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1.
Cell ; 184(4): 957-968.e21, 2021 02 18.
Article in English | MEDLINE | ID: mdl-33567265

ABSTRACT

Ligand-gated ion channels mediate signal transduction at chemical synapses and transition between resting, open, and desensitized states in response to neurotransmitter binding. Neurotransmitters that produce maximum open channel probabilities (Po) are full agonists, whereas those that yield lower than maximum Po are partial agonists. Cys-loop receptors are an important class of neurotransmitter receptors, yet a structure-based understanding of the mechanism of partial agonist action has proven elusive. Here, we study the glycine receptor with the full agonist glycine and the partial agonists taurine and γ-amino butyric acid (GABA). We use electrophysiology to show how partial agonists populate agonist-bound, closed channel states and cryo-EM reconstructions to illuminate the structures of intermediate, pre-open states, providing insights into previously unseen conformational states along the receptor reaction pathway. We further correlate agonist-induced conformational changes to Po across members of the receptor family, providing a hypothetical mechanism for partial and full agonist action at Cys-loop receptors.


Subject(s)
Ion Channel Gating , Receptors, Glycine/agonists , Receptors, Glycine/metabolism , Animals , Binding Sites , Cell Line , Cryoelectron Microscopy , Glycine , HEK293 Cells , Humans , Imaging, Three-Dimensional , Maleates/chemistry , Models, Molecular , Mutant Proteins/chemistry , Mutant Proteins/metabolism , Mutation/genetics , Neurotransmitter Agents/metabolism , Protein Domains , Receptors, Glycine/genetics , Receptors, Glycine/ultrastructure , Styrene/chemistry , Zebrafish , gamma-Aminobutyric Acid/metabolism
2.
Cell ; 179(4): 864-879.e19, 2019 10 31.
Article in English | MEDLINE | ID: mdl-31675497

ABSTRACT

Physical or mental stress leads to neuroplasticity in the brain and increases the risk of depression and anxiety. Stress exposure causes the dysfunction of peripheral T lymphocytes. However, the pathological role and underlying regulatory mechanism of peripheral T lymphocytes in mood disorders have not been well established. Here, we show that the lack of CD4+ T cells protects mice from stress-induced anxiety-like behavior. Physical stress-induced leukotriene B4 triggers severe mitochondrial fission in CD4+ T cells, which further leads to a variety of behavioral abnormalities including anxiety, depression, and social disorders. Metabolomic profiles and single-cell transcriptome reveal that CD4+ T cell-derived xanthine acts on oligodendrocytes in the left amygdala via adenosine receptor A1. Mitochondrial fission promotes the de novo synthesis of purine via interferon regulatory factor 1 accumulation in CD4+ T cells. Our study implicates a critical link between a purine metabolic disorder in CD4+ T cells and stress-driven anxiety-like behavior.


Subject(s)
Anxiety/metabolism , Behavior, Animal/physiology , Brain Diseases, Metabolic/metabolism , Stress, Psychological/metabolism , Amygdala/metabolism , Amygdala/pathology , Animals , Anxiety/genetics , Anxiety/immunology , Anxiety/physiopathology , Brain Diseases, Metabolic/genetics , Brain Diseases, Metabolic/physiopathology , CD4-Positive T-Lymphocytes/metabolism , CD4-Positive T-Lymphocytes/pathology , Disease Models, Animal , Humans , Mice , Mitochondrial Dynamics/genetics , Oligodendroglia/metabolism , Oligodendroglia/pathology , Single-Cell Analysis , Stress, Psychological/genetics , Stress, Psychological/physiopathology , Transcriptome/genetics , Xanthine/metabolism
3.
Immunity ; 56(7): 1533-1547.e7, 2023 07 11.
Article in English | MEDLINE | ID: mdl-37354904

ABSTRACT

The crosstalk between the immune and neuroendocrine systems is critical for intestinal homeostasis and gut-brain communications. However, it remains unclear how immune cells participate in gut sensation of hormones and neurotransmitters release in response to environmental cues, such as self-lipids and microbial lipids. We show here that lipid-mediated engagement of invariant natural killer T (iNKT) cells with enterochromaffin (EC) cells, a subset of intestinal epithelial cells, promoted peripheral serotonin (5-HT) release via a CD1d-dependent manner, regulating gut motility and hemostasis. We also demonstrated that inhibitory sphingolipids from symbiotic microbe Bacteroides fragilis represses 5-HT release. Mechanistically, CD1d ligation on EC cells transduced a signal and restrained potassium conductance through activation of protein tyrosine kinase Pyk2, leading to calcium influx and 5-HT secretion. Together, our data reveal that by engaging with iNKT cells, gut chemosensory cells selectively perceive lipid antigens via CD1d to control 5-HT release, modulating intestinal and systemic homeostasis.


