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1.
Cell ; 179(6): 1276-1288.e14, 2019 11 27.
Article in English | MEDLINE | ID: mdl-31778654

ABSTRACT

Although human genetic studies have implicated many susceptible genes associated with plasma lipid levels, their physiological and molecular functions are not fully characterized. Here we demonstrate that orphan G protein-coupled receptor 146 (GPR146) promotes activity of hepatic sterol regulatory element binding protein 2 (SREBP2) through activation of the extracellular signal-regulated kinase (ERK) signaling pathway, thereby regulating hepatic very low-density lipoprotein (VLDL) secretion, and subsequently circulating low-density lipoprotein cholesterol (LDL-C) and triglycerides (TG) levels. Remarkably, GPR146 deficiency reduces plasma cholesterol levels substantially in both wild-type and LDL receptor (LDLR)-deficient mice. Finally, aortic atherosclerotic lesions are reduced by 90% and 70%, respectively, in male and female LDLR-deficient mice upon GPR146 depletion. Taken together, these findings outline a regulatory role for the GPR146/ERK axis in systemic cholesterol metabolism and suggest that GPR146 inhibition could be an effective strategy to reduce plasma cholesterol levels and atherosclerosis.


Subject(s)
Atherosclerosis/metabolism , Hypercholesterolemia/metabolism , Receptors, G-Protein-Coupled/deficiency , Animals , Atherosclerosis/blood , Base Sequence , Cholesterol/blood , Dependovirus/metabolism , Extracellular Signal-Regulated MAP Kinases/metabolism , Fasting , Female , Hepatocytes/metabolism , Humans , Hypercholesterolemia/blood , Lipoproteins, VLDL/metabolism , Liver/metabolism , Mice , Mice, Inbred C57BL , RNA, Small Interfering/metabolism , Receptors, G-Protein-Coupled/metabolism , Receptors, LDL/metabolism , Signal Transduction , Sterol Regulatory Element Binding Protein 2/metabolism , Triglycerides/blood , Up-Regulation
2.
Mol Cell ; 83(7): 1109-1124.e4, 2023 04 06.
Article in English | MEDLINE | ID: mdl-36921607

ABSTRACT

The Polycomb-group chromatin modifiers play important roles to repress or switch off gene expression in plants and animals. How the active chromatin state is switched to a Polycomb-repressed state is unclear. In Arabidopsis, prolonged cold induces the switching of the highly active chromatin state at the potent floral repressor FLC to a Polycomb-repressed state, which is epigenetically maintained when temperature rises to confer "cold memory," enabling plants to flower in spring. We report that the cis-acting cold memory element (CME) region at FLC bears bivalent marks of active histone H3K4me3 and repressive H3K27me3 that are read and interpreted by an assembly of bivalent chromatin readers to drive cold-induced switching of the FLC chromatin state. In response to cold, the 47-bp CME and its associated bivalent chromatin feature drive the switching of active chromatin state at a recombinant gene to a Polycomb-repressed domain, conferring cold memory. We reveal a paradigm for environment-induced chromatin-state switching at bivalent loci in plants.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Chromatin/genetics , Chromatin/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , MADS Domain Proteins/genetics , MADS Domain Proteins/metabolism , Polycomb-Group Proteins/genetics , Polycomb-Group Proteins/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , Cold Temperature , Gene Expression Regulation, Plant , Flowers/genetics , Flowers/metabolism
3.
Immunity ; 53(6): 1315-1330.e9, 2020 12 15.
Article in English | MEDLINE | ID: mdl-33275896

ABSTRACT

Various vaccine strategies have been proposed in response to the global COVID-19 pandemic, each with unique strategies for eliciting immune responses. Here, we developed nanoparticle vaccines by covalently conjugating the self-assembled 24-mer ferritin to the receptor binding domain (RBD) and/or heptad repeat (HR) subunits of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) spike (S) protein. Compared to monomer vaccines, nanoparticle vaccines elicited more robust neutralizing antibodies and cellular immune responses. RBD and RBD-HR nanoparticle vaccinated hACE2 transgenic mice vaccinated with RBD and/or RBD-HR nanoparticles exhibited reduced viral load in the lungs after SARS-CoV-2 challenge. RBD-HR nanoparticle vaccines also promoted neutralizing antibodies and cellular immune responses against other coronaviruses. The nanoparticle vaccination of rhesus macaques induced neutralizing antibodies, and T and B cell responses prior to boost immunization; these responses persisted for more than three months. RBD- and HR-based nanoparticles thus present a promising vaccination approach against SARS-CoV-2 and other coronaviruses.


