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1.
Cell ; 187(7): 1719-1732.e14, 2024 Mar 28.
Article in English | MEDLINE | ID: mdl-38513663

ABSTRACT

The glycine transporter 1 (GlyT1) plays a crucial role in the regulation of both inhibitory and excitatory neurotransmission by removing glycine from the synaptic cleft. Given its close association with glutamate/glycine co-activated NMDA receptors (NMDARs), GlyT1 has emerged as a central target for the treatment of schizophrenia, which is often linked to hypofunctional NMDARs. Here, we report the cryo-EM structures of GlyT1 bound with substrate glycine and drugs ALX-5407, SSR504734, and PF-03463275. These structures, captured at three fundamental states of the transport cycle-outward-facing, occluded, and inward-facing-enable us to illustrate a comprehensive blueprint of the conformational change associated with glycine reuptake. Additionally, we identified three specific pockets accommodating drugs, providing clear insights into the structural basis of their inhibitory mechanism and selectivity. Collectively, these structures offer significant insights into the transport mechanism and recognition of substrate and anti-schizophrenia drugs, thus providing a platform to design small molecules to treat schizophrenia.


Subject(s)
Glycine Plasma Membrane Transport Proteins , Humans , Biological Transport , Glycine/metabolism , Glycine Plasma Membrane Transport Proteins/chemistry , Glycine Plasma Membrane Transport Proteins/metabolism , Glycine Plasma Membrane Transport Proteins/ultrastructure , Receptors, N-Methyl-D-Aspartate/metabolism , Schizophrenia/metabolism , Synaptic Transmission , Imidazoles/chemistry , Sarcosine/analogs & derivatives , Piperidines/chemistry
2.
Cell ; 186(18): 3793-3809.e26, 2023 08 31.
Article in English | MEDLINE | ID: mdl-37562401

ABSTRACT

Hepatocytes, the major metabolic hub of the body, execute functions that are human-specific, altered in human disease, and currently thought to be regulated through endocrine and cell-autonomous mechanisms. Here, we show that key metabolic functions of human hepatocytes are controlled by non-parenchymal cells (NPCs) in their microenvironment. We developed mice bearing human hepatic tissue composed of human hepatocytes and NPCs, including human immune, endothelial, and stellate cells. Humanized livers reproduce human liver architecture, perform vital human-specific metabolic/homeostatic processes, and model human pathologies, including fibrosis and non-alcoholic fatty liver disease (NAFLD). Leveraging species mismatch and lipidomics, we demonstrate that human NPCs control metabolic functions of human hepatocytes in a paracrine manner. Mechanistically, we uncover a species-specific interaction whereby WNT2 secreted by sinusoidal endothelial cells controls cholesterol uptake and bile acid conjugation in hepatocytes through receptor FZD5. These results reveal the essential microenvironmental regulation of hepatic metabolism and its human-specific aspects.


Subject(s)
Endothelial Cells , Liver , Animals , Humans , Mice , Endothelial Cells/metabolism , Hepatocytes/metabolism , Kupffer Cells/metabolism , Liver/cytology , Liver/metabolism , Non-alcoholic Fatty Liver Disease/metabolism , Fibrosis/metabolism
3.
Cell ; 180(6): 1212-1227.e14, 2020 03 19.
Article in English | MEDLINE | ID: mdl-32169215

ABSTRACT

The paternal genome undergoes a massive exchange of histone with protamine for compaction into sperm during spermiogenesis. Upon fertilization, this process is potently reversed, which is essential for parental genome reprogramming and subsequent activation; however, it remains poorly understood how this fundamental process is initiated and regulated. Here, we report that the previously characterized splicing kinase SRPK1 initiates this life-beginning event by catalyzing site-specific phosphorylation of protamine, thereby triggering protamine-to-histone exchange in the fertilized oocyte. Interestingly, protamine undergoes a DNA-dependent phase transition to gel-like condensates and SRPK1-mediated phosphorylation likely helps open up such structures to enhance protamine dismissal by nucleoplasmin (NPM2) and enable the recruitment of HIRA for H3.3 deposition. Remarkably, genome-wide assay for transposase-accessible chromatin sequencing (ATAC-seq) analysis reveals that selective chromatin accessibility in both sperm and MII oocytes is largely erased in early pronuclei in a protamine phosphorylation-dependent manner, suggesting that SRPK1-catalyzed phosphorylation initiates a highly synchronized reorganization program in both parental genomes.


