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1.
Cell ; 185(22): 4082-4098.e22, 2022 10 27.
Article in English | MEDLINE | ID: mdl-36198318

ABSTRACT

The mechanism that initiates autophagosome formation on the ER in multicellular organisms is elusive. Here, we showed that autophagy stimuli trigger Ca2+ transients on the outer surface of the ER membrane, whose amplitude, frequency, and duration are controlled by the metazoan-specific ER transmembrane autophagy protein EPG-4/EI24. Persistent Ca2+ transients/oscillations on the cytosolic ER surface in EI24-depleted cells cause accumulation of FIP200 autophagosome initiation complexes on the ER. This defect is suppressed by attenuating ER Ca2+ transients. Multi-modal SIM analysis revealed that Ca2+ transients on the ER trigger the formation of dynamic and fusion-prone liquid-like FIP200 puncta. Starvation-induced Ca2+ transients on lysosomes also induce FIP200 puncta that further move to the ER. Multiple FIP200 puncta on the ER, whose association depends on the ER proteins VAPA/B and ATL2/3, assemble into autophagosome formation sites. Thus, Ca2+ transients are crucial for triggering phase separation of FIP200 to specify autophagosome initiation sites in metazoans.


Subject(s)
Autophagosomes , Calcium , Animals , Autophagosomes/metabolism , Calcium/metabolism , Endoplasmic Reticulum/metabolism , Autophagy-Related Proteins/metabolism , Autophagy , Cell Cycle Proteins/metabolism
2.
Cell ; 183(3): 730-738.e13, 2020 10 29.
Article in English | MEDLINE | ID: mdl-32979942

ABSTRACT

SARS-CoV-2 is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins, the detailed architecture of the intact virus remains to be unveiled. Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryoelectron tomography (cryo-ET) and subtomogram averaging (STA). Native structures of the S proteins in pre- and postfusion conformations were determined to average resolutions of 8.7-11 Å. Compositions of the N-linked glycans from the native spikes were analyzed by mass spectrometry, which revealed overall processing states of the native glycans highly similar to that of the recombinant glycoprotein glycans. The native conformation of the ribonucleoproteins (RNPs) and their higher-order assemblies were revealed. Overall, these characterizations revealed the architecture of the SARS-CoV-2 virus in exceptional detail and shed light on how the virus packs its ∼30-kb-long single-segmented RNA in the ∼80-nm-diameter lumen.


Subject(s)
Betacoronavirus/physiology , Betacoronavirus/ultrastructure , Virus Assembly , Animals , Chlorocebus aethiops , Cryoelectron Microscopy , Humans , Mass Spectrometry , Models, Molecular , Protein Conformation , SARS-CoV-2 , Vero Cells , Viral Proteins/chemistry , Viral Proteins/ultrastructure , Virus Cultivation
3.
Cell ; 182(3): 563-577.e20, 2020 08 06.
Article in English | MEDLINE | ID: mdl-32615086

ABSTRACT

Adipose tissues dynamically remodel their cellular composition in response to external cues by stimulating beige adipocyte biogenesis; however, the developmental origin and pathways regulating this process remain insufficiently understood owing to adipose tissue heterogeneity. Here, we employed single-cell RNA-seq and identified a unique subset of adipocyte progenitor cells (APCs) that possessed the cell-intrinsic plasticity to give rise to beige fat. This beige APC population is proliferative and marked by cell-surface proteins, including PDGFRα, Sca1, and CD81. Notably, CD81 is not only a beige APC marker but also required for de novo beige fat biogenesis following cold exposure. CD81 forms a complex with αV/ß1 and αV/ß5 integrins and mediates the activation of integrin-FAK signaling in response to irisin. Importantly, CD81 loss causes diet-induced obesity, insulin resistance, and adipose tissue inflammation. These results suggest that CD81 functions as a key sensor of external inputs and controls beige APC proliferation and whole-body energy homeostasis.


Subject(s)
Adipogenesis/genetics , Adipose Tissue, Beige/metabolism , Energy Metabolism/genetics , Focal Adhesion Kinase 1/metabolism , Signal Transduction/genetics , Stem Cells/metabolism , Tetraspanin 28/metabolism , Adipocytes/metabolism , Adipose Tissue, Beige/cytology , Adipose Tissue, Beige/growth & development , Adipose Tissue, White/metabolism , Adult , Animals , Ataxin-1/metabolism , Female , Fibronectins/pharmacology , Focal Adhesion Kinase 1/genetics , Humans , Inflammation/genetics , Inflammation/metabolism , Insulin Resistance/genetics , Integrins/metabolism , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Middle Aged , Obesity/genetics , Obesity/metabolism , RNA-Seq , Receptor, Platelet-Derived Growth Factor alpha/metabolism , Signal Transduction/drug effects , Single-Cell Analysis , Stem Cells/cytology , Tetraspanin 28/genetics
4.
Cell ; 170(5): 1028-1043.e19, 2017 Aug 24.
Article in English | MEDLINE | ID: mdl-28841410

