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1.
Cell ; 187(13): 3427-3444.e21, 2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38733990

ABSTRACT

Many behaviors require the coordinated actions of somatic and autonomic functions. However, the underlying mechanisms remain elusive. By opto-stimulating different populations of descending spinal projecting neurons (SPNs) in anesthetized mice, we show that stimulation of excitatory SPNs in the rostral ventromedial medulla (rVMM) resulted in a simultaneous increase in somatomotor and sympathetic activities. Conversely, opto-stimulation of rVMM inhibitory SPNs decreased both activities. Anatomically, these SPNs innervate both sympathetic preganglionic neurons and motor-related regions in the spinal cord. Fiber-photometry recording indicated that the activities of rVMM SPNs correlate with different levels of muscle and sympathetic tone during distinct arousal states. Inhibiting rVMM excitatory SPNs reduced basal muscle and sympathetic tone, impairing locomotion initiation and high-speed performance. In contrast, silencing the inhibitory population abolished muscle atonia and sympathetic hypoactivity during rapid eye movement (REM) sleep. Together, these results identify rVMM SPNs as descending spinal projecting pathways controlling the tone of both the somatomotor and sympathetic systems.


Subject(s)
Medulla Oblongata , Spinal Cord , Sympathetic Nervous System , Animals , Male , Mice , Locomotion/physiology , Medulla Oblongata/physiology , Mice, Inbred C57BL , Motor Neurons/physiology , Neurons/physiology , Sleep, REM/physiology , Spinal Cord/physiology , Sympathetic Nervous System/physiology , Behavior, Animal , Cell Count , Muscle, Skeletal
2.
Immunity ; 55(9): 1627-1644.e7, 2022 09 13.
Article in English | MEDLINE | ID: mdl-35977543

ABSTRACT

The apolipoprotein E4 (APOE4) allele is associated with an increased risk of Alzheimer disease and a decreased risk of glaucoma, but the underlying mechanisms remain poorly understood. Here, we found that in two mouse glaucoma models, microglia transitioned to a neurodegenerative phenotype characterized by upregulation of Apoe and Lgals3 (Galectin-3), which were also upregulated in human glaucomatous retinas. Mice with targeted deletion of Apoe in microglia or carrying the human APOE4 allele were protected from retinal ganglion cell (RGC) loss, despite elevated intraocular pressure (IOP). Similarly to Apoe-/- retinal microglia, APOE4-expressing microglia did not upregulate neurodegeneration-associated genes, including Lgals3, following IOP elevation. Genetic and pharmacologic targeting of Galectin-3 ameliorated RGC degeneration, and Galectin-3 expression was attenuated in human APOE4 glaucoma samples. These results demonstrate that impaired activation of APOE4 microglia is protective in glaucoma and that the APOE-Galectin-3 signaling can be targeted to treat this blinding disease.


Subject(s)
Apolipoprotein E4 , Glaucoma , Animals , Apolipoprotein E4/genetics , Apolipoprotein E4/metabolism , Apolipoprotein E4/therapeutic use , Apolipoproteins E/genetics , Apolipoproteins E/metabolism , Disease Models, Animal , Galectin 3/genetics , Galectin 3/metabolism , Galectin 3/therapeutic use , Glaucoma/drug therapy , Glaucoma/genetics , Glaucoma/metabolism , Humans , Mice , Microglia/metabolism
3.
Nature ; 624(7991): 403-414, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38092914

ABSTRACT

The brain controls nearly all bodily functions via spinal projecting neurons (SPNs) that carry command signals from the brain to the spinal cord. However, a comprehensive molecular characterization of brain-wide SPNs is still lacking. Here we transcriptionally profiled a total of 65,002 SPNs, identified 76 region-specific SPN types, and mapped these types into a companion atlas of the whole mouse brain1. This taxonomy reveals a three-component organization of SPNs: (1) molecularly homogeneous excitatory SPNs from the cortex, red nucleus and cerebellum with somatotopic spinal terminations suitable for point-to-point communication; (2) heterogeneous populations in the reticular formation with broad spinal termination patterns, suitable for relaying commands related to the activities of the entire spinal cord; and (3) modulatory neurons expressing slow-acting neurotransmitters and/or neuropeptides in the hypothalamus, midbrain and reticular formation for 'gain setting' of brain-spinal signals. In addition, this atlas revealed a LIM homeobox transcription factor code that parcellates the reticulospinal neurons into five molecularly distinct and spatially segregated populations. Finally, we found transcriptional signatures of a subset of SPNs with large soma size and correlated these with fast-firing electrophysiological properties. Together, this study establishes a comprehensive taxonomy of brain-wide SPNs and provides insight into the functional organization of SPNs in mediating brain control of bodily functions.