Subject(s)
Chromatin/metabolism , Protamines/metabolism , Protein Serine-Threonine Kinases/metabolism , Animals , Cell Cycle Proteins/metabolism , Cell Nucleus/metabolism , Chromatin/physiology , Chromatin Assembly and Disassembly/genetics , Chromatin Assembly and Disassembly/physiology , Fertilization/genetics , Histones/metabolism , Male , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Mice, Knockout , Oocytes/metabolism , Oocytes/physiology , Phosphorylation , Protamine Kinase/genetics , Protamine Kinase/metabolism , Protamines/genetics , Protein Serine-Threonine Kinases/physiology , RNA Splicing/genetics , RNA Splicing/physiology , Spermatozoa/metabolism , Transcription Factors/metabolism , Zygote/metabolism
4.
Cell ; 180(1): 50-63.e12, 2020 01 09.
Article in English | MEDLINE | ID: mdl-31923399

ABSTRACT

Mucosal barrier immunity is essential for the maintenance of the commensal microflora and combating invasive bacterial infection. Although immune and epithelial cells are thought to be the canonical orchestrators of this complex equilibrium, here, we show that the enteric nervous system (ENS) plays an essential and non-redundant role in governing the antimicrobial protein (AMP) response. Using confocal microscopy and single-molecule fluorescence in situ mRNA hybridization (smFISH) studies, we observed that intestinal neurons produce the pleiotropic cytokine IL-18. Strikingly, deletion of IL-18 from the enteric neurons alone, but not immune or epithelial cells, rendered mice susceptible to invasive Salmonella typhimurium (S.t.) infection. Mechanistically, unbiased RNA sequencing and single-cell sequencing revealed that enteric neuronal IL-18 is specifically required for homeostatic goblet cell AMP production. Together, we show that neuron-derived IL-18 signaling controls tissue-wide intestinal immunity and has profound consequences on the mucosal barrier and invasive bacterial killing.


Subject(s)
Immunity, Mucosal/immunology , Interleukin-18/immunology , Intestinal Mucosa/immunology , Animals , Cytokines/immunology , Enteric Nervous System/immunology , Enteric Nervous System/metabolism , Epithelial Cells/immunology , Female , Goblet Cells/immunology , Interleukin-18/biosynthesis , Intestinal Mucosa/metabolism , Intestine, Small/immunology , Male , Mice , Mice, Inbred C57BL , Neurons/immunology , Rats , Rats, Sprague-Dawley , Salmonella Infections/immunology , Salmonella typhimurium/immunology , Signal Transduction/immunology
5.
Cell ; 178(5): 1176-1188.e15, 2019 08 22.
Article in English | MEDLINE | ID: mdl-31442406

ABSTRACT

Adaptive immunity provides life-long protection by generating central and effector memory T cells and the most recently described tissue resident memory T (TRM) cells. However, the cellular origin of CD4 TRM cells and their contribution to host defense remain elusive. Using IL-17A tracking-fate mouse models, we found that a significant fraction of lung CD4 TRM cells derive from IL-17A-producing effector (TH17) cells following immunization with heat-killed Klebsiella pneumonia (Kp). These exTH17 TRM cells are maintained in the lung by IL-7, produced by lymphatic endothelial cells. During a memory response, neither antibodies, γδ T cells, nor circulatory T cells are sufficient for the rapid host defense required to eliminate Kp. Conversely, using parabiosis and depletion studies, we demonstrated that exTH17 TRM cells play an important role in bacterial clearance. Thus, we delineate the origin and function of airway CD4 TRM cells during bacterial infection, offering novel strategies for targeted vaccine design.


Subject(s)
Klebsiella Infections/immunology , Th17 Cells/immunology , Animals , CD4-Positive T-Lymphocytes/cytology , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/metabolism , Diphtheria Toxin/pharmacology , Disease Models, Animal , Female , Immunologic Memory , Interleukin-17/genetics , Interleukin-17/metabolism , Klebsiella Infections/pathology , Klebsiella pneumoniae/immunology , Klebsiella pneumoniae/pathogenicity , Lung/drug effects , Lung/metabolism , Lung/microbiology , Mice , Mice, Inbred C57BL , Th17 Cells/cytology , Th17 Cells/metabolism
7.
Nature ; 626(7998): 427-434, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38081299