ABSTRACT

Cis-regulatory elements (CREs) are commonly recognized by correlative chromatin features, yet the molecular composition of the vast majority of CREs in chromatin remains unknown. Here, we describe a CRISPR affinity purification in situ of regulatory elements (CAPTURE) approach to unbiasedly identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated nuclease-deficient Cas9 protein and sequence-specific guide RNAs, we show high-resolution and selective isolation of chromatin interactions at a single-copy genomic locus. Purification of human telomeres using CAPTURE identifies known and new telomeric factors. In situ capture of individual constituents of the enhancer cluster controlling human ß-globin genes establishes evidence for composition-based hierarchical organization. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally regulated super-enhancers reveals spatial features that causally control gene transcription. Thus, comprehensive and unbiased analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease.


Subject(s)
CRISPR-Cas Systems , Endonucleases/metabolism , Genetic Techniques , Regulatory Elements, Transcriptional , Animals , Biotinylation , Cells, Cultured , Embryonic Stem Cells/metabolism , Endonucleases/genetics , Enhancer Elements, Genetic , Humans , K562 Cells , Mice , RNA, Guide, Kinetoplastida/metabolism , Telomere/metabolism , beta-Globins/genetics
5.
Mol Cell ; 82(20): 3810-3825.e8, 2022 10 20.
Article in English | MEDLINE | ID: mdl-36108631

ABSTRACT

Human mixed-lineage leukemia (MLL) family methyltransferases methylate histone H3 lysine 4 to different methylation states (me1/me2/me3) with distinct functional outputs, but the mechanism underlying the different product specificities of MLL proteins remains unclear. Here, we develop methodologies to quantitatively measure the methylation rate difference between mono-, di-, and tri-methylation steps and demonstrate that MLL proteins possess distinct product specificities in the context of the minimum MLL-RBBP5-ASH2L complex. Comparative structural analyses of MLL complexes by X-ray crystal structures, fluorine-19 nuclear magnetic resonance, and molecular dynamics simulations reveal that the dynamics of two conserved tyrosine residues at the "F/Y (phenylalanine/tyrosine) switch" positions fine-tune the product specificity. The variation in the intramolecular interaction between SET-N and SET-C affects the F/Y switch dynamics, thus determining the product specificities of MLL proteins. These results indicate a modified F/Y switch rule applicable for most SET domain methyltransferases and implicate the functional divergence of MLL proteins.


Subject(s)
Histone-Lysine N-Methyltransferase , Leukemia , Humans , Histone-Lysine N-Methyltransferase/metabolism , Histones/metabolism , Methyltransferases/genetics , Methyltransferases/metabolism , Lysine/metabolism , Fluorine/metabolism , Myeloid-Lymphoid Leukemia Protein/metabolism , Tyrosine , Phenylalanine
6.
Nature ; 600(7888): 314-318, 2021 12.
Article in English | MEDLINE | ID: mdl-34819664

ABSTRACT

Thermogenesis in brown and beige adipose tissue has important roles in maintaining body temperature and countering the development of metabolic disorders such as obesity and type 2 diabetes1,2. Although much is known about commitment and activation of brown and beige adipose tissue, its multiple and abundant immunological factors have not been well characterized3-6. Here we define a critical role of IL-27-IL-27Rα signalling in improving thermogenesis, protecting against diet-induced obesity and ameliorating insulin resistance. Mechanistic studies demonstrate that IL-27 directly targets adipocytes, activating p38 MAPK-PGC-1α signalling and stimulating the production of UCP1. Notably, therapeutic administration of IL-27 ameliorated metabolic morbidities in well-established mouse models of obesity. Consistently, individuals with obesity show significantly decreased levels of serum IL-27, which can be restored after bariatric surgery. Collectively, these findings show that IL-27 has an important role in orchestrating metabolic programs, and is a highly promising target for anti-obesity immunotherapy.