Subject(s)
Bacterial Proteins/immunology , COVID-19 Vaccines/immunology , COVID-19/immunology , Ferritins/immunology , Helicobacter pylori/metabolism , Recombinant Fusion Proteins/immunology , SARS-CoV-2/physiology , Spike Glycoprotein, Coronavirus/immunology , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/metabolism , Animals , Antibodies, Neutralizing/metabolism , Antibodies, Viral/metabolism , Bacterial Proteins/chemistry , COVID-19 Vaccines/chemistry , Ferritins/chemistry , Humans , Macaca mulatta , Mice , Mice, Inbred BALB C , Nanoparticles/chemistry , Pandemics , Protein Binding , Spike Glycoprotein, Coronavirus/chemistry , Vaccination
4.
Nature ; 620(7974): 545-551, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37224876

ABSTRACT

Doping of perovskite semiconductors1 and passivation of their grain boundaries2 remain challenging but essential for advancing high-efficiency perovskite solar cells. Particularly, it is crucial to build perovskite/indium tin oxide (ITO) Schottky contact based inverted devices without predepositing a layer of hole-transport material3-5. Here we report a dimethylacridine-based molecular doping process used to construct a well-matched p-perovskite/ITO contact, along with all-round passivation of grain boundaries, achieving a certified power conversion efficiency (PCE) of 25.39%. The molecules are shown to be extruded from the precursor solution to the grain boundaries and the bottom of the film surface in the chlorobenzene-quenched crystallization process, which we call a molecule-extrusion process. The core coordination complex between the deprotonated phosphonic acid group of the molecule and lead polyiodide of perovskite is responsible for both mechanical absorption and electronic charge transfer, and leads to p-type doping of the perovskite film. We created an efficient device with a PCE of 25.86% (reverse scan) and that maintained 96.6% of initial PCE after 1,000 h of light soaking.

5.
Nature ; 607(7918): 339-344, 2022 07.
Article in English | MEDLINE | ID: mdl-35768511

ABSTRACT

Extreme weather conditions associated with climate change affect many aspects of plant and animal life, including the response to infectious diseases. Production of salicylic acid (SA), a central plant defence hormone1-3, is particularly vulnerable to suppression by short periods of hot weather above the normal plant growth temperature range via an unknown mechanism4-7. Here we show that suppression of SA production in Arabidopsis thaliana at 28 °C is independent of PHYTOCHROME B8,9 (phyB) and EARLY FLOWERING 310 (ELF3), which regulate thermo-responsive plant growth and development. Instead, we found that formation of GUANYLATE BINDING PROTEIN-LIKE 3 (GBPL3) defence-activated biomolecular condensates11 (GDACs) was reduced at the higher growth temperature. The altered GDAC formation in vivo is linked to impaired recruitment of GBPL3 and SA-associated Mediator subunits to the promoters of CBP60g and SARD1, which encode master immune transcription factors. Unlike many other SA signalling components, including the SA receptor and biosynthetic genes, optimized CBP60g expression was sufficient to broadly restore SA production, basal immunity and effector-triggered immunity at the elevated growth temperature without significant growth trade-offs. CBP60g family transcription factors are widely conserved in plants12. These results have implications for safeguarding the plant immune system as well as understanding the concept of the plant-pathogen-environment disease triangle and the emergence of new disease epidemics in a warming climate.