Subject(s)
Brain , Gene Expression Profiling , Neural Pathways , Neurons , Spinal Cord , Animals , Mice , Hypothalamus , Neurons/metabolism , Neuropeptides , Spinal Cord/cytology , Spinal Cord/metabolism , Brain/cytology , Brain/metabolism , Neurotransmitter Agents , Mesencephalon/cytology , Reticular Formation/cytology , Electrophysiology , Cerebellum/cytology , Cerebral Cortex/cytology
4.
EMBO J ; 2024 Aug 19.
Article in English | MEDLINE | ID: mdl-39160276

ABSTRACT

Metabolic dysfunction-associated steatohepatitis (MASH, previously termed non-alcoholic steatohepatitis (NASH)), is a major complication of obesity that promotes fatty liver disease. MASH is characterized by progressive tissue fibrosis and sterile liver inflammation that can lead to liver cirrhosis, cancer, and death. The molecular mechanisms of fibrosis in MASH and its systemic control remain poorly understood. Here, we identified the secreted-type pro-fibrotic protein, procollagen C-endopeptidase enhancer-1 (PCPE-1), as a brown adipose tissue (BAT)-derived adipokine that promotes liver fibrosis in a murine obesity-induced MASH model. BAT-specific or systemic PCPE-1 depletion in mice ameliorated liver fibrosis, whereas, PCPE-1 gain of function in BAT enhanced hepatic fibrosis. High-calorie diet-induced ER stress increased PCPE-1 production in BAT through the activation of IRE-1/JNK/c-Fos/c-Jun signaling. Circulating PCPE-1 levels are increased in the plasma of MASH patients, suggesting a therapeutic possibility. In sum, our results uncover PCPE-1 as a novel systemic control factor of liver fibrosis.

5.
Nature ; 606(7912): 94-101, 2022 06.
Article in English | MEDLINE | ID: mdl-35650358

ABSTRACT

Neurotransmitters play essential roles in regulating neural circuit dynamics both in the central nervous system as well as at the peripheral, including the gastrointestinal tract1-3. Their real-time monitoring will offer critical information for understanding neural function and diagnosing disease1-3. However, bioelectronic tools to monitor the dynamics of neurotransmitters in vivo, especially in the enteric nervous systems, are underdeveloped. This is mainly owing to the limited availability of biosensing tools that are capable of examining soft, complex and actively moving organs. Here we introduce a tissue-mimicking, stretchable, neurochemical biological interface termed NeuroString, which is prepared by laser patterning of a metal-complexed polyimide into an interconnected graphene/nanoparticle network embedded in an elastomer. NeuroString sensors allow chronic in vivo real-time, multichannel and multiplexed monoamine sensing in the brain of behaving mouse, as well as measuring serotonin dynamics in the gut without undesired stimulations and perturbing peristaltic movements. The described elastic and conformable biosensing interface has broad potential for studying the impact of neurotransmitters on gut microbes, brain-gut communication and may ultimately be extended to biomolecular sensing in other soft organs across the body.


Subject(s)
Brain , Enteric Nervous System , Gastrointestinal Tract , Neurotransmitter Agents , Animals , Biosensing Techniques , Brain/metabolism , Brain-Gut Axis , Elastomers , Enteric Nervous System/metabolism , Gastrointestinal Tract/innervation , Gastrointestinal Tract/physiology , Graphite , Lasers , Mice , Nanoparticles , Neurotransmitter Agents/analysis , Serotonin/analysis
6.
Nature ; 612(7939): 301-309, 2022 12.
Article in English | MEDLINE | ID: mdl-36450978