Subject(s)
Adipocytes/metabolism , Energy Metabolism , Interleukin-27/metabolism , Thermogenesis , Animals , Bariatric Surgery , Disease Models, Animal , Female , Humans , Insulin Resistance , Interleukin-27/blood , Interleukin-27/therapeutic use , Male , Mice , Obesity/blood , Obesity/drug therapy , Obesity/metabolism , Obesity/prevention & control , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism , Receptors, Interleukin/metabolism , Signal Transduction , Uncoupling Protein 1/biosynthesis , p38 Mitogen-Activated Protein Kinases/metabolism
7.
Mol Cell ; 73(6): 1127-1137.e5, 2019 03 21.
Article in English | MEDLINE | ID: mdl-30772175

ABSTRACT

We have previously proposed that selective inheritance, the limited transmission of damaging mtDNA mutations from mother to offspring, is based on replication competition in Drosophila melanogaster. This model, which stems from our observation that wild-type mitochondria propagate much more vigorously in the fly ovary than mitochondria carrying fitness-impairing mutations, implies that germ cells recognize the fitness of individual mitochondria and selectively boost the propagation of healthy ones. Here, we demonstrate that the protein kinase PINK1 preferentially accumulates on mitochondria enriched for a deleterious mtDNA mutation. PINK1 phosphorylates Larp to inhibit protein synthesis on the mitochondrial outer membrane. Impaired local translation on defective mitochondria in turn limits the replication of their mtDNA and hence the transmission of deleterious mutations to the offspring. Our work confirms that selective inheritance occurs at the organelle level during Drosophila oogenesis and provides molecular entry points to test this model in other systems.


Subject(s)
DNA Replication , DNA, Mitochondrial/genetics , Drosophila Proteins/metabolism , Drosophila melanogaster/enzymology , Mitochondria/enzymology , Mitochondrial Membranes/enzymology , Mitochondrial Proteins/biosynthesis , Mutation , Oocytes/enzymology , Protein Serine-Threonine Kinases/metabolism , Animals , Animals, Genetically Modified , DNA, Mitochondrial/biosynthesis , Drosophila Proteins/genetics , Drosophila melanogaster/genetics , Female , Inheritance Patterns , Mitochondria/genetics , Mitochondrial Proteins/genetics , Oogenesis , Organelle Biogenesis , Phosphorylation , Protein Serine-Threonine Kinases/genetics , Protein Stability , Transcription Factors/genetics , Transcription Factors/metabolism
8.
Proc Natl Acad Sci U S A ; 121(1): e2313773120, 2024 Jan 02.
Article in English | MEDLINE | ID: mdl-38147648

ABSTRACT

Climate change is a new disrupter to global fisheries systems and their governance frameworks. It poses a pressing management challenge, particularly in China, which is renowned as the world's largest fishing country and seafood producer. As climate change continues to intensify in the region and climate awareness grows within the country's national policy, the need to understand China's fisheries' resilience to the escalating climate crisis becomes paramount. In this study, we conduct an interdisciplinary analysis to assess the vulnerability and risk of China's marine capture fisheries in response to climate change. This study employs a spatially explicit, indicator-based approach with a coupled social-ecological framework, focusing on 67 species and 11 coastal regions. By integrating diverse sets of climatic, ecological, economic, societal, and governance indicators and information, we elucidate the factors that could hinder climate adaptation, including a limited understanding of fish early life stages, uncertainty in seafood production, unequal allocation and accessibility of resources, and inadequate consideration of inclusive governance and adaptive management. Our results show that species, which have managed to survive the stress of overfishing, demonstrate a remarkable ability to adapt to climate change. However, collapsing stocks such as large yellow croaker face a high risk due to the synergistic effects of inherent biological traits and external management interventions. We emphasize the imperative to build institutional, scientific, and social capacity to support fisheries adaptation. The scientific insights provided by this study can inform fisheries management decisions and promote the operationalization of climate-resilient fisheries in China and other regions.


Subject(s)
Conservation of Natural Resources , Fisheries , Animals , Climate Change , Social Environment , China , Ecosystem , Fishes
9.
Hum Mol Genet ; 33(9): 752-767, 2024 Apr 18.
Article in English | MEDLINE | ID: mdl-38271183