Subject(s)
Natural Killer T-Cells , Serotonin , Serotonin/metabolism , Lipids , Antigens, CD1d/metabolism
4.
Nature ; 630(8016): 509-515, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38750366

ABSTRACT

Temperature profoundly affects macromolecular function, particularly in proteins with temperature sensitivity1,2. However, its impact is often overlooked in biophysical studies that are typically performed at non-physiological temperatures, potentially leading to inaccurate mechanistic and pharmacological insights. Here we demonstrate temperature-dependent changes in the structure and function of TRPM4, a temperature-sensitive Ca2+-activated ion channel3-7. By studying TRPM4 prepared at physiological temperature using single-particle cryo-electron microscopy, we identified a 'warm' conformation that is distinct from those observed at lower temperatures. This conformation is driven by a temperature-dependent Ca2+-binding site in the intracellular domain, and is essential for TRPM4 function in physiological contexts. We demonstrated that ligands, exemplified by decavanadate (a positive modulator)8 and ATP (an inhibitor)9, bind to different locations of TRPM4 at physiological temperatures than at lower temperatures10,11, and that these sites have bona fide functional relevance. We elucidated the TRPM4 gating mechanism by capturing structural snapshots of its different functional states at physiological temperatures, revealing the channel opening that is not observed at lower temperatures. Our study provides an example of temperature-dependent ligand recognition and modulation of an ion channel, underscoring the importance of studying macromolecules at physiological temperatures. It also provides a potential molecular framework for deciphering how thermosensitive TRPM channels perceive temperature changes.


Subject(s)
Ion Channel Gating , TRPM Cation Channels , Temperature , Humans , Adenosine Triphosphate/metabolism , Adenosine Triphosphate/pharmacology , Binding Sites , Calcium/metabolism , Cryoelectron Microscopy , HEK293 Cells , Ion Channel Gating/drug effects , Ligands , Models, Molecular , Protein Binding , Protein Domains , Substrate Specificity , TRPM Cation Channels/agonists , TRPM Cation Channels/antagonists & inhibitors , TRPM Cation Channels/chemistry , TRPM Cation Channels/metabolism , Vanadates/chemistry , Vanadates/pharmacology , Vanadates/metabolism
5.
Nature ; 627(8004): 656-663, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38418883

ABSTRACT

Understanding the cellular processes that underlie early lung adenocarcinoma (LUAD) development is needed to devise intervention strategies1. Here we studied 246,102 single epithelial cells from 16 early-stage LUADs and 47 matched normal lung samples. Epithelial cells comprised diverse normal and cancer cell states, and diversity among cancer cells was strongly linked to LUAD-specific oncogenic drivers. KRAS mutant cancer cells showed distinct transcriptional features, reduced differentiation and low levels of aneuploidy. Non-malignant areas surrounding human LUAD samples were enriched with alveolar intermediate cells that displayed elevated KRT8 expression (termed KRT8+ alveolar intermediate cells (KACs) here), reduced differentiation, increased plasticity and driver KRAS mutations. Expression profiles of KACs were enriched in lung precancer cells and in LUAD cells and signified poor survival. In mice exposed to tobacco carcinogen, KACs emerged before lung tumours and persisted for months after cessation of carcinogen exposure. Moreover, they acquired Kras mutations and conveyed sensitivity to targeted KRAS inhibition in KAC-enriched organoids derived from alveolar type 2 (AT2) cells. Last, lineage-labelling of AT2 cells or KRT8+ cells following carcinogen exposure showed that KACs are possible intermediates in AT2-to-tumour cell transformation. This study provides new insights into epithelial cell states at the root of LUAD development, and such states could harbour potential targets for prevention or intervention.