ABSTRACT

Clonal haematopoiesis involves the expansion of certain blood cell lineages and has been associated with ageing and adverse health outcomes1-5. Here we use exome sequence data on 628,388 individuals to identify 40,208 carriers of clonal haematopoiesis of indeterminate potential (CHIP). Using genome-wide and exome-wide association analyses, we identify 24 loci (21 of which are novel) where germline genetic variation influences predisposition to CHIP, including missense variants in the lymphocytic antigen coding gene LY75, which are associated with reduced incidence of CHIP. We also identify novel rare variant associations with clonal haematopoiesis and telomere length. Analysis of 5,041 health traits from the UK Biobank (UKB) found relationships between CHIP and severe COVID-19 outcomes, cardiovascular disease, haematologic traits, malignancy, smoking, obesity, infection and all-cause mortality. Longitudinal and Mendelian randomization analyses revealed that CHIP is associated with solid cancers, including non-melanoma skin cancer and lung cancer, and that CHIP linked to DNMT3A is associated with the subsequent development of myeloid but not lymphoid leukaemias. Additionally, contrary to previous findings from the initial 50,000 UKB exomes6, our results in the full sample do not support a role for IL-6 inhibition in reducing the risk of cardiovascular disease among CHIP carriers. Our findings demonstrate that CHIP represents a complex set of heterogeneous phenotypes with shared and unique germline genetic causes and varied clinical implications.


Subject(s)
COVID-19 , Cardiovascular Diseases , Humans , Clonal Hematopoiesis/genetics , Cardiovascular Diseases/epidemiology , Cardiovascular Diseases/genetics
7.
EMBO J ; 42(23): e115008, 2023 Dec 01.
Article in English | MEDLINE | ID: mdl-37964598

ABSTRACT

The main goals and challenges for the life science communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially in large-scale data-driven research and computational analyses. Here, we present key findings, procedures, effective measures and recommendations for generating and establishing sustainable life science resources based on the collaborative, cross-disciplinary work done within the EOSC-Life (European Open Science Cloud for Life Sciences) consortium. Bringing together 13 European life science research infrastructures, it has laid the foundation for an open, digital space to support biological and medical research. Using lessons learned from 27 selected projects, we describe the organisational, technical, financial and legal/ethical challenges that represent the main barriers to sustainability in the life sciences. We show how EOSC-Life provides a model for sustainable data management according to FAIR (findability, accessibility, interoperability, and reusability) principles, including solutions for sensitive- and industry-related resources, by means of cross-disciplinary training and best practices sharing. Finally, we illustrate how data harmonisation and collaborative work facilitate interoperability of tools, data, solutions and lead to a better understanding of concepts, semantics and functionalities in the life sciences.


Subject(s)
Biological Science Disciplines , Biomedical Research , Software , Workflow
8.
Proc Natl Acad Sci U S A ; 121(25): e2314036121, 2024 Jun 18.
Article in English | MEDLINE | ID: mdl-38857391

ABSTRACT

Permafrost regions contain approximately half of the carbon stored in land ecosystems and have warmed at least twice as much as any other biome. This warming has influenced vegetation activity, leading to changes in plant composition, physiology, and biomass storage in aboveground and belowground components, ultimately impacting ecosystem carbon balance. Yet, little is known about the causes and magnitude of long-term changes in the above- to belowground biomass ratio of plants (η). Here, we analyzed η values using 3,013 plots and 26,337 species-specific measurements across eight sites on the Tibetan Plateau from 1995 to 2021. Our analysis revealed distinct temporal trends in η for three vegetation types: a 17% increase in alpine wetlands, and a decrease of 26% and 48% in alpine meadows and alpine steppes, respectively. These trends were primarily driven by temperature-induced growth preferences rather than shifts in plant species composition. Our findings indicate that in wetter ecosystems, climate warming promotes aboveground plant growth, while in drier ecosystems, such as alpine meadows and alpine steppes, plants allocate more biomass belowground. Furthermore, we observed a threefold strengthening of the warming effect on η over the past 27 y. Soil moisture was found to modulate the sensitivity of η to soil temperature in alpine meadows and alpine steppes, but not in alpine wetlands. Our results contribute to a better understanding of the processes driving the response of biomass distribution to climate warming, which is crucial for predicting the future carbon trajectory of permafrost ecosystems and climate feedback.