ABSTRACT

Mutations in the Kunitz-type serine protease inhibitor HAI-2, encoded by SPINT2, are responsible for the pathogenesis of syndromic congenital sodium diarrhea (SCSD), an intractable secretory diarrhea of infancy. Some of the mutations cause defects in the functionally required Kunitz domain 1 and/or subcellular targeting signals. Almost all SCSD patients, however, harbor SPINT2 missense mutations that affect the functionally less important Kunitz domain 2. How theses single amino acid substitutions inactivate HAI-2 was, here, investigated by the doxycycline-inducible expression of three of these mutants in HAI-2-knockout Caco-2 human colorectal adenocarcinoma cells. Examining protein expressed from these HAI-2 mutants reveals that roughly 50% of the protein is synthesized as disulfide-linked oligomers that lose protease inhibitory activity due to the distortion of the Kunitz domains by disarrayed disulfide bonding. Although the remaining protein is synthesized as monomers, its glycosylation status suggests that the HAI-2 monomer remains in the immature, lightly glycosylated form, and is not converted to the heavily glycosylated mature form. Heavily glycosylated HAI-2 possesses full anti-protease activity and appropriate subcellular targeting signals, including the one embedded in the complex-type N-glycan. As predicted, these HAI-2 mutants cannot suppress the excessive prostasin proteolysis caused by HAI-2 deletion. The oligomerization and glycosylation defects have also been observed in a colorectal adenocarcinoma line that harbors one of these SPINT2 missense mutations. Our study reveals that the abnormal protein folding and N-glycosylation can cause widespread HAI-2 inactivation in SCSD patents.


Subject(s)
Adenocarcinoma , Colorectal Neoplasms , Serine Endopeptidases , Humans , Membrane Glycoproteins/metabolism , Caco-2 Cells , Glycosylation , Mutation , Diarrhea/congenital , Protein Folding , Colorectal Neoplasms/genetics , Disulfides , Proteinase Inhibitory Proteins, Secretory/genetics
10.
PLoS Biol ; 21(12): e3002433, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38091366

ABSTRACT

The emerging and global spread of a novel plasmid-mediated colistin resistance gene, mcr-1, threatens human health. Expression of the MCR-1 protein affects bacterial fitness and this cost correlates with lipid A perturbation. However, the exact molecular mechanism remains unclear. Here, we identified the MCR-1 M6 variant carrying two-point mutations that conferred co-resistance to ß-lactam antibiotics. Compared to wild-type (WT) MCR-1, this variant caused severe disturbance in lipid A, resulting in up-regulation of L, D-transpeptidases (LDTs) pathway, which explains co-resistance to ß-lactams. Moreover, we show that a lipid A loading pocket is localized at the linker domain of MCR-1 where these 2 mutations are located. This pocket governs colistin resistance and bacterial membrane permeability, and the mutated pocket in M6 enhances the binding affinity towards lipid A. Based on this new information, we also designed synthetic peptides derived from M6 that exhibit broad-spectrum antimicrobial activity, exposing a potential vulnerability that could be exploited for future antimicrobial drug design.


Subject(s)
Colistin , Escherichia coli Proteins , Humans , Colistin/pharmacology , Anti-Bacterial Agents/pharmacology , beta Lactam Antibiotics , Lipid A , Antimicrobial Peptides , Monobactams , Plasmids , Drug Resistance, Bacterial/genetics , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Microbial Sensitivity Tests
11.
Nat Rev Genet ; 21(8): 493-502, 2020 08.
Article in English | MEDLINE | ID: mdl-32235907

ABSTRACT

Accurate prediction of disease risk based on the genetic make-up of an individual is essential for effective prevention and personalized treatment. Nevertheless, to date, individual genetic variants from genome-wide association studies have achieved only moderate prediction of disease risk. The aggregation of genetic variants under a polygenic model shows promising improvements in prediction accuracies. Increasingly, electronic health records (EHRs) are being linked to patient genetic data in biobanks, which provides new opportunities for developing and applying polygenic risk scores in the clinic, to systematically examine and evaluate patient susceptibilities to disease. However, the heterogeneous nature of EHR data brings forth many practical challenges along every step of designing and implementing risk prediction strategies. In this Review, we present the unique considerations for using genotype and phenotype data from biobank-linked EHRs for polygenic risk prediction.


Subject(s)
Electronic Health Records , Genetic Association Studies , Genetic Predisposition to Disease , Multifactorial Inheritance , Algorithms , Computational Biology/methods , Genome-Wide Association Study , Genomics/methods , Genotype , Humans , Phenotype , Reproducibility of Results , Risk Assessment , Risk Factors
12.
Nature ; 579(7797): 152-157, 2020 03.
Article in English | MEDLINE | ID: mdl-32076264

ABSTRACT

GPR52 is a class-A orphan G-protein-coupled receptor that is highly expressed in the brain and represents a promising therapeutic target for the treatment of Huntington's disease and several psychiatric disorders1,2. Pathological malfunction of GPR52 signalling occurs primarily through the heterotrimeric Gs protein2, but it is unclear how GPR52 and Gs couple for signal transduction and whether a native ligand or other activating input is required. Here we present the high-resolution structures of human GPR52 in three states: a ligand-free state, a Gs-coupled self-activation state and a potential allosteric ligand-bound state. Together, our structures reveal that extracellular loop 2 occupies the orthosteric binding pocket and operates as a built-in agonist, conferring an intrinsically high level of basal activity to GPR523. A fully active state is achieved when Gs is coupled to GPR52 in the absence of an external agonist. The receptor also features a side pocket for ligand binding. These insights into the structure and function of GPR52 could improve our understanding of other self-activated GPCRs, enable the identification of endogenous and tool ligands, and guide drug discovery efforts that target GPR52.