Subject(s)
Adenocarcinoma of Lung , Cell Differentiation , Epithelial Cells , Lung Neoplasms , Animals , Humans , Mice , Adenocarcinoma of Lung/genetics , Adenocarcinoma of Lung/pathology , Alveolar Epithelial Cells/metabolism , Alveolar Epithelial Cells/pathology , Aneuploidy , Carcinogens/toxicity , Epithelial Cells/classification , Epithelial Cells/metabolism , Epithelial Cells/pathology , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Mutation , Organoids/drug effects , Organoids/metabolism , Precancerous Conditions/metabolism , Proto-Oncogene Proteins p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/metabolism , Survival Rate , Tobacco Products/adverse effects , Tobacco Products/toxicity
6.
Cell ; 159(7): 1578-90, 2014 Dec 18.
Article in English | MEDLINE | ID: mdl-25525876

ABSTRACT

Proteasomes and lysosomes constitute the major cellular systems that catabolize proteins to recycle free amino acids for energy and new protein synthesis. Tripeptidyl peptidase II (TPPII) is a large cytosolic proteolytic complex that functions in tandem with the proteasome-ubiquitin protein degradation pathway. We found that autosomal recessive TPP2 mutations cause recurrent infections, autoimmunity, and neurodevelopmental delay in humans. We show that a major function of TPPII in mammalian cells is to maintain amino acid levels and that TPPII-deficient cells compensate by increasing lysosome number and proteolytic activity. However, the overabundant lysosomes derange cellular metabolism by consuming the key glycolytic enzyme hexokinase-2 through chaperone-mediated autophagy. This reduces glycolysis and impairs the production of effector cytokines, including IFN-γ and IL-1ß. Thus, TPPII controls the balance between intracellular amino acid availability, lysosome number, and glycolysis, which is vital for adaptive and innate immunity and neurodevelopmental health.


Subject(s)
Adaptive Immunity , Aminopeptidases/metabolism , Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/metabolism , Glycolysis , Immunity, Innate , Immunologic Deficiency Syndromes/genetics , Immunologic Deficiency Syndromes/metabolism , Proteolysis , Serine Endopeptidases/metabolism , Amino Acid Sequence , Aminopeptidases/chemistry , Animals , Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/chemistry , Female , Humans , Immunologic Deficiency Syndromes/immunology , Lysosomes/metabolism , Male , Models, Molecular , Molecular Sequence Data , Pedigree , Sequence Alignment , Serine Endopeptidases/chemistry
7.
Immunity ; 50(6): 1401-1411.e4, 2019 06 18.
Article in English | MEDLINE | ID: mdl-31076358

ABSTRACT

Inflammasome activation and subsequent pyroptosis are critical defense mechanisms against microbes. However, overactivation of inflammasome leads to death of the host. Although recent studies have uncovered the mechanism of pyroptosis following inflammasome activation, how pyroptotic cell death drives pathogenesis, eventually leading to death of the host, is unknown. Here, we identified inflammasome activation as a trigger for blood clotting through pyroptosis. We have shown that canonical inflammasome activation by the conserved type III secretion system (T3SS) rod proteins from Gram-negative bacteria or noncanonical inflammasome activation by lipopolysaccharide (LPS) induced systemic blood clotting and massive thrombosis in tissues. Following inflammasome activation, pyroptotic macrophages released tissue factor (TF), an essential initiator of coagulation cascades. Genetic or pharmacological inhibition of TF abolishes inflammasome-mediated blood clotting and protects against death. Our data reveal that blood clotting is the major cause of host death following inflammasome activation and demonstrate that inflammasome bridges inflammation with thrombosis.


Subject(s)
Blood Coagulation , Inflammasomes/metabolism , Pyroptosis , Thrombosis/etiology , Thrombosis/metabolism , Animals , Bacterial Infections/complications , Bacterial Infections/microbiology , Biomarkers , Caspases/metabolism , Cell-Derived Microparticles/immunology , Cell-Derived Microparticles/metabolism , Disease Models, Animal , Humans , Lipopolysaccharides/immunology , Macrophages/immunology , Macrophages/metabolism , Mice , Monocytes/immunology , Monocytes/metabolism , Signal Transduction , Thromboplastin/metabolism , Thrombosis/blood , Thrombosis/mortality
8.
Nature ; 608(7923): 626-631, 2022 08.
Article in English | MEDLINE | ID: mdl-35896743

ABSTRACT

Emissions of the critical ozone-depleting and greenhouse gas nitrous oxide (N2O) from soils and industrial processes have increased considerably over the last decades1-3. As the final step of bacterial denitrification, N2O is reduced to chemically inert N2 (refs. 1,4) in a reaction that is catalysed by the copper-dependent nitrous oxide reductase (N2OR) (ref. 5). The assembly of its unique [4Cu:2S] active site cluster CuZ requires both the ATP-binding-cassette (ABC) complex NosDFY and the membrane-anchored copper chaperone NosL (refs. 4,6). Here we report cryo-electron microscopy structures of Pseudomonas stutzeri NosDFY and its complexes with NosL and N2OR, respectively. We find that the periplasmic NosD protein contains a binding site for a Cu+ ion and interacts specifically with NosL in its nucleotide-free state, whereas its binding to N2OR requires a conformational change that is triggered by ATP binding. Mutually exclusive structures of NosDFY in complex with NosL and with N2OR reveal a sequential metal-trafficking and assembly pathway for a highly complex copper site. Within this pathway, NosDFY acts as a mechanical energy transducer rather than as a transporter. It links ATP hydrolysis in the cytoplasm to a conformational transition of the NosD subunit in the periplasm, which is required for NosDFY to switch its interaction partner so that copper ions are handed over from the chaperone NosL to the enzyme N2OR.