Subject(s)
Acclimatization , Arabidopsis Proteins , Arabidopsis , Environment , Global Warming , Plant Immunity , Temperature , Arabidopsis/growth & development , Arabidopsis/immunology , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Calmodulin-Binding Proteins/genetics , Gene Expression Regulation, Plant , Global Warming/statistics & numerical data , Host-Pathogen Interactions , Phytochrome B , Plant Diseases/genetics , Plant Immunity/genetics , Salicylic Acid/metabolism , Transcription Factors
6.
Mol Cell ; 77(1): 95-107.e5, 2020 01 02.
Article in English | MEDLINE | ID: mdl-31628042

ABSTRACT

GTP cyclohydrolase I (GTPCH), 6-pyruvoyltetrahydropterin synthase (PTPS), and sepiapterin reductase (SR) are sequentially responsible for de novo synthesis of tetrahydrobiopterin (BH4), a known co-factor for nitric oxide synthase (NOS). The implication of BH4-biosynthesis process in tumorigenesis remains to be investigated. Here, we show that PTPS, which is highly expressed in early-stage colorectal cancer, is phosphorylated at Thr 58 by AMPK under hypoxia; this phosphorylation promotes PTPS binding to LTBP1 and subsequently drives iNOS-mediated LTBP1 S-nitrosylation through proximal-coupling BH4 production within the PTPS/iNOS/LTBP1 complex. In turn, LTBP1 S-nitrosylation results in proteasome-dependent LTBP1 protein degradation, revealing an inverse relationship between PTPS pT58 and LTBP1 stability. Physiologically, the repressive effect of PTPS on LTBP1 leads to impaired transforming growth factor ß (TGF-ß) secretion and thereby maintains tumor cell growth under hypoxia. Our findings illustrate a molecular mechanism underlying the regulation of LTBP1-TGF-ß signaling by the BH4-biosynthesis pathway and highlight the specific requirement of PTPS for tumor growth.


Subject(s)
Cell Proliferation/physiology , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , Hypoxia/metabolism , Latent TGF-beta Binding Proteins/metabolism , Phosphorus-Oxygen Lyases/metabolism , Animals , Cell Line , Cell Line, Tumor , HCT116 Cells , HEK293 Cells , HT29 Cells , Humans , Mice , Mice, Inbred BALB C , Mice, Nude , Nitric Oxide Synthase/metabolism , Phosphorylation/physiology , Proteasome Endopeptidase Complex/metabolism , Proteolysis , Signal Transduction/physiology , Transforming Growth Factor beta/metabolism
7.
J Immunol ; 212(7): 1207-1220, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38345351

ABSTRACT

Teleost fish type I IFNs and the associated receptors from the cytokine receptor family B (CRFB) are characterized by remarkable diversity and complexity. How the fish type I IFNs bind to their receptors is still not fully understood. In this study, we demonstrate that CRFB1 and CRFB5 constitute the receptor pair through which type I subgroup d IFN (IFNd) from large yellow croaker, Larimichthys crocea, activates the conserved JAK-STAT signaling pathway as a part of the antiviral response. Our data suggest that L. crocea IFNd (LcIFNd) has a higher binding affinity with L. crocea CRFB5 (LcCRFB5) than with LcCRFB1. Furthermore, we report the crystal structure of LcIFNd at a 1.49-Å resolution and construct structural models of LcIFNd in binary complexes with predicted structures of extracellular regions of LcCRFB1 and LcCRFB5, respectively. Despite striking similarities in overall architectures of LcIFNd and its ortholog human IFN-ω, the receptor binding patterns between LcIFNd and its receptors show that teleost and mammalian type I IFNs may have differentially selected helices that bind to their homologous receptors. Correspondingly, key residues mediating binding of LcIFNd to LcCRFB1 and LcCRFB5 are largely distinct from the receptor-interacting residues in other fish and mammalian type I IFNs. Our findings reveal a ligand/receptor complex binding mechanism of IFNd in teleost fish, thus providing new insights into the function and evolution of type I IFNs.