Subject(s)
Biomass , Ecosystem , Permafrost , Tibet , Wetlands , Plants/metabolism , Climate Change , Temperature , Carbon Cycle , Plant Development/physiology , Soil/chemistry , Grassland
9.
EMBO J ; 41(6): e109102, 2022 03 15.
Article in English | MEDLINE | ID: mdl-35146778

ABSTRACT

The microbiome plays an important role in shaping plant growth and immunity, but few plant genes and pathways impacting plant microbiome composition have been reported. In Arabidopsis thaliana, the phosphate starvation response (PSR) was recently found to modulate the root microbiome upon phosphate (Pi) starvation through the transcriptional regulator PHR1. Here, we report that A. thaliana PHR1 directly binds to the promoters of rapid alkalinization factor (RALF) genes, and activates their expression under phosphate-starvation conditions. RALFs in turn suppress complex formation of pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) receptor through FERONIA, a previously-identified PTI modulator that increases resistance to certain detrimental microorganisms. Suppression of immunity via the PHR1-RALF-FERONIA axis allows colonization by specialized root microbiota that help to alleviate phosphate starvation by upregulating the expression of PSR genes. These findings provide a new paradigm for coordination of host-microbe homeostasis through modulating plant innate immunity after environmental perturbations.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Microbiota , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Gene Expression Regulation, Plant , Phosphates/metabolism , Plant Immunity/genetics , Plants/metabolism , Transcription Factors/metabolism
10.
Brief Bioinform ; 25(5)2024 Jul 25.
Article in English | MEDLINE | ID: mdl-39073832

ABSTRACT

Herbal medicines, particularly traditional Chinese medicines (TCMs), are a rich source of natural products with significant therapeutic potential. However, understanding their mechanisms of action is challenging due to the complexity of their multi-ingredient compositions. We introduced Herb-CMap, a multimodal fusion framework leveraging protein-protein interactions and herb-perturbed gene expression signatures. Utilizing a network-based heat diffusion algorithm, Herb-CMap creates a connectivity map linking herb perturbations to their therapeutic targets, thereby facilitating the prioritization of active ingredients. As a case study, we applied Herb-CMap to Suhuang antitussive capsule (Suhuang), a TCM formula used for treating cough variant asthma (CVA). Using in vivo rat models, our analysis established the transcriptomic signatures of Suhuang and identified its key compounds, such as quercetin and luteolin, and their target genes, including IL17A, PIK3CB, PIK3CD, AKT1, and TNF. These drug-target interactions inhibit the IL-17 signaling pathway and deactivate PI3K, AKT, and NF-κB, effectively reducing lung inflammation and alleviating CVA. The study demonstrates the efficacy of Herb-CMap in elucidating the molecular mechanisms of herbal medicines, offering valuable insights for advancing drug discovery in TCM.


Subject(s)
Antitussive Agents , Drugs, Chinese Herbal , Medicine, Chinese Traditional , Animals , Drugs, Chinese Herbal/pharmacology , Drugs, Chinese Herbal/therapeutic use , Medicine, Chinese Traditional/methods , Rats , Antitussive Agents/pharmacology , Antitussive Agents/therapeutic use , Protein Interaction Maps/drug effects , Asthma/drug therapy , Asthma/metabolism , Asthma/genetics , Signal Transduction/drug effects , Cough/drug therapy , Transcriptome , Humans
11.
PLoS Pathog ; 20(8): e1012479, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39178325

ABSTRACT

Alveolar echinococcosis (AE) is a highly lethal helminth infection. Current chemotherapeutic strategies for AE primarily involve the use of benzimidazoles (BZs) such as mebendazole (MDZ) and albendazole (ABZ), which exhibit limited efficacy. In a previous study, the vaccine of recombinant Echinococcus granulosus P29 (rEgP29) showed significant immunoprotection against E. granulosus in both mice and sheep. In the current study, we utilized hybridoma technology to generate five monoclonal antibodies (mAbs) against P29, among which 4G10F4 mAb exhibited the highest antigen-specific binding capacity. This mAb was selected for further investigation of anti-AE therapy, both in vivo and in vitro. In vitro, 4G10F4 inhibited a noteworthy inhibition of E. multilocularis protoscoleces and primary cells viability through complement-dependent cytotoxicity (CDC) mechanism. In vivo, two experiments were conducted. In the first experiment, mice were intraperitoneally injected with Em protoscoleces, and subsequently treated with 4G10F4 mAb (2.5/5/10 mg/kg) at 12 weeks postinfection once per week for 8 times via tail vein injection. Mice that were treated with 4G10F4 mAb only in dosage of 5mg/kg exhibited a significant lower mean parasite burden (0.89±0.97 g) compared to isotype mAb treated control mice (2.21±1.30 g). In the second experiment, mice were infected through hepatic portal vein and treated with 4G10F4 mAb (5mg/kg) at one week after surgery once per week for 8 times. The numbers of hepatic metacestode lesions of the 4G10F4 treatment group were significantly lower in comparison to the isotype control group. Pathological analysis revealed severe disruption of the inner structure of the metacestode in both experiments, particularly affecting the germinal and laminated layers, resulting in the transformation into infertile vesicles after treatment with 4G10F4. In addition, the safety of 4G10F4 for AE treatment was confirmed through assessment of mouse weight and evaluation of liver and kidney function. This study presents antigen-specific monoclonal antibody immunotherapy as a promising therapeutic approach against E. multilocularis induced AE.