Subject(s)
Bacterial Proteins , Cryoelectron Microscopy , Nitrous Oxide , Oxidoreductases , Pseudomonas stutzeri , Adenosine Triphosphate/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/ultrastructure , Binding Sites , Copper/chemistry , Copper/metabolism , Cytoplasm/enzymology , Molecular Chaperones/metabolism , Nitrous Oxide/metabolism , Oxidoreductases/chemistry , Oxidoreductases/metabolism , Oxidoreductases/ultrastructure , Periplasm/enzymology , Protein Binding , Protein Conformation , Pseudomonas stutzeri/cytology , Pseudomonas stutzeri/enzymology
9.
Genome Res ; 34(1): 134-144, 2024 Feb 07.
Article in English | MEDLINE | ID: mdl-38191205

ABSTRACT

Large-scale genetic mutant libraries are powerful approaches to interrogating genotype-phenotype correlations and identifying genes responsible for certain environmental stimuli, both of which are the central goal of life science study. We produced the first large-scale CRISPR-Cas9-induced library in a nonmodel multicellular organism, Bombyx mori We developed a piggyBac-delivered binary genome editing strategy, which can simultaneously meet the requirements of mixed microinjection, efficient multipurpose genetic operation, and preservation of growth-defect lines. We constructed a single-guide RNA (sgRNA) plasmid library containing 92,917 sgRNAs targeting promoters and exons of 14,645 protein-coding genes, established 1726 transgenic sgRNA lines following microinjection of 66,650 embryos, and generated 300 mutant lines with diverse phenotypic changes. Phenomic characterization of mutant lines identified a large set of genes responsible for visual phenotypic or economically valuable trait changes. Next, we performed pooled context-specific positive screens for tolerance to environmental pollutant cadmium exposure, and identified KWMTBOMO12902 as a strong candidate gene for breeding applications in sericulture industry. Collectively, our results provide a novel and versatile approach for functional B. mori genomics, as well as a powerful resource for identifying the potential of key candidate genes for improving various economic traits. This study also shows the effectiveness, practicality, and convenience of large-scale mutant libraries in other nonmodel organisms.


Subject(s)
Bombyx , Animals , Bombyx/genetics , RNA, Guide, CRISPR-Cas Systems , Mutagenesis , Gene Editing/methods , Animals, Genetically Modified/genetics , CRISPR-Cas Systems
10.
Nature ; 584(7822): 646-651, 2020 08.
Article in English | MEDLINE | ID: mdl-32494015

ABSTRACT

Pannexin 1 (PANX1) is an ATP-permeable channel with critical roles in a variety of physiological functions such as blood pressure regulation1, apoptotic cell clearance2 and human oocyte development3. Here we present several structures of human PANX1 in a heptameric assembly at resolutions of up to 2.8 angström, including an apo state, a caspase-7-cleaved state and a carbenoxolone-bound state. We reveal a gating mechanism that involves two ion-conducting pathways. Under normal cellular conditions, the intracellular entry of the wide main pore is physically plugged by the C-terminal tail. Small anions are conducted through narrow tunnels in the intracellular domain. These tunnels connect to the main pore and are gated by a long linker between the N-terminal helix and the first transmembrane helix. During apoptosis, the C-terminal tail is cleaved by caspase, allowing the release of ATP through the main pore. We identified a carbenoxolone-binding site embraced by W74 in the extracellular entrance and a role for carbenoxolone as a channel blocker. We identified a gap-junction-like structure using a glycosylation-deficient mutant, N255A. Our studies provide a solid foundation for understanding the molecular mechanisms underlying the channel gating and inhibition of PANX1 and related large-pore channels.