Subject(s)
Interferon Type I , Perciformes , Animals , Humans , Phylogeny , Fishes/metabolism , Interferon Type I/metabolism , Fish Proteins/genetics , Mammals/metabolism
8.
Nature ; 580(7805): 653-657, 2020 04.
Article in English | MEDLINE | ID: mdl-32350464

ABSTRACT

The aboveground parts of terrestrial plants, collectively called the phyllosphere, have a key role in the global balance of atmospheric carbon dioxide and oxygen. The phyllosphere represents one of the most abundant habitats for microbiota colonization. Whether and how plants control phyllosphere microbiota to ensure plant health is not well understood. Here we show that the Arabidopsis quadruple mutant (min7 fls2 efr cerk1; hereafter, mfec)1, simultaneously defective in pattern-triggered immunity and the MIN7 vesicle-trafficking pathway, or a constitutively activated cell death1 (cad1) mutant, carrying a S205F mutation in a membrane-attack-complex/perforin (MACPF)-domain protein, harbour altered endophytic phyllosphere microbiota and display leaf-tissue damage associated with dysbiosis. The Shannon diversity index and the relative abundance of Firmicutes were markedly reduced, whereas Proteobacteria were enriched in the mfec and cad1S205F mutants, bearing cross-kingdom resemblance to some aspects of the dysbiosis that occurs in human inflammatory bowel disease. Bacterial community transplantation experiments demonstrated a causal role of a properly assembled leaf bacterial community in phyllosphere health. Pattern-triggered immune signalling, MIN7 and CAD1 are found in major land plant lineages and are probably key components of a genetic network through which terrestrial plants control the level and nurture the diversity of endophytic phyllosphere microbiota for survival and health in a microorganism-rich environment.


Subject(s)
Arabidopsis/genetics , Arabidopsis/microbiology , Gene Regulatory Networks/genetics , Plant Components, Aerial/genetics , Plant Components, Aerial/microbiology , Plant Diseases/genetics , Plant Diseases/prevention & control , Arabidopsis/immunology , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Cell Death , Environment , Firmicutes/genetics , Firmicutes/isolation & purification , Genes, Plant/genetics , Genotype , Guanine Nucleotide Exchange Factors/genetics , Guanine Nucleotide Exchange Factors/metabolism , Homeostasis , Microbiota/genetics , Microbiota/physiology , Mutation , Phenotype , Plant Diseases/immunology , Plant Diseases/microbiology , Plant Immunity/genetics , Plant Leaves/genetics , Plant Leaves/microbiology , Proteobacteria/genetics , Proteobacteria/isolation & purification
9.
Nature ; 577(7790): 341-345, 2020 01.
Article in English | MEDLINE | ID: mdl-31942054

ABSTRACT

Classification is an important task at which both biological and artificial neural networks excel1,2. In machine learning, nonlinear projection into a high-dimensional feature space can make data linearly separable3,4, simplifying the classification of complex features. Such nonlinear projections are computationally expensive in conventional computers. A promising approach is to exploit physical materials systems that perform this nonlinear projection intrinsically, because of their high computational density5, inherent parallelism and energy efficiency6,7. However, existing approaches either rely on the systems' time dynamics, which requires sequential data processing and therefore hinders parallel computation5,6,8, or employ large materials systems that are difficult to scale up7. Here we use a parallel, nanoscale approach inspired by filters in the brain1 and artificial neural networks2 to perform nonlinear classification and feature extraction. We exploit the nonlinearity of hopping conduction9-11 through an electrically tunable network of boron dopant atoms in silicon, reconfiguring the network through artificial evolution to realize different computational functions. We first solve the canonical two-input binary classification problem, realizing all Boolean logic gates12 up to room temperature, demonstrating nonlinear classification with the nanomaterial system. We then evolve our dopant network to realize feature filters2 that can perform four-input binary classification on the Modified National Institute of Standards and Technology handwritten digit database. Implementation of our material-based filters substantially improves the classification accuracy over that of a linear classifier directly applied to the original data13. Our results establish a paradigm of silicon-based electronics for small-footprint and energy-efficient computation14.