Subject(s)
Receptors, G-Protein-Coupled/chemistry , Receptors, G-Protein-Coupled/metabolism , Allosteric Regulation , Allosteric Site , Amino Acid Motifs , Amino Acid Sequence , Apoproteins/agonists , Apoproteins/chemistry , Apoproteins/metabolism , Binding Sites , Cryoelectron Microscopy , Crystallography, X-Ray , GTP-Binding Protein alpha Subunits, Gs/chemistry , GTP-Binding Protein alpha Subunits, Gs/metabolism , GTP-Binding Protein alpha Subunits, Gs/ultrastructure , Humans , Ligands , Models, Molecular , Receptors, G-Protein-Coupled/agonists , Receptors, G-Protein-Coupled/ultrastructure
13.
Proc Natl Acad Sci U S A ; 120(50): e2309359120, 2023 Dec 12.
Article in English | MEDLINE | ID: mdl-38048463

ABSTRACT

Tandem DNA repeats are often organized into heterochromatin that is crucial for genome organization and stability. Recent studies revealed that individual repeats within tandem DNA repeats can behave very differently. How DNA repeats are assembled into distinct heterochromatin structures remains poorly understood. Here, we developed a genome-wide genetic screen using a reporter gene at different units in a repeat array. This screen led to identification of a conserved protein Rex1BD required for heterochromatin silencing. Our structural analysis revealed that Rex1BD forms a four-helix bundle structure with a distinct charged electrostatic surface. Mechanistically, Rex1BD facilitates the recruitment of Clr6 histone deacetylase (HDAC) by interacting with histones. Interestingly, Rex1BD also interacts with the 14-3-3 protein Rad25, which is responsible for recruiting the RITS (RNA-induced transcriptional silencing) complex to DNA repeats. Our results suggest that coordinated action of Rex1BD and Rad25 mediates formation of distinct heterochromatin structure at DNA repeats via linking RNAi and HDAC pathways.


Subject(s)
Schizosaccharomyces pombe Proteins , Schizosaccharomyces , RNA Interference , Heterochromatin/genetics , Heterochromatin/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/metabolism , 14-3-3 Proteins/genetics , 14-3-3 Proteins/metabolism , Histone Deacetylases/metabolism , DNA/metabolism , Tandem Repeat Sequences
14.
Proc Natl Acad Sci U S A ; 120(18): e2213332120, 2023 05 02.
Article in English | MEDLINE | ID: mdl-37094167

ABSTRACT

Among the current five Variants of Concern, infections caused by SARS-CoV-2 B.1.617.2 (Delta) variant are often associated with the greatest severity. Despite recent advances on the molecular basis of elevated pathogenicity using recombinant proteins, the architecture of intact Delta virions remains veiled. Moreover, pieces of molecular evidence for the detailed mechanism of S-mediated membrane fusion are missing. Here, we showed the pleomorphic nature of Delta virions from electron beam inactivated samples and reported the in situ structure and distribution of S on the authentic Delta variant. We also captured the virus-virus fusion events, which provided pieces of structural evidence for Delta's attenuated dependency on cellular factors for fusion activation, and proposed a model of S-mediated membrane fusion. Besides, site-specific glycan analysis revealed increased oligomannose-type glycosylation of native Delta S than that of the WT S. Together, these results disclose distinctive factors of Delta being the most virulent SARS-CoV-2 variant.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Membrane Fusion , Glycosylation , Spike Glycoprotein, Coronavirus
15.
J Cell Sci ; 136(12)2023 06 15.
Article in English | MEDLINE | ID: mdl-37232206