Subject(s)
Connexins/chemistry , Connexins/metabolism , Cryoelectron Microscopy , Ion Channel Gating , Nerve Tissue Proteins/chemistry , Nerve Tissue Proteins/metabolism , Patch-Clamp Techniques , Adenosine Triphosphate/metabolism , Animals , Apoproteins/chemistry , Apoproteins/metabolism , Apoproteins/ultrastructure , Apoptosis , Binding Sites/drug effects , Carbenoxolone/chemistry , Carbenoxolone/metabolism , Carbenoxolone/pharmacology , Caspase 7/metabolism , Cell Line , Connexins/ultrastructure , Gap Junctions , Glycosylation , Humans , Ion Channel Gating/drug effects , Models, Molecular , Mutation , Nerve Tissue Proteins/ultrastructure , Protein Subunits/chemistry , Protein Subunits/metabolism , Sf9 Cells
11.
Nature ; 588(7837): 350-354, 2020 12.
Article in English | MEDLINE | ID: mdl-33149300

ABSTRACT

The proton-activated chloride channel (PAC) is active across a wide range of mammalian cells and is involved in acid-induced cell death and tissue injury1-3. PAC has recently been shown to represent a novel and evolutionarily conserved protein family4,5. Here we present two cryo-electron microscopy structures of human PAC in a high-pH resting closed state and a low-pH proton-bound non-conducting state. PAC is a trimer in which each subunit consists of a transmembrane domain (TMD), which is formed of two helices (TM1 and TM2), and an extracellular domain (ECD). Upon a decrease of pH from 8 to 4, we observed marked conformational changes in the ECD-TMD interface and the TMD. The rearrangement of the ECD-TMD interface is characterized by the movement of the histidine 98 residue, which is, after acidification, decoupled from the resting position and inserted into an acidic pocket that is about 5 Å away. Within the TMD, TM1 undergoes a rotational movement, switching its interaction partner from its cognate TM2 to the adjacent TM2. The anion selectivity of PAC is determined by the positively charged lysine 319 residue on TM2, and replacing lysine 319 with a glutamate residue converts PAC to a cation-selective channel. Our data provide a glimpse of the molecular assembly of PAC, and a basis for understanding the mechanism of proton-dependent activation.


Subject(s)
Chloride Channels/chemistry , Chloride Channels/metabolism , Cryoelectron Microscopy , Ion Channel Gating , Patch-Clamp Techniques , Single Molecule Imaging , Anions/metabolism , Binding Sites , Chloride Channels/ultrastructure , Chlorides/metabolism , Glutamic Acid/metabolism , Humans , Hydrogen-Ion Concentration , Ion Transport , Lysine/metabolism , Models, Molecular , Protein Subunits/chemistry , Protein Subunits/metabolism , Protons , Rotation , Substrate Specificity
12.
Nature ; 587(7832): 126-132, 2020 11.
Article in English | MEDLINE | ID: mdl-32879494

ABSTRACT

Chromosomal instability in cancer consists of dynamic changes to the number and structure of chromosomes1,2. The resulting diversity in somatic copy number alterations (SCNAs) may provide the variation necessary for tumour evolution1,3,4. Here we use multi-sample phasing and SCNA analysis of 1,421 samples from 394 tumours across 22 tumour types to show that continuous chromosomal instability results in pervasive SCNA heterogeneity. Parallel evolutionary events, which cause disruption in the same genes (such as BCL9, MCL1, ARNT (also known as HIF1B), TERT and MYC) within separate subclones, were present in 37% of tumours. Most recurrent losses probably occurred before whole-genome doubling, that was found as a clonal event in 49% of tumours. However, loss of heterozygosity at the human leukocyte antigen (HLA) locus and loss of chromosome 8p to a single haploid copy recurred at substantial subclonal frequencies, even in tumours with whole-genome doubling, indicating ongoing karyotype remodelling. Focal amplifications that affected chromosomes 1q21 (which encompasses BCL9, MCL1 and ARNT), 5p15.33 (TERT), 11q13.3 (CCND1), 19q12 (CCNE1) and 8q24.1 (MYC) were frequently subclonal yet appeared to be clonal within single samples. Analysis of an independent series of 1,024 metastatic samples revealed that 13 focal SCNAs were enriched in metastatic samples, including gains in chromosome 8q24.1 (encompassing MYC) in clear cell renal cell carcinoma and chromosome 11q13.3 (encompassing CCND1) in HER2+ breast cancer. Chromosomal instability may enable the continuous selection of SCNAs, which are established as ordered events that often occur in parallel, throughout tumour evolution.