10.
Mol Cell ; 70(5): 801-813.e6, 2018 06 07.
Article in English | MEDLINE | ID: mdl-29804829

ABSTRACT

The RNA-guided DNA endonuclease Cas9 is a powerful tool for genome editing. Little is known about the kinetics and fidelity of the double-strand break (DSB) repair process that follows a Cas9 cutting event in living cells. Here, we developed a strategy to measure the kinetics of DSB repair for single loci in human cells. Quantitative modeling of repaired DNA in time series after Cas9 activation reveals variable and often slow repair rates, with half-life times up to ∼10 hr. Furthermore, repair of the DSBs tends to be error prone. Both classical and microhomology-mediated end joining pathways contribute to the erroneous repair. Estimation of their individual rate constants indicates that the balance between these two pathways changes over time and can be altered by additional ionizing radiation. Our approach provides quantitative insights into DSB repair kinetics and fidelity in single loci and indicates that Cas9-induced DSBs are repaired in an unusual manner.


Subject(s)
CRISPR-Associated Protein 9/genetics , CRISPR-Cas Systems , Clustered Regularly Interspaced Short Palindromic Repeats , DNA Breaks, Double-Stranded , DNA End-Joining Repair , Gene Editing/methods , CRISPR-Associated Protein 9/metabolism , Humans , INDEL Mutation , K562 Cells , Kinetics , Models, Genetic
11.
EMBO J ; 40(10): e106632, 2021 05 17.
Article in English | MEDLINE | ID: mdl-33739466

ABSTRACT

HIV-1 latency is a major obstacle to achieving a functional cure for AIDS. Reactivation of HIV-1-infected cells followed by their elimination via immune surveillance is one proposed strategy for eradicating the viral reservoir. However, current latency-reversing agents (LRAs) show high toxicity and low efficiency, and new targets are needed to develop more promising LRAs. Here, we found that the histone chaperone CAF-1 (chromatin assembly factor 1) is enriched on the HIV-1 long terminal repeat (LTR) and forms nuclear bodies with liquid-liquid phase separation (LLPS) properties. CAF-1 recruits epigenetic modifiers and histone chaperones to the nuclear bodies to establish and maintain HIV-1 latency in different latency models and primary CD4+ T cells. Three disordered regions of the CHAF1A subunit are important for phase-separated CAF-1 nuclear body formation and play a key role in maintaining HIV-1 latency. Disruption of phase-separated CAF-1 bodies could be a potential strategy to reactivate latent HIV-1.


Subject(s)
HIV-1/metabolism , CD4-Positive T-Lymphocytes/metabolism , Chromatin Assembly Factor-1/genetics , Chromatin Assembly Factor-1/metabolism , Epigenesis, Genetic/genetics , Epigenesis, Genetic/physiology , HEK293 Cells , Humans , Promoter Regions, Genetic/genetics
12.
N Engl J Med ; 386(12): 1109-1120, 2022 03 24.
Article in English | MEDLINE | ID: mdl-35320642