ABSTRACT

Vesicular monoamine transporter 2 (VMAT2) accumulates monoamines in presynaptic vesicles for storage and exocytotic release, and has a vital role in monoaminergic neurotransmission1-3. Dysfunction of monoaminergic systems causes many neurological and psychiatric disorders, including Parkinson's disease, hyperkinetic movement disorders and depression4-6. Suppressing VMAT2 with reserpine and tetrabenazine alleviates symptoms of hypertension and Huntington's disease7,8, respectively. Here we describe cryo-electron microscopy structures of human VMAT2 complexed with serotonin and three clinical drugs at 3.5-2.8 Å, demonstrating the structural basis for transport and inhibition. Reserpine and ketanserin occupy the substrate-binding pocket and lock VMAT2 in cytoplasm-facing and lumen-facing states, respectively, whereas tetrabenazine binds in a VMAT2-specific pocket and traps VMAT2 in an occluded state. The structures in three distinct states also reveal the structural basis of the VMAT2 transport cycle. Our study establishes a structural foundation for the mechanistic understanding of substrate recognition, transport, drug inhibition and pharmacology of VMAT2 while shedding light on the rational design of potential therapeutic agents.


Subject(s)
Cryoelectron Microscopy , Vesicular Monoamine Transport Proteins , Humans , Binding Sites , Cytoplasm/drug effects , Cytoplasm/metabolism , Ketanserin/chemistry , Ketanserin/metabolism , Ketanserin/pharmacology , Reserpine/chemistry , Reserpine/metabolism , Reserpine/pharmacology , Serotonin/chemistry , Serotonin/metabolism , Substrate Specificity , Tetrabenazine/chemistry , Tetrabenazine/metabolism , Tetrabenazine/pharmacology , Vesicular Monoamine Transport Proteins/antagonists & inhibitors , Vesicular Monoamine Transport Proteins/chemistry , Vesicular Monoamine Transport Proteins/metabolism , Vesicular Monoamine Transport Proteins/ultrastructure
8.
Nature ; 606(7914): 585-593, 2022 06.
Article in English | MEDLINE | ID: mdl-35483404

ABSTRACT

Severe COVID-19 is characterized by persistent lung inflammation, inflammatory cytokine production, viral RNA and a sustained interferon (IFN) response, all of which are recapitulated and required for pathology in the SARS-CoV-2-infected MISTRG6-hACE2 humanized mouse model of COVID-19, which has a human immune system1-20. Blocking either viral replication with remdesivir21-23 or the downstream IFN-stimulated cascade with anti-IFNAR2 antibodies in vivo in the chronic stages of disease attenuates the overactive immune inflammatory response, especially inflammatory macrophages. Here we show that SARS-CoV-2 infection and replication in lung-resident human macrophages is a critical driver of disease. In response to infection mediated by CD16 and ACE2 receptors, human macrophages activate inflammasomes, release interleukin 1 (IL-1) and IL-18, and undergo pyroptosis, thereby contributing to the hyperinflammatory state of the lungs. Inflammasome activation and the accompanying inflammatory response are necessary for lung inflammation, as inhibition of the NLRP3 inflammasome pathway reverses chronic lung pathology. Notably, this blockade of inflammasome activation leads to the release of infectious virus by the infected macrophages. Thus, inflammasomes oppose host infection by SARS-CoV-2 through the production of inflammatory cytokines and suicide by pyroptosis to prevent a productive viral cycle.


Subject(s)
COVID-19 , Inflammasomes , Macrophages , SARS-CoV-2 , Angiotensin-Converting Enzyme 2 , Animals , COVID-19/pathology , COVID-19/physiopathology , COVID-19/virology , Humans , Inflammasomes/metabolism , Interleukin-1 , Interleukin-18 , Lung/pathology , Lung/virology , Macrophages/metabolism , Macrophages/pathology , Macrophages/virology , Mice , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Pneumonia/metabolism , Pneumonia/virology , Pyroptosis , Receptors, IgG , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity
9.
Immunity ; 48(4): 716-729.e8, 2018 04 17.
Article in English | MEDLINE | ID: mdl-29625895