Subject(s)
Chromosomal Instability/genetics , Evolution, Molecular , Karyotype , Neoplasm Metastasis/genetics , Neoplasms/genetics , Chromosomes, Human, Pair 11/genetics , Chromosomes, Human, Pair 8/genetics , Clone Cells/metabolism , Clone Cells/pathology , Cyclin E/genetics , DNA Copy Number Variations/genetics , Female , Humans , Loss of Heterozygosity/genetics , Male , Mutagenesis , Neoplasm Metastasis/pathology , Neoplasms/pathology , Oncogene Proteins/genetics
13.
Nucleic Acids Res ; 52(7): 3938-3949, 2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38477328

ABSTRACT

In the hypothetical RNA world, ribozymes could have acted as modern aminoacyl-tRNA synthetases (ARSs) to charge tRNAs, thus giving rise to the peptide synthesis along with the evolution of a primitive translation apparatus. We previously reported a T-boxzyme, Tx2.1, which selectively charges initiator tRNA with N-biotinyl-phenylalanine (BioPhe) in situ in a Flexible In-vitro Translation (FIT) system to produce BioPhe-initiating peptides. Here, we performed in vitro selection of elongation-capable T-boxzymes (elT-boxzymes), using para-azido-l-phenylalanine (PheAZ) as an acyl-donor. We implemented a new strategy to enrich elT-boxzyme-tRNA conjugates that self-aminoacylated on the 3'-terminus selectively. One of them, elT32, can charge PheAZ onto tRNA in trans in response to its cognate anticodon. Further evolution of elT32 resulted in elT49, with enhanced aminoacylation activity. We have demonstrated the translation of a PheAZ-containing peptide in an elT-boxzyme-integrated FIT system, revealing that elT-boxzymes are able to generate the PheAZ-tRNA in response to the cognate anticodon in situ of a custom-made translation system. This study, together with Tx2.1, illustrates a scenario where a series of ribozymes could have overseen aminoacylation and co-evolved with a primitive RNA-based translation system.


Subject(s)
Anticodon , Protein Biosynthesis , RNA, Catalytic , RNA, Transfer, Amino Acyl , RNA, Catalytic/metabolism , RNA, Catalytic/genetics , Anticodon/genetics , RNA, Transfer, Amino Acyl/metabolism , RNA, Transfer, Amino Acyl/genetics , Phenylalanine/metabolism , Phenylalanine/analogs & derivatives , Amino Acyl-tRNA Synthetases/metabolism , Amino Acyl-tRNA Synthetases/genetics , Transfer RNA Aminoacylation , Aminoacylation , Peptide Chain Elongation, Translational
14.
Proc Natl Acad Sci U S A ; 120(31): e2305273120, 2023 08.
Article in English | MEDLINE | ID: mdl-37487072

ABSTRACT

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here, we provide a detailed analysis of the heterogeneous graph structures of spider webs and use deep learning as a way to model and then synthesize artificial, bioinspired 3D web structures. The generative models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) an analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation; 2) a discrete diffusion model with full neighbor representation; and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bioinspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose an algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles toward integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.


Subject(s)
Deep Learning , Spiders , Animals , Algorithms , Commerce , Cytoskeleton
15.
Hepatology ; 79(4): 882-897, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-36999536

ABSTRACT

BACKGROUND AND AIMS: NASH, characterized by inflammation and fibrosis, is emerging as a leading etiology of HCC. Lipidomics analyses in the liver have shown that the levels of polyunsaturated phosphatidylcholine (PC) are decreased in patients with NASH, but the roles of membrane PC composition in the pathogenesis of NASH have not been investigated. Lysophosphatidylcholine acyltransferase 3 (LPCAT3), a phospholipid (PL) remodeling enzyme that produces polyunsaturated PLs, is a major determinant of membrane PC content in the liver. APPROACH AND RESULTS: The expression of LPCAT3 and the correlation between its expression and NASH severity were analyzed in human patient samples. We examined the effect of Lpcat3 deficiency on NASH progression using Lpcat3 liver-specific knockout (LKO) mice. RNA sequencing, lipidomics, and metabolomics were performed in liver samples. Primary hepatocytes and hepatic cell lines were used for in vitro analyses. We showed that LPCAT3 was dramatically suppressed in human NASH livers, and its expression was inversely correlated with NAFLD activity score and fibrosis stage. Loss of Lpcat3 in mouse liver promotes both spontaneous and diet-induced NASH/HCC. Mechanistically, Lpcat3 deficiency enhances reactive oxygen species production due to impaired mitochondrial homeostasis. Loss of Lpcat3 increases inner mitochondrial membrane PL saturation and elevates stress-induced autophagy, resulting in reduced mitochondrial content and increased fragmentation. Furthermore, overexpression of Lpcat3 in the liver ameliorates inflammation and fibrosis of NASH. CONCLUSIONS: These results demonstrate that membrane PL composition modulates the progression of NASH and that manipulating LPCAT3 expression could be an effective therapeutic for NASH.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Non-alcoholic Fatty Liver Disease , Humans , Animals , Mice , Phospholipids , Inflammation , Fibrosis , 1-Acylglycerophosphocholine O-Acyltransferase
16.
Hepatology ; 79(2): 425-437, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-37611260