ABSTRACT

Mitochondrial dynamics regulate the quality and morphology of mitochondria. Calcium (Ca2+) plays an important role in regulating mitochondrial function. Here, we investigated the effects of optogenetically engineered Ca2+ signaling on mitochondrial dynamics. More specifically, customized illumination conditions could trigger unique Ca2+ oscillation waves to trigger specific signaling pathways. In this study, we found that modulating Ca2+ oscillations by increasing the light frequency, intensity and exposure time could drive mitochondria toward the fission state, mitochondrial dysfunction, autophagy and cell death. Moreover, illumination triggered phosphorylation at the Ser616 residue but not the Ser637 residue of the mitochondrial fission protein, dynamin-related protein 1 (DRP1, encoded by DNM1L), via the activation of Ca2+-dependent kinases CaMKII, ERK and CDK1. However, optogenetically engineered Ca2+ signaling did not activate calcineurin phosphatase to dephosphorylate DRP1 at Ser637. In addition, light illumination had no effect on the expression levels of the mitochondrial fusion proteins mitofusin 1 (MFN1) and 2 (MFN2). Overall, this study provides an effective and innovative approach to altering Ca2+ signaling for controlling mitochondrial fission with a more precise resolution than pharmacological approaches in the temporal dimension.


Subject(s)
Calcium , Mitochondrial Dynamics , Mitochondrial Dynamics/physiology , Calcium/metabolism , Dynamins/genetics , Dynamins/metabolism , Mitochondria/metabolism , Phosphorylation , Cell Death , Mitochondrial Proteins/metabolism
16.
Brief Bioinform ; 24(6)2023 09 22.
Article in English | MEDLINE | ID: mdl-37769630

ABSTRACT

Single-cell RNA sequencing (scRNA-seq) is a widely used technique for characterizing individual cells and studying gene expression at the single-cell level. Clustering plays a vital role in grouping similar cells together for various downstream analyses. However, the high sparsity and dimensionality of large scRNA-seq data pose challenges to clustering performance. Although several deep learning-based clustering algorithms have been proposed, most existing clustering methods have limitations in capturing the precise distribution types of the data or fully utilizing the relationships between cells, leaving a considerable scope for improving the clustering performance, particularly in detecting rare cell populations from large scRNA-seq data. We introduce DeepScena, a novel single-cell hierarchical clustering tool that fully incorporates nonlinear dimension reduction, negative binomial-based convolutional autoencoder for data fitting, and a self-supervision model for cell similarity enhancement. In comprehensive evaluation using multiple large-scale scRNA-seq datasets, DeepScena consistently outperformed seven popular clustering tools in terms of accuracy. Notably, DeepScena exhibits high proficiency in identifying rare cell populations within large datasets that contain large numbers of clusters. When applied to scRNA-seq data of multiple myeloma cells, DeepScena successfully identified not only previously labeled large cell types but also subpopulations in CD14 monocytes, T cells and natural killer cells, respectively.


Subject(s)
Single-Cell Analysis , Single-Cell Gene Expression Analysis , Sequence Analysis, RNA/methods , Single-Cell Analysis/methods , Algorithms , Cluster Analysis , Gene Expression Profiling/methods
17.
PLoS Pathog ; 19(3): e1011187, 2023 03.
Article in English | MEDLINE | ID: mdl-36888692

ABSTRACT

The current study reveals that in chronic TB, the B cell-deficient µMT strain, relative to wild-type (WT) C57BL/6 mice, displays in the lungs lower levels of inflammation that are associated with decreased CD4+ T cell proliferation, diminished Th1 response, and enhanced levels of interleukin (IL)-10. The latter result raises the possibility that B cells may restrict lung expression of IL-10 in chronic TB. These observations are recapitulated in WT mice depleted for B cells using anti-CD20 antibodies. IL-10 receptor (IL-10R) blockade reverses the phenotypes of decreased inflammation and attenuated CD4+ T cell responses in B cell-depleted mice. Together, these results suggest that in chronic murine TB, B cells, by virtue of their capacity to restrict expression of the anti-inflammatory and immunosuppressive IL-10 in the lungs, promote the development of a robust protective Th1 response, thereby optimizing anti-TB immunity. This vigorous Th1 immunity and restricted IL-10 expression may, however, allow the development of inflammation to a level that can be detrimental to the host. Indeed, decreased lung inflammation observed in chronically infected B cell-deficient mice, which exhibit augmented lung IL-10 levels, is associated with a survival advantage relative to WT animals. Collectively, the results reveal that in chronic murine TB, B cells play a role in modulating the protective Th1 immunity and the anti-inflammatory IL-10 response, which results in augmentation of lung inflammation that can be host-detrimental. Intriguingly, in tuberculous human lungs, conspicuous B cell aggregates are present in close proximity to tissue-damaging lesions manifesting necrosis and cavitation, suggesting the possibility that in human TB, B cells may contribute to the development of exacerbated pathology that is known to promote transmission. Since transmission is a major hindrance to TB control, investigating into whether B cells can shape the development of severe pulmonic pathological responses in tuberculous individuals is warranted.