ABSTRACT

Protective immunity against pathogens depends on the efficient generation of functionally diverse effector and memory T lymphocytes. However, whether plasticity during effector-to-memory CD8+ T cell differentiation affects memory lineage specification and functional versatility remains unclear. Using genetic fate mapping analysis of highly cytotoxic KLRG1+ effector CD8+ T cells, we demonstrated that KLRG1+ cells receiving intermediate amounts of activating and inflammatory signals downregulated KLRG1 during the contraction phase in a Bach2-dependent manner and differentiated into all memory T cell linages, including CX3CR1int peripheral memory cells and tissue-resident memory cells. "ExKLRG1" memory cells retained high cytotoxic and proliferative capacity distinct from other populations, which contributed to effective anti-influenza and anti-tumor immunity. Our work demonstrates that developmental plasticity of KLRG1+ effector CD8+ T cells is important in promoting functionally versatile memory cells and long-term protective immunity.


Subject(s)
CD8-Positive T-Lymphocytes/cytology , CD8-Positive T-Lymphocytes/immunology , Immunologic Memory/immunology , Lymphocyte Activation/immunology , Receptors, Immunologic/metabolism , Animals , Basic-Leucine Zipper Transcription Factors/genetics , Cell Differentiation/immunology , Cell Line, Tumor , Cell Lineage/immunology , Influenza A virus/immunology , Interleukin-12 Subunit p35/immunology , Lectins, C-Type , Listeria monocytogenes/immunology , Melanoma, Experimental , Mice , Mice, Inbred C57BL , Mice, Knockout , Receptors, Immunologic/genetics , Vesicular stomatitis Indiana virus/immunology
10.
Genes Dev ; 33(19-20): 1361-1366, 2019 10 01.
Article in English | MEDLINE | ID: mdl-31488580

ABSTRACT

The ubiquitin-specific protease (USP) family is the largest group of cysteine proteases. Cancer genomic analysis identified frequent amplification of USP21 (22%) in human pancreatic ductal adenocarcinoma (PDAC). USP21 overexpression correlates with human PDAC progression, and enforced expression of USP21 accelerates murine PDAC tumor growth and drives PanIN to PDAC progression in immortalized human pancreatic ductal cells. Conversely, depletion of USP21 impairs PDAC tumor growth. Mechanistically, USP21 deubiquitinates and stabilizes the TCF/LEF transcription factor TCF7, which promotes cancer cell stemness. Our work identifies and validates USP21 as a PDAC oncogene, providing a potential druggable target for this intractable disease.


Subject(s)
Gene Expression Regulation, Neoplastic/genetics , Pancreatic Neoplasms/enzymology , Ubiquitin Thiolesterase/genetics , Ubiquitin Thiolesterase/metabolism , Wnt Signaling Pathway/genetics , Animals , Cell Line, Tumor , Humans , Mice , Neoplastic Stem Cells/pathology , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/physiopathology , T Cell Transcription Factor 1 , Ubiquitination , Pancreatic Neoplasms
11.
Immunity ; 47(2): 284-297.e5, 2017 08 15.
Article in English | MEDLINE | ID: mdl-28813659

ABSTRACT

Ten-Eleven-Translocation-2 (Tet2) is a DNA methylcytosine dioxygenase that functions as a tumor suppressor in hematopoietic malignancies. We examined the role of Tet2 in tumor-tissue myeloid cells and found that Tet2 sustains the immunosuppressive function of these cells. We found that Tet2 expression is increased in intratumoral myeloid cells both in mouse models of melanoma and in melanoma patients and that this increased expression is dependent on an IL-1R-MyD88 pathway. Ablation of Tet2 in myeloid cells suppressed melanoma growth in vivo and shifted the immunosuppressive gene expression program in tumor-associated macrophages to a proinflammatory one, with a concomitant reduction of the immunosuppressive function. This resulted in increased numbers of effector T cells in the tumor, and T cell depletion abolished the reduced tumor growth observed upon myeloid-specific deletion of Tet2. Our findings reveal a non-cell-intrinsic, tumor-promoting function for Tet2 and suggest that Tet2 may present a therapeutic target for the treatment of non-hematologic malignancies.