ABSTRACT

BACKGROUND AND AIMS: The predominantly progressive, indeterminate, and predominantly regressive (P-I-R) classification extends beyond staging and provides information on dynamic changes of liver fibrosis. However, the prognostic implication of P-I-R classification is not elucidated. Therefore, in the present research, we investigated the utility of P-I-R classification in predicting the on-treatment clinical outcomes. APPROACH AND RESULTS: In an extension study on a randomized controlled trial, we originally enrolled 1000 patients with chronic hepatitis B and biopsy-proven histological significant fibrosis, and treated them for more than 7 years with entecavir-based therapy. Among the 727 patients with a second biopsy at treatment week 72, we compared P-I-R classification and Ishak score changes in 646 patients with adequate liver sections for the histological evaluation. Progressive, indeterminate, and regressive cases were observed in 70%, 17%, and 13% of patients before treatments and 20%, 14%, and 64% after 72-week treatment, respectively, which could further differentiate the histological outcomes of patients with stable Ishak scores. The 7-year cumulative incidence of HCC was 1.5% for the regressive cases, 4.3% for the indeterminate cases, and 22.8% for the progressive cases ( p <0.001). After adjusting for age, treatment regimen, platelet counts, cirrhosis, Ishak fibrosis score changes, and Laennec staging, the posttreatment progressive had a HR of 17.77 (vs. posttreatment regressive; 95% CI: 5.55-56.88) for the incidence of liver-related events (decompensation, HCC, and death/liver transplantation). CONCLUSIONS: The P-I-R classification can be a meaningful complement to the Ishak fibrosis score not only in evaluating the histological changes but also in predicting the clinical outcomes.


Subject(s)
Carcinoma, Hepatocellular , Hepatitis B, Chronic , Liver Neoplasms , Humans , Carcinoma, Hepatocellular/pathology , Antiviral Agents/therapeutic use , Liver Neoplasms/pathology , Liver Cirrhosis/pathology , Liver/pathology , Hepatitis B, Chronic/complications , Hepatitis B, Chronic/drug therapy , Hepatitis B, Chronic/pathology , Fibrosis , Biopsy/adverse effects
17.
Immunity ; 45(1): 145-58, 2016 07 19.
Article in English | MEDLINE | ID: mdl-27421703

ABSTRACT

Fibroproliferative diseases are driven by dysregulated tissue repair responses and are a major cause of morbidity and mortality because they affect nearly every organ system. Type 2 cytokine responses are critically involved in tissue repair; however, the mechanisms that regulate beneficial regeneration versus pathological fibrosis are not well understood. Here, we have shown that the type 2 effector cytokine interleukin-13 simultaneously, yet independently, directed hepatic fibrosis and the compensatory proliferation of hepatocytes and biliary cells in progressive models of liver disease induced by interleukin-13 overexpression or after infection with Schistosoma mansoni. Using transgenic mice with interleukin-13 signaling genetically disrupted in hepatocytes, cholangiocytes, or resident tissue fibroblasts, we have revealed direct and distinct roles for interleukin-13 in fibrosis, steatosis, cholestasis, and ductular reaction. Together, these studies show that these mechanisms are simultaneously controlled but distinctly regulated by interleukin-13 signaling. Thus, it may be possible to promote interleukin-13-dependent hepatobiliary expansion without generating pathological fibrosis. VIDEO ABSTRACT.