Subject(s)
Antibodies, Monoclonal , Echinococcosis , Animals , Echinococcosis/drug therapy , Echinococcosis/immunology , Antibodies, Monoclonal/pharmacology , Mice , Helminth Proteins/immunology , Helminth Proteins/pharmacology , Mice, Inbred BALB C , Echinococcus multilocularis/immunology , Echinococcus multilocularis/drug effects , Female , Echinococcus granulosus/immunology , Sheep , Antibodies, Helminth/immunology , Antigens, Helminth/immunology
12.
Proc Natl Acad Sci U S A ; 120(34): e2300856120, 2023 Aug 22.
Article in English | MEDLINE | ID: mdl-37579165

ABSTRACT

Space heating and cooling consume ~13% of global energy every year. The development of advanced materials that promote energy savings in heating and cooling is gaining increasing attention. To thermally isolate the space of concern and minimize the heat exchange with the outside environment has been recognized as one effective solution. To this end, here, we develop a universal category of colorful low-emissivity paints to form bilayer coatings consisting of an infrared (IR)-reflective bottom layer and an IR-transparent top layer in colors. The colorful visual appearance ensures the aesthetical effect comparable to conventional paints. High mid-infrared reflectance (up to ~80%) is achieved, which is more than 10 times as conventional paints in the same colors, efficiently reducing both heat gain and loss from/to the outside environment. The high near-IR reflectance also benefits reducing solar heat gain in hot days. The advantageous features of these paints strike a balance between energy savings and penalties for heating and cooling throughout the year, providing a comprehensive year-round energy-saving solution adaptable to a wide variety of climatic zones. Taking a typical midrise apartment building as an example, the application of our colorful low-emissivity paints can realize positive heating, ventilation, and air conditioning energy saving, up to 27.24 MJ/m2/y (corresponding to the 7.4% saving ratio). Moreover, the versatility of the paint, along with its applicability to diverse surfaces of various shapes and materials, makes the paints extensively useful in a range of scenarios, including building envelopes, transportation, and storage.

13.
Proc Natl Acad Sci U S A ; 120(22): e2220148120, 2023 05 30.
Article in English | MEDLINE | ID: mdl-37216506

ABSTRACT

Exploring the potential lead compounds for Alzheimer's disease (AD) remains one of the challenging tasks. Here, we report that the plant extract conophylline (CNP) impeded amyloidogenesis by preferentially inhibiting BACE1 translation via the 5' untranslated region (5'UTR) and rescued cognitive decline in an animal model of APP/PS1 mice. ADP-ribosylation factor-like protein 6-interacting protein 1 (ARL6IP1) was then found to mediate the effect of CNP on BACE1 translation, amyloidogenesis, glial activation, and cognitive function. Through analysis of the 5'UTR-targetd RNA-binding proteins by RNA pulldown combined with LC-MS/MS, we found that FMR1 autosomal homolog 1 (FXR1) interacted with ARL6IP1 and mediated CNP-induced reduction of BACE1 by regulating the 5'UTR activity. Without altering the protein levels of ARL6IP1 and FXR1, CNP treatment promoted ARL6IP1 interaction with FXR1 and inhibited FXR1 binding to the 5'UTR both in vitro and in vivo. Collectively, CNP exhibited a therapeutic potential for AD via ARL6IP1. Through pharmacological manipulation, we uncovered a dynamic interaction between FXR1 and the 5'UTR in translational control of BACE1, adding to the understanding of the pathophysiology of AD.