Subject(s)
Carcinogenesis , DNA-Binding Proteins/metabolism , Melanoma/immunology , Myeloid-Derived Suppressor Cells/immunology , Proto-Oncogene Proteins/metabolism , Skin Neoplasms/immunology , T-Lymphocytes/immunology , Animals , Dioxygenases , Female , Humans , Male , Melanoma, Experimental , Mice , Mice, Inbred C57BL , Mice, Knockout , Tumor Burden , Tumor Escape
12.
Nature ; 580(7804): 524-529, 2020 04.
Article in English | MEDLINE | ID: mdl-32322056

ABSTRACT

The initiation of an intestinal tumour is a probabilistic process that depends on the competition between mutant and normal epithelial stem cells in crypts1. Intestinal stem cells are closely associated with a diverse but poorly characterized network of mesenchymal cell types2,3. However, whether the physiological mesenchymal microenvironment of mutant stem cells affects tumour initiation remains unknown. Here we provide in vivo evidence that the mesenchymal niche controls tumour initiation in trans. By characterizing the heterogeneity of the intestinal mesenchyme using single-cell RNA-sequencing analysis, we identified a population of rare pericryptal Ptgs2-expressing fibroblasts that constitutively process arachidonic acid into highly labile prostaglandin E2 (PGE2). Specific ablation of Ptgs2 in fibroblasts was sufficient to prevent tumour initiation in two different models of sporadic, autochthonous tumorigenesis. Mechanistically, single-cell RNA-sequencing analyses of a mesenchymal niche model showed that fibroblast-derived PGE2 drives the expansion οf a population of Sca-1+ reserve-like stem cells. These express a strong regenerative/tumorigenic program, driven by the Hippo pathway effector Yap. In vivo, Yap is indispensable for Sca-1+ cell expansion and early tumour initiation and displays a nuclear localization in both mouse and human adenomas. Using organoid experiments, we identified a molecular mechanism whereby PGE2 promotes Yap dephosphorylation, nuclear translocation and transcriptional activity by signalling through the receptor Ptger4. Epithelial-specific ablation of Ptger4 misdirected the regenerative reprogramming of stem cells and prevented Sca-1+ cell expansion and sporadic tumour initiation in mutant mice, thereby demonstrating the robust paracrine control of tumour-initiating stem cells by PGE2-Ptger4. Analyses of patient-derived organoids established that PGE2-PTGER4 also regulates stem-cell function in humans. Our study demonstrates that initiation of colorectal cancer is orchestrated by the mesenchymal niche and reveals a mechanism by which rare pericryptal Ptgs2-expressing fibroblasts exert paracrine control over tumour-initiating stem cells via the druggable PGE2-Ptger4-Yap signalling axis.


Subject(s)
Carcinogenesis , Colorectal Neoplasms/pathology , Intestines/pathology , Mesoderm/pathology , Neoplastic Stem Cells/pathology , Paracrine Communication , Stem Cell Niche , Adaptor Proteins, Signal Transducing/metabolism , Animals , Antigens, Ly/metabolism , Arachidonic Acid/metabolism , Cell Cycle Proteins/metabolism , Cell Proliferation , Colorectal Neoplasms/metabolism , Cyclooxygenase 2/metabolism , Dinoprostone/metabolism , Female , Fibroblasts/metabolism , Fibroblasts/pathology , Humans , Intestinal Mucosa/metabolism , Intestinal Mucosa/pathology , Male , Membrane Proteins/metabolism , Mesoderm/metabolism , Mice , Neoplastic Stem Cells/metabolism , Organoids/metabolism , Organoids/pathology , Receptors, Prostaglandin E, EP4 Subtype/metabolism , Single-Cell Analysis , YAP-Signaling Proteins
13.
Nucleic Acids Res ; 52(D1): D293-D303, 2024 Jan 05.
Article in English | MEDLINE | ID: mdl-37889053

ABSTRACT

Gene regulatory networks (GRNs) are interpretable graph models encompassing the regulatory interactions between transcription factors (TFs) and their downstream target genes. Making sense of the topology and dynamics of GRNs is fundamental to interpreting the mechanisms of disease etiology and translating corresponding findings into novel therapies. Recent advances in single-cell multi-omics techniques have prompted the computational inference of GRNs from single-cell transcriptomic and epigenomic data at an unprecedented resolution. Here, we present scGRN (https://bio.liclab.net/scGRN/), a comprehensive single-cell multi-omics gene regulatory network platform of human and mouse. The current version of scGRN catalogs 237 051 cell type-specific GRNs (62 999 692 TF-target gene pairs), covering 160 tissues/cell lines and 1324 single-cell samples. scGRN is the first resource documenting large-scale cell type-specific GRN information of diverse human and mouse conditions inferred from single-cell multi-omics data. We have implemented multiple online tools for effective GRN analysis, including differential TF-target network analysis, TF enrichment analysis, and pathway downstream analysis. We also provided details about TF binding to promoters, super-enhancers and typical enhancers of target genes in GRNs. Taken together, scGRN is an integrative and useful platform for searching, browsing, analyzing, visualizing and downloading GRNs of interest, enabling insight into the differences in regulatory mechanisms across diverse conditions.