Subject(s)
Fatty Liver/immunology , Fibroblasts/immunology , Interleukin-13/metabolism , Liver Cirrhosis, Biliary/immunology , Liver/pathology , Schistosoma mansoni/immunology , Schistosomiasis mansoni/immunology , Animals , Bile Acids and Salts/biosynthesis , Cell Proliferation , Cells, Cultured , Fibrosis , Humans , Interleukin-13/genetics , Interleukin-13/immunology , Mice , Mice, Inbred C57BL , Mice, Knockout , Signal Transduction , Th2 Cells/immunology
18.
PLoS Biol ; 20(11): e3001812, 2022 11.
Article in English | MEDLINE | ID: mdl-36318572

ABSTRACT

Sleep is an essential process that consolidates memories by modulating synapses through poorly understood mechanisms. Here, we report that GABAergic synapses in hippocampal CA1 pyramidal neurons undergo daily rhythmic alterations. Specifically, wake inhibits phasic inhibition, whereas it promotes tonic inhibition compared to sleep. We further utilize a model of chemically induced inhibitory long-term potentiation (iLTP) to examine inhibitory plasticity. Intriguingly, while CA1 pyramidal neurons in both wake and sleep mice undergo iLTP, wake mice have a much higher magnitude. We also employ optogenetics and observe that inhibitory inputs from parvalbumin-, but not somatostatin-, expressing interneurons contribute to dynamic iLTP during sleep and wake. Finally, we demonstrate that synaptic insertion of α5-GABAA receptors underlies the wake-specific enhancement of iLTP at parvalbumin-synapses, which is independent of time of the day. These data reveal a previously unappreciated daily oscillation of inhibitory LTP in hippocampal neurons and uncover a dynamic contribution of inhibitory synapses in memory mechanisms across sleep and wake.


Subject(s)
Hippocampus , Parvalbumins , Animals , Mice , Hippocampus/physiology , Interneurons/metabolism , Neuronal Plasticity/physiology , Parvalbumins/metabolism , Sleep , Wakefulness
19.
Nature ; 576(7785): 163-167, 2019 12.
Article in English | MEDLINE | ID: mdl-31776515

ABSTRACT

Calcium homeostasis modulators (CALHMs) are voltage-gated, Ca2+-inhibited nonselective ion channels that act as major ATP release channels, and have important roles in gustatory signalling and neuronal toxicity1-3. Dysfunction of CALHMs has previously been linked to neurological disorders1. Here we present cryo-electron microscopy structures of the human CALHM2 channel in the Ca2+-free active or open state and in the ruthenium red (RUR)-bound inhibited state, at resolutions up to 2.7 Å. Our work shows that purified CALHM2 channels form both gap junctions and undecameric hemichannels. The protomer shows a mirrored arrangement of the transmembrane domains (helices S1-S4) relative to other channels with a similar topology, such as connexins, innexins and volume-regulated anion channels4-8. Upon binding to RUR, we observed a contracted pore with notable conformational changes of the pore-lining helix S1, which swings nearly 60° towards the pore axis from a vertical to a lifted position. We propose a two-section gating mechanism in which the S1 helix coarsely adjusts, and the N-terminal helix fine-tunes, the pore size. We identified a RUR-binding site near helix S1 that may stabilize this helix in the lifted conformation, giving rise to channel inhibition. Our work elaborates on the principles of CALHM2 channel architecture and symmetry, and the mechanism that underlies channel inhibition.


Subject(s)
Ion Channel Gating , Cryoelectron Microscopy , Humans , Models, Molecular , Protein Structure, Quaternary , Protein Structure, Secondary , Protein Structure, Tertiary
20.
Nature ; 575(7783): 473-479, 2019 11.
Article in English | MEDLINE | ID: mdl-31748722

ABSTRACT

Traditional technologies for virtual reality (VR) and augmented reality (AR) create human experiences through visual and auditory stimuli that replicate sensations associated with the physical world. The most widespread VR and AR systems use head-mounted displays, accelerometers and loudspeakers as the basis for three-dimensional, computer-generated environments that can exist in isolation or as overlays on actual scenery. In comparison to the eyes and the ears, the skin is a relatively underexplored sensory interface for VR and AR technology that could, nevertheless, greatly enhance experiences at a qualitative level, with direct relevance in areas such as communications, entertainment and medicine1,2. Here we present a wireless, battery-free platform of electronic systems and haptic (that is, touch-based) interfaces capable of softly laminating onto the curved surfaces of the skin to communicate information via spatio-temporally programmable patterns of localized mechanical vibrations. We describe the materials, device structures, power delivery strategies and communication schemes that serve as the foundations for such platforms. The resulting technology creates many opportunities for use where the skin provides an electronically programmable communication and sensory input channel to the body, as demonstrated through applications in social media and personal engagement, prosthetic control and feedback, and gaming and entertainment.


Subject(s)
Augmented Reality , Equipment Design , Skin , Touch , User-Computer Interface , Virtual Reality , Wireless Technology/instrumentation , Communication , Epidermis , Feedback , Female , Humans , Male , Prostheses and Implants , Robotics , Social Media , Vibration , Video Games
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