ABSTRACT

BACKGROUND: Cryptococcal meningitis is a leading cause of human immunodeficiency virus (HIV)-related death in sub-Saharan Africa. Whether a treatment regimen that includes a single high dose of liposomal amphotericin B would be efficacious is not known. METHODS: In this phase 3 randomized, controlled, noninferiority trial conducted in five African countries, we assigned HIV-positive adults with cryptococcal meningitis in a 1:1 ratio to receive either a single high dose of liposomal amphotericin B (10 mg per kilogram of body weight) on day 1 plus 14 days of flucytosine (100 mg per kilogram per day) and fluconazole (1200 mg per day) or the current World Health Organization-recommended treatment, which includes amphotericin B deoxycholate (1 mg per kilogram per day) plus flucytosine (100 mg per kilogram per day) for 7 days, followed by fluconazole (1200 mg per day) for 7 days (control). The primary end point was death from any cause at 10 weeks; the trial was powered to show noninferiority at a 10-percentage-point margin. RESULTS: A total of 844 participants underwent randomization; 814 were included in the intention-to-treat population. At 10 weeks, deaths were reported in 101 participants (24.8%; 95% confidence interval [CI], 20.7 to 29.3) in the liposomal amphotericin B group and 117 (28.7%; 95% CI, 24.4 to 33.4) in the control group (difference, -3.9 percentage points); the upper boundary of the one-sided 95% confidence interval was 1.2 percentage points (within the noninferiority margin; P<0.001 for noninferiority). Fungal clearance from cerebrospinal fluid was -0.40 log10 colony-forming units (CFU) per milliliter per day in the liposomal amphotericin B group and -0.42 log10 CFU per milliliter per day in the control group. Fewer participants had grade 3 or 4 adverse events in the liposomal amphotericin B group than in the control group (50.0% vs. 62.3%). CONCLUSIONS: Single-dose liposomal amphotericin B combined with flucytosine and fluconazole was noninferior to the WHO-recommended treatment for HIV-associated cryptococcal meningitis and was associated with fewer adverse events. (Funded by the European and Developing Countries Clinical Trials Partnership and others; Ambition ISRCTN number, ISRCTN72509687.).


Subject(s)
AIDS-Related Opportunistic Infections/drug therapy , Amphotericin B/administration & dosage , Antifungal Agents/administration & dosage , Fluconazole/administration & dosage , Flucytosine/administration & dosage , Meningitis, Cryptococcal/drug therapy , AIDS-Related Opportunistic Infections/mortality , Administration, Oral , Africa South of the Sahara , Amphotericin B/adverse effects , Antifungal Agents/adverse effects , Drug Administration Schedule , Drug Therapy, Combination , Fluconazole/adverse effects , Flucytosine/adverse effects , HIV Infections/complications , Meningitis, Cryptococcal/mortality
13.
Plant Physiol ; 194(3): 1764-1778, 2024 Feb 29.
Article in English | MEDLINE | ID: mdl-38035763

ABSTRACT

Clubroot, caused by the soil-borne protist pathogen Plasmodiophora brassicae, is one of the most devastating diseases of Brassica oil and vegetable crops worldwide. Understanding the pathogen infection strategy is crucial for the development of disease control. However, because of its obligate biotrophic nature, the molecular mechanism by which this pathogen promotes infection remains largely unknown. P. brassicae E3 ubiquitin ligase 2 (PbE3-2) is a Really Interesting New Gene (RING)-type E3 ubiquitin ligase in P. brassicae with E3 ligase activity in vitro. Yeast (Saccharomyces cerevisiae) invertase assay and apoplast washing fluid extraction showed that PbE3-2 harbors a functional signal peptide. Overexpression of PbE3-2 in Arabidopsis (Arabidopsis thaliana) resulted in higher susceptibility to P. brassicae and decreases in chitin-triggered reactive oxygen species burst and expression of marker genes in salicylic acid signaling. PbE3-2 interacted with and ubiquitinated host cysteine protease RESPONSIVE TO DEHYDRATION 21A (RD21A) in vitro and in vivo. Mutant plants deficient in RD21A exhibited similar susceptibility and compromised immune responses as in PbE3-2 overexpression plants. We show that PbE3-2, which targets RD21A, is an important virulence factor for P. brassicae. Two other secretory RING-type E3 ubiquitin ligases in P. brassicae performed the same function as PbE3-2 and ubiquitinated RD21A. This study reveals a substantial virulence functional role of protist E3 ubiquitin ligases and demonstrates a mechanism by which protist E3 ubiquitin ligases degrade host immune-associated cysteine proteases to impede host immunity.