Subject(s)
Gene Expression Profiling , Gene Regulatory Networks , Single-Cell Analysis , Transcription Factors , Animals , Humans , Mice , Protein Binding , Transcription Factors/genetics , Transcription Factors/metabolism , Transcriptome
14.
J Biol Chem ; 300(3): 105721, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38311175

ABSTRACT

Histone H3 tyrosine-99 sulfation (H3Y99sulf) is a recently identified histone mark that can cross-talk with H4R3me2a to regulate gene transcription, but its role in cancer biology is less studied. Here, we report that H3Y99sulf is a cancer-associated histone mark that can mediate hepatocellular carcinoma (HCC) cells responding to hypoxia. Hypoxia-stimulated SNAIL pathway elevates the expression of PAPSS2, which serves as a source of adenosine 3'-phosphate 5'-phos-phosulfate for histone sulfation and results in upregulation of H3Y99sulf. The transcription factor TDRD3 is the downstream effector of H3Y99sulf-H4R3me2a axis in HCC. It reads and co-localizes with the H3Y99sulf-H4R3me2a dual mark in the promoter regions of HIF1A and PDK1 to regulate gene transcription. Depletion of SULT1B1 can effectively reduce the occurrence of H3Y99sulf-H4R3me2a-TDRD3 axis in gene promoter regions and lead to downregulation of targeted gene transcription. Hypoxia-inducible factor 1-alpha and PDK1 are master regulators for hypoxic responses and cancer metabolism. Disruption of the H3Y99sulf-H4R3me2a-TDRD3 axis can inhibit the expression and functions of hypoxia-inducible factor 1-alpha and PDK1, resulting in suppressed proliferation, tumor growth, and survival of HCC cells suffering hypoxia stress. The present study extends the regulatory and functional mechanisms of H3Y99sulf and improves our understanding of its role in cancer biology.


Subject(s)
Carcinoma, Hepatocellular , Histones , Liver Neoplasms , Tyrosine , Humans , Carcinoma, Hepatocellular/metabolism , Cell Line, Tumor , Cell Proliferation , Gene Expression Regulation, Neoplastic , Histones/metabolism , Hypoxia/genetics , Hypoxia-Inducible Factor 1/metabolism , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Liver Neoplasms/metabolism , Tyrosine/metabolism
15.
Acc Chem Res ; 57(6): 992-1006, 2024 Mar 19.
Article in English | MEDLINE | ID: mdl-38417011

ABSTRACT

ConspectusMechanically interlocked polymers (MIPs) such as polyrotaxanes and polycatenanes are polymer architectures that incorporate mechanical bonds, which represent a compelling frontier in polymer science. MIPs with cross-linked structures are known as mechanically interlocked networks (MINs) and are widely utilized in materials science. Leveraging the motion of mechanical bonds, MINs hold the potential for achieving a combination of robustness and dynamicity. Currently, the reported MINs predominantly consist of networks with discrete mechanical bonds as cross-linking points, exemplified by well-known slide-ring materials and rotaxane/catenane cross-linked polymers. The motion of these mechanically interlocked cross-linking points facilitates the redistribution of tension throughout the network, effectively preventing stress concentration and thereby enhancing material toughness. In these instances, the impact of mechanical bonds can be likened to the adage "small things can make a big difference", whereby a limited number of mechanical bonds substantially elevate the mechanical performance of conventional polymers. In addition to MINs cross-linked by mechanical bonds, there is another type of MIN in which their principal parts are polymer chains composed of dense mechanical bonds. Within these MINs, mechanical bonds generally serve as repeating units, and their unique properties stem from integrating and amplifying the function of a large amount of mechanical bonds. Consequently, MINs with dense mechanical bonds tend to reflect the intrinsic properties of mechanical interlocked polymers, making their exploration critical for a comprehensive understanding of MIPs. Nevertheless, investigations into MINs featuring dense mechanical bonds remain relatively scarce.This Account presents a comprehensive overview of our investigation and insights into MINs featuring dense mechanical bonds. First, we delve into the synthetic strategies employed to effectively prepare MINs with dense mechanical bonds, while critically evaluating their advantages and limitations. Through meticulous control of the core interlocking step, three distinct strategies have emerged: mechanical interlocking followed by polymerization, supramolecular polymerization followed by mechanical interlocking, and dynamic interlocking. Furthermore, we underscore the structure-property relationships of MINs with dense mechanical bonds. The macroscopic properties of MINs originate from integrating and amplifying countless microscopic motions of mechanical bonds, a phenomenon we define as an integration and amplification mechanism. Our investigation has revealed detailed motion characteristics of mechanical bonds in bulk mechanically interlocked materials, encompassing the quantification of motion activation energy, discrimination of varying motion distances, and elucidation of the recovery process. Additionally, we have elucidated their influence on the mechanical performance of the respective materials. Moreover, we have explored potential applications of MINs, leveraging their exceptional mechanical properties and dynamicity. These applications include enhancing the toughness of conventional polymers, engineering mechanically adaptive and multifunctional aerogels, and mitigating Li protrusion as interfacial layers in lithium-ion batteries. Finally, we offer our personal perspectives on the promises, opportunities, and key challenges in the future development of MINs with dense mechanical bonds, underscoring the potential for transformative advancements in this burgeoning field.