Subject(s)
Mycobacterium tuberculosis , Tuberculosis, Pulmonary , Tuberculosis , Mice , Humans , Animals , Interleukin-10/metabolism , Mice, Inbred C57BL , Inflammation , Th1 Cells
18.
PLoS Pathog ; 19(5): e1011380, 2023 05.
Article in English | MEDLINE | ID: mdl-37155712

ABSTRACT

Many herbivorous insects rely on plant volatiles to locate their host plants. Vector-borne viral infections induce changes in plant volatiles, which render infected plants more attractive to insect vectors. However, the detailed mechanisms underlying the olfactory responses of insect vectors induced by the volatiles produced by virus-infected plants are poorly understood. Here, we show that volatiles emitted by pepper (Capsicum annuum) plants infected with tomato zonate spot virus (TZSV), particularly the volatile cis-3-hexenal, which is recognized by chemosensory protein 1 of the thrips Frankliniella intonsa (FintCSP1), are more attractive to F. intonsa than the volatiles emitted by non-infected pepper plants. FintCSP1 is highly abundant in the antenna of F. intonsa. Silencing of FintCSP1 significantly decreased electroantennogram responses of F. intonsa antennae to cis-3-hexenal and impaired thrips' responses to TZSV-infected pepper plants and cis-3-hexenal, as assessed using a Y-tube olfactometer. Three-dimensional model predictions indicated that FintCSP1 consists of seven α-helixes and two disulfide bridges. Molecular docking analysis suggested that cis-3-hexenal is positioned deep inside the binding pocket of FintCSP1 and binds to residues of the protein. We combined site-directed mutagenesis and fluorescence binding assays and identified three hydrophilic residues, Lys26, Thr28, and Glu67, of FintCSP1 as being critical for cis-3-hexenal binding. Furthermore, CSP of F. occidentalis (FoccCSP) is also a key olfactory protein involved in modulating the behaviour of F. occidentalis to TZSV-infected pepper. This study revealed the specific binding characteristics of CSPs to cis-3-hexenal and confirmed the general hypothesis that virus infections induce changes in host volatiles, which can be recognized by the olfactory proteins of the insect vector to enhance vector attraction and this may facilitate viral spread and transmission.


Subject(s)
Capsicum , Plant Viruses , Solanum lycopersicum , Thysanoptera , Animals , Thysanoptera/physiology , Molecular Docking Simulation
19.
Circ Res ; 132(2): e59-e77, 2023 01 20.
Article in English | MEDLINE | ID: mdl-36583384

ABSTRACT

BACKGROUND: PKA (protein kinase A)-mediated phosphorylation of cardiac RyR2 (ryanodine receptor 2) has been extensively studied for decades, but the physiological significance of PKA phosphorylation of RyR2 remains poorly understood. Recent determination of high-resolution 3-dimensional structure of RyR2 in complex with CaM (calmodulin) reveals that the major PKA phosphorylation site in RyR2, serine-2030 (S2030), is located within a structural pathway of CaM-dependent inactivation of RyR2. This novel structural insight points to a possible role of PKA phosphorylation of RyR2 in CaM-dependent inactivation of RyR2, which underlies the termination of Ca2+ release and induction of cardiac Ca2+ alternans. METHODS: We performed single-cell endoplasmic reticulum Ca2+ imaging to assess the impact of S2030 mutations on Ca2+ release termination in human embryonic kidney 293 cells. Here we determined the role of the PKA site RyR2-S2030 in a physiological setting, we generated a novel mouse model harboring the S2030L mutation and carried out confocal Ca2+ imaging. RESULTS: We found that mutations, S2030D, S2030G, S2030L, S2030V, and S2030W reduced the endoplasmic reticulum luminal Ca2+ level at which Ca2+ release terminates (the termination threshold), whereas S2030P and S2030R increased the termination threshold. S2030A and S2030T had no significant impact on release termination. Furthermore, CaM-wild-type increased, whereas Ca2+ binding deficient CaM mutant (CaM-M [a loss-of-function CaM mutation with all 4 EF-hand motifs mutated]), PKA, and Ca2+/CaMKII (CaM-dependent protein kinase II) reduced the termination threshold. The S2030L mutation abolished the actions of CaM-wild-type, CaM-M, and PKA, but not CaMKII, in Ca2+ release termination. Moreover, we showed that isoproterenol and CaM-M suppressed pacing-induced Ca2+ alternans and accelerated Ca2+ transient recovery in intact working hearts, whereas CaM-wild-type exerted an opposite effect. The impact of isoproterenol was partially and fully reversed by the PKA inhibitor N-[2-(p-bromocinnamylamino)ethyl]-5-isoquinoline-sulfonamide and the CaMKII inhibitor N-[2-[N-(4-chlorocinnamyl)-N-methylaminomethyl]phenyl]-N-(2-hydroxyethyl)-4-methoxybenzenesulfonamide individually and together, respectively. S2030L abolished the impact of CaM-wild-type, CaM-M, and N-[2-(p-bromocinnamylamino)ethyl]-5-isoquinoline-sulfonamide-sensitive component, but not the N-[2-[N-(4-chlorocinnamyl)-N-methylaminomethyl]phenyl]-N-(2-hydroxyethyl)-4-methoxybenzenesulfonamide-sensitive component, of isoproterenol.