Subject(s)
Arabidopsis , Cysteine Proteases , Arabidopsis/genetics , Cysteine Proteases/genetics , Plant Immunity/genetics , Saccharomyces cerevisiae , Ubiquitin , Ubiquitin-Protein Ligases/genetics , Ubiquitination
14.
Plant Cell ; 34(10): 3718-3736, 2022 09 27.
Article in English | MEDLINE | ID: mdl-35861414

ABSTRACT

Pollen tube guidance regulates the growth direction and ovule targeting of pollen tubes in pistils, which is crucial for the completion of sexual reproduction in flowering plants. The Arabidopsis (Arabidopsis thaliana) pollen-specific receptor kinase (PRK) family members PRK3 and PRK6 are specifically tip-localized and essential for pollen tube growth and guidance. However, the mechanisms controlling the polar localization of PRKs at the pollen tube tip are unclear. The Arabidopsis P4-ATPase ALA3 helps establish the polar localization of apical phosphatidylserine (PS) in pollen tubes. Here, we discovered that loss of ALA3 function caused pollen tube defects in growth and ovule targeting and significantly affected the polar localization pattern of PRK3 and PRK6. Both PRK3 and PRK6 contain two polybasic clusters in the intracellular juxtamembrane domain, and they bound to PS in vitro. PRK3 and PRK6 with polybasic cluster mutations showed reduced or abolished binding to PS and altered polar localization patterns, and they failed to effectively complement the pollen tube-related phenotypes of prk mutants. These results suggest that ALA3 influences the precise localization of PRK3, PRK6, and other PRKs by regulating the distribution of PS, which plays a key role in regulating pollen tube growth and guidance.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Adenosine Triphosphatases/metabolism , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , Phosphatidylserines/metabolism , Phospholipids/metabolism , Pollen Tube , Protein Serine-Threonine Kinases
15.
Mol Psychiatry ; 2024 Jul 13.
Article in English | MEDLINE | ID: mdl-39003414

ABSTRACT

Neuroligin-3 (Nlgn3) is an autism-associated cell-adhesion molecule that interacts with neurexins and is robustly expressed in both neurons and astrocytes. Neuronal Nlgn3 is an essential regulator of synaptic transmission but the function of astrocytic Nlgn3 is largely unknown. Given the high penetrance of Nlgn3 mutations in autism and the emerging role of astrocytes in neuropsychiatric disorders, we here asked whether astrocytic Nlgn3 might shape neural circuit properties in the cerebellum similar to neuronal Nlgn3. Imaging of tagged Nlgn3 protein produced by CRISPR/Cas9-mediated genome editing showed that Nlgn3 is enriched in the cell body but not the fine processes of cerebellar astrocytes (Bergmann glia). Astrocyte-specific knockout of Nlgn3 did not detectably alter the number of synapses, synaptic transmission, or astrocyte morphology in mouse cerebellum. However, spatial transcriptomic analyses revealed a significant shift in gene expression among multiple cerebellar cell types after the deletion of astrocytic Nlgn3. Hence, in contrast to neuronal Nlgn3, astrocytic Nlgn3 in the cerebellum is not involved in shaping synapses but may modulate gene expression in specific brain areas.

16.
PLoS Biol ; 20(7): e3001699, 2022 07.
Article in English | MEDLINE | ID: mdl-35776767

ABSTRACT

Both the composition of cell types and their spatial distribution in a tissue play a critical role in cellular function, organ development, and disease progression. For example, intratumor heterogeneity and the distribution of transcriptional and genetic events in single cells drive the genesis and development of cancer. However, it can be challenging to fully characterize the molecular profile of cells in a tissue with high spatial resolution because microscopy has limited ability to extract comprehensive genomic information, and the spatial resolution of genomic techniques tends to be limited by dissection. There is a growing need for tools that can be used to explore the relationship between histological features, gene expression patterns, and spatially correlated genomic alterations in healthy and diseased tissue samples. Here, we present a technique that combines label-free histology with spatially resolved multiomics in unfixed and unstained tissue sections. This approach leverages stimulated Raman scattering microscopy to provide chemical contrast that reveals histological tissue architecture, allowing for high-resolution in situ laser microdissection of regions of interests. These microtissue samples are then processed for DNA and RNA sequencing to identify unique genetic profiles that correspond to distinct anatomical regions. We demonstrate the capabilities of this technique by mapping gene expression and copy number alterations to histologically defined regions in human oral squamous cell carcinoma (OSCC). Our approach provides complementary insights in tumorigenesis and offers an integrative tool for macroscale cancer tissues with spatial multiomics assessments.