16.
Mol Psychiatry ; 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38589563

ABSTRACT

The associations of synaptic loss with amyloid-ß (Aß) and tau pathology measured by positron emission tomography (PET) and plasma analysis in Alzheimer's disease (AD) patients are unknown. Seventy-five participants, including 26 AD patients, 19 mild cognitive impairment (MCI) patients, and 30 normal controls (NCs), underwent [18F]SynVesT-1 PET/MR scans to assess synaptic density and [18F]florbetapir and [18F]MK6240 PET/CT scans to evaluate Aß plaques and tau tangles. Among them, 19 AD patients, 12 MCI patients, and 29 NCs had plasma Aß42/40 and p-tau181 levels measured by the Simoa platform. Twenty-three individuals, 6 AD patients, 4 MCI patients, and 13 NCs, underwent [18F]SynVesT-1 PET/MRI and [18F]MK6240 PET/CT scans during a one-year follow-up assessment. The associations of Aß and tau pathology with cross-sectional and longitudinal synaptic loss were investigated using Pearson correlation analyses, generalized linear models and mediation analyses. AD patients exhibited lower synaptic density than NCs and MCI patients. In the whole cohort, global Aß deposition was associated with synaptic loss in the medial (r = -0.431, p < 0.001) and lateral (r = -0.406, p < 0.001) temporal lobes. Synaptic density in almost all regions was related to the corresponding regional tau tangles independent of global Aß deposition in the whole cohort and stratified groups. Synaptic density in the medial and lateral temporal lobes was correlated with plasma Aß42/40 (r = 0.300, p = 0.020/r = 0.289, p = 0.025) and plasma p-tau 181 (r = -0.412, p = 0.001/r = -0.529, p < 0.001) levels in the whole cohort. Mediation analyses revealed that tau tangles mediated the relationship between Aß plaques and synaptic density in the whole cohort. Baseline tau pathology was positively associated with longitudinal synaptic loss. This study suggested that tau burden is strongly linked to synaptic density independent of Aß plaques, and also can predict longitudinal synaptic loss.