Subject(s)
Alzheimer Disease , Animals , Mice , 5' Untranslated Regions , Alzheimer Disease/drug therapy , Alzheimer Disease/genetics , Alzheimer Disease/metabolism , Amyloid Precursor Protein Secretases/genetics , Amyloid Precursor Protein Secretases/metabolism , Aspartic Acid Endopeptidases/genetics , Aspartic Acid Endopeptidases/metabolism , Chromatography, Liquid , Fragile X Mental Retardation Protein/genetics , Protein Biosynthesis , Tandem Mass Spectrometry
14.
Brief Bioinform ; 24(1)2023 01 19.
Article in English | MEDLINE | ID: mdl-36403090

ABSTRACT

The label-free quantification (LFQ) has emerged as an exceptional technique in proteomics owing to its broad proteome coverage, great dynamic ranges and enhanced analytical reproducibility. Due to the extreme difficulty lying in an in-depth quantification, the LFQ chains incorporating a variety of transformation, pretreatment and imputation methods are required and constructed. However, it remains challenging to determine the well-performing chain, owing to its strong dependence on the studied data and the diverse possibility of integrated chains. In this study, an R package EVALFQ was therefore constructed to enable a performance evaluation on >3000 LFQ chains. This package is unique in (a) automatically evaluating the performance using multiple criteria, (b) exploring the quantification accuracy based on spiking proteins and (c) discovering the well-performing chains by comprehensive assessment. All in all, because of its superiority in assessing from multiple perspectives and scanning among over 3000 chains, this package is expected to attract broad interests from the fields of proteomic quantification. The package is available at https://github.com/idrblab/EVALFQ.


Subject(s)
Proteome , Proteomics , Proteome/metabolism , Proteomics/methods , Reproducibility of Results
15.
Brief Bioinform ; 25(1)2023 11 22.
Article in English | MEDLINE | ID: mdl-38168839

ABSTRACT

Cell clustering is typically the initial step in single-cell RNA sequencing (scRNA-seq) analyses. The performance of clustering considerably impacts the validity and reproducibility of cell identification. A variety of clustering algorithms have been developed for scRNA-seq data. These algorithms generate cell label sets that assign each cell to a cluster. However, different algorithms usually yield different label sets, which can introduce variations in cell-type identification based on the generated label sets. Currently, the performance of these algorithms has not been systematically evaluated in single-cell transcriptome studies. Herein, we performed a critical assessment of seven state-of-the-art clustering algorithms including four deep learning-based clustering algorithms and commonly used methods Seurat, Cosine-based Tanimoto similarity-refined graph for community detection using Leiden's algorithm (CosTaL) and Single-cell consensus clustering (SC3). We used diverse evaluation indices based on 10 different scRNA-seq benchmarks to systematically evaluate their clustering performance. Our results show that CosTaL, Seurat, Deep Embedding for Single-cell Clustering (DESC) and SC3 consistently outperformed Single-Cell Clustering Assessment Framework and scDeepCluster based on nine effectiveness scores. Notably, CosTaL and DESC demonstrated superior performance in clustering specific cell types. The performance of the single-cell Variational Inference tools varied across different datasets, suggesting its sensitivity to certain dataset characteristics. Notably, DESC exhibited promising results for cell subtype identification and capturing cellular heterogeneity. In addition, SC3 requires more memory and exhibits slower computation speed compared to other algorithms for the same dataset. In sum, this study provides useful guidance for selecting appropriate clustering methods in scRNA-seq data analysis.


Subject(s)
Single-Cell Analysis , Transcriptome , Sequence Analysis, RNA/methods , Reproducibility of Results , Single-Cell Analysis/methods , Algorithms , Cluster Analysis , Gene Expression Profiling/methods
16.
Bioinformatics ; 40(1)2024 01 02.
Article in English | MEDLINE | ID: mdl-38070161

ABSTRACT

MOTIVATION: Drug repositioning is an effective strategy to identify new indications for existing drugs, providing the quickest possible transition from bench to bedside. With the rapid development of deep learning, graph convolutional networks (GCNs) have been widely adopted for drug repositioning tasks. However, prior GCNs based methods exist limitations in deeply integrating node features and topological structures, which may hinder the capability of GCNs. RESULTS: In this study, we propose an adaptive GCNs approach, termed AdaDR, for drug repositioning by deeply integrating node features and topological structures. Distinct from conventional graph convolution networks, AdaDR models interactive information between them with adaptive graph convolution operation, which enhances the expression of model. Concretely, AdaDR simultaneously extracts embeddings from node features and topological structures and then uses the attention mechanism to learn adaptive importance weights of the embeddings. Experimental results show that AdaDR achieves better performance than multiple baselines for drug repositioning. Moreover, in the case study, exploratory analyses are offered for finding novel drug-disease associations. AVAILABILITY AND IMPLEMENTATION: The soure code of AdaDR is available at: https://github.com/xinliangSun/AdaDR.