Subject(s)
Ryanodine Receptor Calcium Release Channel , Serine , Mice , Animals , Humans , Isoproterenol/pharmacology , Ryanodine Receptor Calcium Release Channel/metabolism , Serine/metabolism , Serine/pharmacology , Cyclic AMP-Dependent Protein Kinases/metabolism , Calmodulin/metabolism , Calcium-Calmodulin-Dependent Protein Kinase Type 2/genetics , Calcium-Calmodulin-Dependent Protein Kinase Type 2/metabolism , Isoquinolines/pharmacology , Sulfonamides/pharmacology , Calcium/metabolism , Myocytes, Cardiac/metabolism , Sarcoplasmic Reticulum/metabolism
20.
Circ Res ; 133(2): 177-192, 2023 07 07.
Article in English | MEDLINE | ID: mdl-37325910

ABSTRACT

BACKGROUND: A loss-of-function cardiac ryanodine receptor (RyR2) mutation, I4855M+/-, has recently been linked to a new cardiac disorder termed RyR2 Ca2+ release deficiency syndrome (CRDS) as well as left ventricular noncompaction (LVNC). The mechanism by which RyR2 loss-of-function causes CRDS has been extensively studied, but the mechanism underlying RyR2 loss-of-function-associated LVNC is unknown. Here, we determined the impact of a CRDS-LVNC-associated RyR2-I4855M+/- loss-of-function mutation on cardiac structure and function. METHODS: We generated a mouse model expressing the CRDS-LVNC-associated RyR2-I4855M+/- mutation. Histological analysis, echocardiography, ECG recording, and intact heart Ca2+ imaging were performed to characterize the structural and functional consequences of the RyR2-I4855M+/- mutation. RESULTS: As in humans, RyR2-I4855M+/- mice displayed LVNC characterized by cardiac hypertrabeculation and noncompaction. RyR2-I4855M+/- mice were highly susceptible to electrical stimulation-induced ventricular arrhythmias but protected from stress-induced ventricular arrhythmias. Unexpectedly, the RyR2-I4855M+/- mutation increased the peak Ca2+ transient but did not alter the L-type Ca2+ current, suggesting an increase in Ca2+-induced Ca2+ release gain. The RyR2-I4855M+/- mutation abolished sarcoplasmic reticulum store overload-induced Ca2+ release or Ca2+ leak, elevated sarcoplasmic reticulum Ca2+ load, prolonged Ca2+ transient decay, and elevated end-diastolic Ca2+ level upon rapid pacing. Immunoblotting revealed increased level of phosphorylated CaMKII (Ca2+-calmodulin dependent protein kinases II) but unchanged levels of CaMKII, calcineurin, and other Ca2+ handling proteins in the RyR2-I4855M+/- mutant compared with wild type. CONCLUSIONS: The RyR2-I4855M+/- mutant mice represent the first RyR2-associated LVNC animal model that recapitulates the CRDS-LVNC overlapping phenotype in humans. The RyR2-I4855M+/- mutation increases the peak Ca2+ transient by increasing the Ca2+-induced Ca2+ release gain and the end-diastolic Ca2+ level by prolonging Ca2+ transient decay. Our data suggest that the increased peak-systolic and end-diastolic Ca2+ levels may underlie RyR2-associated LVNC.


Subject(s)
Heart Defects, Congenital , Ryanodine Receptor Calcium Release Channel , Animals , Humans , Mice , Arrhythmias, Cardiac/metabolism , Calcium/metabolism , Calcium Signaling/physiology , Calcium-Calmodulin-Dependent Protein Kinase Type 2/metabolism , Heart Defects, Congenital/metabolism , Myocytes, Cardiac/metabolism , Ryanodine Receptor Calcium Release Channel/genetics , Ryanodine Receptor Calcium Release Channel/metabolism , Sarcoplasmic Reticulum/metabolism
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