18.
Nature ; 571(7765): 403-407, 2019 07.
Article in English | MEDLINE | ID: mdl-31217581

ABSTRACT

Activated CD4 T cells proliferate rapidly and remodel epigenetically before exiting the cell cycle and engaging acquired effector functions. Metabolic reprogramming from the naive state is required throughout these phases of activation1. In CD4 T cells, T-cell-receptor ligation-along with co-stimulatory and cytokine signals-induces a glycolytic anabolic program that is required for biomass generation, rapid proliferation and effector function2. CD4 T cell differentiation (proliferation and epigenetic remodelling) and function are orchestrated coordinately by signal transduction and transcriptional remodelling. However, it remains unclear whether these processes are regulated independently of one another by cellular biochemical composition. Here we demonstrate that distinct modes of mitochondrial metabolism support differentiation and effector functions of mouse T helper 1 (TH1) cells by biochemically uncoupling these two processes. We find that the tricarboxylic acid cycle is required for the terminal effector function of TH1 cells through succinate dehydrogenase (complex II), but that the activity of succinate dehydrogenase suppresses TH1 cell proliferation and histone acetylation. By contrast, we show that complex I of the electron transport chain, the malate-aspartate shuttle and mitochondrial citrate export are required to maintain synthesis of aspartate, which is necessary for the proliferation of T helper cells. Furthermore, we find that mitochondrial citrate export and the malate-aspartate shuttle promote histone acetylation, and specifically regulate the expression of genes involved in T cell activation. Combining genetic, pharmacological and metabolomics approaches, we demonstrate that the differentiation and terminal effector functions of T helper cells are biochemically uncoupled. These findings support a model in which the malate-aspartate shuttle, mitochondrial citrate export and complex I supply the substrates needed for proliferation and epigenetic remodelling early during T cell activation, whereas complex II consumes the substrates of these pathways, which antagonizes differentiation and enforces terminal effector function. Our data suggest that transcriptional programming acts together with a parallel biochemical network to enforce cell state.


Subject(s)
Cell Differentiation , Mitochondria/metabolism , Th1 Cells/cytology , Th1 Cells/immunology , Acetylation , Animals , Aspartic Acid/metabolism , Cell Differentiation/genetics , Cell Line , Cell Proliferation/genetics , Citric Acid/metabolism , Citric Acid Cycle , Electron Transport , Female , Histones/metabolism , Humans , Lymphocyte Activation/genetics , Malates/metabolism , Male , Mice , Succinate Dehydrogenase/metabolism , Th1 Cells/metabolism , Transcription, Genetic
19.
Nucleic Acids Res ; 51(D1): D280-D290, 2023 01 06.
Article in English | MEDLINE | ID: mdl-36318264

ABSTRACT

Super-enhancers (SEs) are cell-specific DNA cis-regulatory elements that can supervise the transcriptional regulation processes of downstream genes. SEdb 2.0 (http://www.licpathway.net/sedb) aims to provide a comprehensive SE resource and annotate their potential roles in gene transcriptions. Compared with SEdb 1.0, we have made the following improvements: (i) Newly added the mouse SEs and expanded the scale of human SEs. SEdb 2.0 contained 1 167 518 SEs from 1739 human H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) samples and 550 226 SEs from 931 mouse H3K27ac ChIP-seq samples, which was five times that of SEdb 1.0. (ii) Newly added transcription factor binding sites (TFBSs) in SEs identified by TF motifs and TF ChIP-seq data. (iii) Added comprehensive (epi)genetic annotations of SEs, including chromatin accessibility regions, methylation sites, chromatin interaction regions and topologically associating domains (TADs). (iv) Newly embedded and updated search and analysis tools, including 'Search SE by TF-based', 'Differential-Overlapping-SE analysis' and 'SE-based TF-Gene analysis'. (v) Newly provided quality control (QC) metrics for ChIP-seq processing. In summary, SEdb 2.0 is a comprehensive update of SEdb 1.0, which curates more SEs and annotation information than SEdb 1.0. SEdb 2.0 provides a friendly platform for researchers to more comprehensively clarify the important role of SEs in the biological process.


Subject(s)
Databases, Genetic , Enhancer Elements, Genetic , Animals , Humans , Mice , Chromatin/genetics , Gene Expression Regulation , Transcription Factors/genetics , Transcription Factors/metabolism
20.
Proc Natl Acad Sci U S A ; 119(28): e2122534119, 2022 Jul 12.
Article in English | MEDLINE | ID: mdl-35867737

ABSTRACT

Photoinduced phase transition (PIPT) is always treated as a coherent process, but ultrafast disordering in PIPT is observed in recent experiments. Utilizing the real-time time-dependent density functional theory method, here we track the motion of individual vanadium (V) ions during PIPT in VO2 and uncover that their coherent or disordered dynamics can be manipulated by tuning the laser fluence. We find that the photoexcited holes generate a force on each V-V dimer to drive their collective coherent motion, in competing with the thermal-induced vibrations. If the laser fluence is so weak that the photoexcited hole density is too low to drive the phase transition alone, the PIPT is a disordered process due to the interference of thermal phonons. We also reveal that the photoexcited holes populated by the V-V dimerized bonding states will become saturated if the laser fluence is too strong, limiting the timescale of photoinduced phase transition.

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