. , Leuzinger Karoline , Alexander Leila T , Wilhelm Maud , Pereira Joana , Hillenbrand Caroline A. , Weissbach Fabian H. , Schwede Torsten , Hirsch Hans H.
Published: December 2023

BK polyomavirus (BKPyV) is a double-stranded DNA virus causing nephropathy, hemorrhagic cystitis, and urothelial cancer in transplant patients. The BKPyV-encoded capsid protein Vp1 and large T-antigen (LTag) are key targets of neutralizing antibodies and cytotoxic T-cells, respectively. Our single-center data suggested that variability in Vp1 and LTag may contribute to failing BKPyV-specific immune control, and impact vaccine design. We therefore analyzed all available entries in GenBank (1516VP1; 742LTAG)and explored potential structural effects using computational approaches. BKPyV-genotype (gt)1 was found in 71.18% of entries, followed by BKPyV-gt4 (19.26%), BKPyV-gt2 (8.11%) and BKPyV-gt3 (1.45%), but rates differed according to country and specimen type. Vp1-mutations matched a serotype different than the assigned one or were serotype-independent in 43%, 18% affected more than one amino acid. Notable Vp1-mutations altered antibody-binding domains, interactions with sialic acid receptors, or were predicted to change conformation. LTag-sequences were more conserved, with only 16 mutations detectable in more than one entry and without significant effects on LTag-structure or interaction domains. However, LTag changes were predicted to affect HLA-class I presentation of immunodominant 9mers to cytotoxic T-cells. These global data strengthen single center observations and specifically our earlier findings revealing mutant 9mer epitopes conferring immune escape from HLA-I cytotoxic T cells. We conclude that variability of BKPyV-Vp1 and LTag may have important implications for diagnostic assays assessing BKPyV-specific immune control and for vaccine design.

IMPORTANCE

Type and rate of amino acid variations in BKPyV may provide important insights into BKPyV diversity in human populations and an important step towards defining determinants of BKPyV-specific immunity needed to protect vulnerable patients from BKPyV diseases. Our analysis of BKPyV sequences obtained from human specimens reveals an unexpectedly high genetic variability for this double-stranded DNA virus that strongly relies on host cell DNA replication machinery with its proof reading and error correction mechanisms. BKPyV variability and immune escape should be taken into account when designing further approaches to antivirals, monoclonal antibodies and vaccines for patients at risk of BKPyV diseases.
Modelling the age-related deceleration of clonal haematopoiesis in UK Biobank
Authors: MacGregor Hamish AJ , Easton Douglas F , Blundell Jamie R
Published: December 2023

Somatic mutations acquired in haematopoietic stem cells can drive clonal expansions, a phenomenon called clonal haematopoiesis (CH). CH has been associated with higher risk of haematological cancer, cardiovascular disease and lower life expectancy and is strongly age-dependent, becoming almost ubiquitous in older adults. However, the dynamics of CH are not yet fully understood, and an accurate quantitative model of clonal expansion in healthy people could inform early detection strategies. Here, we analyse the age-dependence of the variant allele frequency (VAF) distributions of common CH driver variants from the exomes of 400,000 cancer-free UK Biobank participants. We find evidence of a substantial deceleration of clonal expansion with age taking place in younger people. This deceleration appears to be general: different CH hotspot variants all displayed a ∼ 3-fold reduction in growth rate between young and old. We develop several alternative models of clonal dynamics that might explain this age-related deceleration. First we show that variation in fitness of variants among individuals (e.g., due to genetic susceptibility) is unable to produce the required deceleration. Second, we consider a clonal competition model in which clonal expansion in later life is inhibited by competition with an unobserved background of other expanding clones. Finally, we consider an ageing model where HSC division slows down with increasing age. The observed age-specific VAF distributions are consistent with the ageing model with plausible parameters. To further interrogate these models, we consider a large data set of longitudinal growth rates obtained from serial samples of blood. These data suggest that a general slowdown of HSC division rates plays a key role in shaping the genetic diversity of ageing blood.
The multiscale topological organization of the functional brain network in adolescent PTSD
Authors: Corredor David , Segobin Shailendra , Hinault Thomas , Eustache Francis , Dayan Jacques , Guillery-Girard Bérengère , Naveau Mikaël
Published: December 2023

The experience of an extremely aversive event can produce enduring deleterious behavioral and neural consequences, among which posttraumatic stress disorder (PTSD) is a representative example. In this work, we aim to study the whole-cortex functional organization of adolescents with PTSD without thea prioriselection of specific regions of interest or functional networks. To do so, we built on the network neuroscience framework and specifically on multisubject community analysis to study the functional connectivity of the brain. We show, across different topological scales (the number of communities composing the cortex), an increased coupling between regions belonging to unimodal (sensory) regions and a reduced coupling between transmodal (association) regions in the adolescent PTSD group. These results open up an intriguing possibility concerning an altered large-scale cortical organization in adolescent PTSD.

Significance Statement

The understanding of brain responses following the experience of a traumatic event and the eventual apparition of posttraumatic stress disorder (PTSD) symptoms during youth remains an active topic of research in clinical neuroscience. We adapted a multisubject community detection algorithm to study the functional brain organization of PTSD from a whole cortex and multiscale topological perspective, thereby taking into account the complex (network) organization of the brain. PTSD patients and control subjects presented a different whole cortex functional organization that remained present across topological scales. PTSD patients showed a decreased interaction in transmodal cortices and, inversely, an enhanced interaction in unimodal cortices. This investigation highlights the importance of studying the brain from a complex and whole cortex perspective.