Subject(s)
Drug Repositioning , Computational Biology
17.
FASEB J ; 38(13): e23706, 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-38877842

ABSTRACT

The etiology of preeclampsia (PE), a complex and multifactorial condition, remains incompletely understood. DNA methylation, which is primarily regulated by three DNA methyltransferases (DNMTs), DNMT1, DNMT3A, and DNMT3B, plays a vital role in early embryonic development and trophectoderm differentiation. Yet, how DNMTs modulate trophoblast fusion and PE development remains unclear. In this study, we found that the DNMTs expression was downregulated during trophoblast cells fusion. Downregulation of DNMTs was observed during the reconstruction of the denuded syncytiotrophoblast (STB) layer of placental explants. Additionally, overexpression of DNMTs inhibited trophoblast fusion. Conversely, treatment with the DNA methylation inhibitor 5-aza-CdR decreased the expression of DNMTs and promoted trophoblast fusion. A combined analysis of DNA methylation data and gene transcriptome data obtained from the primary cytotrophoblasts (CTBs) fusion process identified 104 potential methylation-regulated differentially expressed genes (MeDEGs) with upregulated expression due to DNA demethylation, including CD59, TNFAIP3, SDC1, and CDK6. The transcription regulation region (TRR) of TNFAIP3 showed a hypomethylation with induction of 5-aza-CdR, which facilitated CREB recruitment and thereby participated in regulating trophoblast fusion. More importantly, clinical correlation analysis of PE showed that the abnormal increase in DNMTs may be involved in the development of PE. This study identified placental DNA methylation-regulated genes that may contribute to PE, offering a novel perspective on the role of epigenetics in trophoblast fusion and its implication in PE development.


Subject(s)
DNA (Cytosine-5-)-Methyltransferases , DNA Methylation , Pre-Eclampsia , Trophoblasts , Trophoblasts/metabolism , Female , Pre-Eclampsia/genetics , Pre-Eclampsia/metabolism , Pre-Eclampsia/pathology , Pregnancy , Humans , DNA (Cytosine-5-)-Methyltransferases/genetics , DNA (Cytosine-5-)-Methyltransferases/metabolism , Cell Fusion , Placenta/metabolism , DNA (Cytosine-5-)-Methyltransferase 1/metabolism , DNA (Cytosine-5-)-Methyltransferase 1/genetics
18.
Mol Psychiatry ; 29(7): 2031-2042, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38361125

ABSTRACT

Running exercise has been shown to alleviate depressive symptoms. However, the mechanism underlying the antidepressant effects of running exercise is not fully understood. The imbalance of M1/M2 microglia phenotype/polarization and concomitant dysregulation of neuroinflammation play crucial roles in the pathogenesis of depression. Running exercise increases circulating levels of adiponectin which is known to cross the blood‒brain barrier and suppress inflammatory responses. AdipoR1 is an adiponectin receptor that is involved in regulating microglial phenotypes and activation states. However, whether running exercise regulates hippocampal microglial phenotypes and neuroinflammation through adiponectin/AdipoR1 to exert its antidepressant effects remains unclear. In the current study, 4 weeks of running exercise significantly alleviated the depressive-like behaviors of chronic unpredictable stress (CUS)-exposed mice. Moreover, running exercise decreased the microglial numbers and altered microglial morphology in three subregions of the hippocampus to restore the M1/M2 balance; these effects were accompanied by regulation of pro-/anti-inflammatory cytokine production and secretion in CUS-exposed mice. These effects may involve elevation of peripheral tissue (adipose tissue and muscle) and plasma adiponectin levels, and hippocampal AdipoR1 levels as well as activation of the AMPK-NF-κB/STAT3 signaling pathway by running exercise. When an adeno-associated virus was used to knock down hippocampal AdipoR1, mice showed depressive-like behaviors and alterations in microglia and inflammatory factor expression in the hippocampus that were similar to those observed in CUS-exposed mice. Together, these results suggest that running exercise maintains the M1/M2 balance and inhibits neuroinflammation in the hippocampus of CUS-exposed mice. These effects might occur via adiponectin/AdipoR1-mediated activation of the AMPK-NF-κB/STAT3 signaling pathway.


Subject(s)
Adiponectin , Depression , Hippocampus , Microglia , Neuroinflammatory Diseases , Physical Conditioning, Animal , Receptors, Adiponectin , Signal Transduction , Stress, Psychological , Animals , Microglia/metabolism , Hippocampus/metabolism , Adiponectin/metabolism , Mice , Stress, Psychological/metabolism , Stress, Psychological/therapy , Receptors, Adiponectin/metabolism , Physical Conditioning, Animal/methods , Physical Conditioning, Animal/physiology , Male , Signal Transduction/physiology , Depression/metabolism , Depression/therapy , Neuroinflammatory Diseases/metabolism , Running/physiology , Mice, Inbred C57BL , Inflammation/metabolism , Disease Models, Animal , Cytokines/metabolism , NF-kappa B/metabolism , STAT3 Transcription Factor/metabolism
19.
Mol Cell ; 66(1): 154-162.e10, 2017 Apr 06.
Article in English | MEDLINE | ID: mdl-28344083

ABSTRACT

Hedgehog (Hh) has been known as the only cholesterol-modified morphogen playing pivotal roles in development and tumorigenesis. A major unsolved question is how Hh signaling regulates the activity of Smoothened (SMO). Here, we performed an unbiased biochemical screen and identified that SMO was covalently modified by cholesterol on the Asp95 (D95) residue through an ester bond. This modification was inhibited by Patched-1 (Ptch1) but enhanced by Hh. The SMO(D95N) mutation, which could not be cholesterol modified, was refractory to Hh-stimulated ciliary localization and failed to activate downstream signaling. Furthermore, homozygous SmoD99N/D99N (the equivalent residue in mouse) knockin mice were embryonic lethal with severe cardiac defects, phenocopying the Smo-/- mice. Together, the results of our study suggest that Hh signaling transduces to SMO through modulating its cholesterylation and provides a therapeutic opportunity to treat Hh-pathway-related cancers by targeting SMO cholesterylation.


Subject(s)
Cholesterol/metabolism , Hedgehog Proteins/metabolism , Signal Transduction , Smoothened Receptor/metabolism , Animals , CHO Cells , Cilia/metabolism , Cricetulus , Gene Expression Regulation, Developmental , Genetic Predisposition to Disease , HEK293 Cells , Heart Defects, Congenital/genetics , Heart Defects, Congenital/metabolism , Hedgehog Proteins/genetics , Humans , Mice , Mice, Transgenic , Mutation , NIH 3T3 Cells , Patched-1 Receptor/genetics , Patched-1 Receptor/metabolism , Phenotype , Protein Processing, Post-Translational , RNA Interference , Smoothened Receptor/genetics , Transfection
20.
BMC Biol ; 22(1): 88, 2024 Apr 19.
Article in English | MEDLINE | ID: mdl-38641823

ABSTRACT

BACKGROUND: Immunosuppressive status is prevalent in cancer patients and increases the complexity of tumor immunotherapy. It has been found that Listeria-vectored tumor vaccines had the potential ability of two-side regulatory effect on the immune response during immunotherapy. RESULTS: The results show that the combined immunotherapy with the LM∆E6E7 and LI∆E6E7, the two cervical cancer vaccine candidate strains constructed by our lab, improves the antitumor immune response and inhibits the suppressive immune response in tumor-bearing mice in vivo, confirming the two-sided regulatory ability of the immune response caused by Listeria-vectored tumor vaccines. The immunotherapy reduces the expression level of myeloid-derived suppressor cells (MDSCs)-inducing factors and then inhibits the phosphorylation level of STAT3 protein, the regulatory factor of MDSCs differentiation, to reduce the MDSCs formation ability. Moreover, vaccines reduce the expression of functional molecules associated with MDSCs may by inhibiting the phosphorylation level of the JAK1-STAT1 and JAK2-STAT3 pathways in tumor tissues to attenuate the immunosuppressive function of MDSCs. CONCLUSIONS: Immunotherapy with Listeria-vectored cervical cancer vaccines significantly reduces the level and function of MDSCs in vivo, which is the key point to the destruction of immunosuppression. The study for the first to elucidate the mechanism of breaking the immunosuppression.


Subject(s)
Cancer Vaccines , Myeloid-Derived Suppressor Cells , Uterine Cervical Neoplasms , Female , Humans , Mice , Animals , Myeloid-Derived Suppressor Cells/metabolism , Myeloid-Derived Suppressor Cells/pathology , Cancer Vaccines/metabolism , Uterine Cervical Neoplasms/prevention & control , Uterine Cervical Neoplasms/metabolism , Phosphorylation , Signal Transduction
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