Subject(s)
Carcinoma, Squamous Cell , Mouth Neoplasms , Carcinoma, Squamous Cell/genetics , DNA Copy Number Variations/genetics , Gene Expression Profiling/methods , Genomics , Humans , Sequence Analysis, RNA
17.
PLoS Genet ; 18(9): e1010351, 2022 09.
Article in English | MEDLINE | ID: mdl-36048878

ABSTRACT

Advances in genomic technology led to a more focused pattern for the distribution of chromosomal proteins and a better understanding of their functions. The recent development of the CUT&RUN technique marks one of the important such advances. Here we develop a modified CUT&RUN technique that we termed nanoCUT&RUN, in which a high affinity nanobody to GFP is used to bring micrococcal nuclease to the binding sites of GFP-tagged chromatin proteins. Subsequent activation of the nuclease cleaves the chromatin, and sequencing of released DNA identifies binding sites. We show that nanoCUT&RUN efficiently produces high quality data for the TRL transcription factor in Drosophila embryos, and distinguishes binding sites specific between two TRL isoforms. We further show that nanoCUT&RUN dissects the distributions of the HipHop and HOAP telomere capping proteins, and uncovers unexpected binding of telomeric proteins at centromeres. nanoCUT&RUN can be readily applied to any system in which a chromatin protein of interest, or its isoforms, carries the GFP tag.


Subject(s)
Drosophila Proteins , Drosophila , Animals , Chromatin/genetics , Chromatin/metabolism , Chromosomal Proteins, Non-Histone/genetics , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Drosophila/genetics , Drosophila Proteins/metabolism , Telomere/genetics , Telomere/metabolism , Transcription Factors/genetics
18.
Proc Natl Acad Sci U S A ; 119(18): e2120340119, 2022 05 03.
Article in English | MEDLINE | ID: mdl-35482922

ABSTRACT

Advanced therapies are commonly administered via injection even when they act within the skin tissue, and this increases the chances of off-target effects. Here we report the use of a skin patch containing a hypobaric chamber that induces skin dome formation to enable needleless delivery of advanced therapies directly into porcine, rat, and mouse skin. Finite element method modeling showed that the hypobaric chamber in the patch opened the skin appendages by 32%, thinned the skin, and compressed the appendage wall epithelia. These changes allowed direct delivery of an H1N1 vaccine antigen and a diclofenac nanotherapeutic into the skin. Fluorescence imaging and infrared mapping of the skin showed needleless delivery via the appendages. The in vivo utility of the patch was demonstrated by a superior immunoglobulin G response to the vaccine antigen in mice compared to intramuscular injection and a 70% reduction in rat paw swelling in vivo over 5 h with diclofenac without skin histology changes.


Subject(s)
Skin , Vaccines , Administration, Cutaneous , Animals , Mice , Needles , Rats , Skin/metabolism , Skin Absorption , Swine
19.
Chem Soc Rev ; 53(2): 606-623, 2024 Jan 22.
Article in English | MEDLINE | ID: mdl-38099593

ABSTRACT

Information storage and security is one of the perennial hot issues in society, while the further advancements of related chemical anti-counterfeiting systems remain a formidable challenge. As emerging anti-counterfeiting materials, stimulus-responsive polymers (SRPs) have attracted extensive attention due to their unique stimulus-responsiveness and charming discoloration performance. At the same time, single-channel decryption technology with low-security levels has been unable to effectively prevent information from being stolen or mimicked. As a result, it would be of great significance to develop SRPs with multi-mode and multi-level anti-counterfeiting characteristics. This study summarizes the latest achievements in advance anti-counterfeiting strategies based on SRPs, including multi-mode anti-counterfeiting (static information) and multi-level anti-counterfeiting (dynamic information). In addition, the promising applications of such materials in anti-counterfeiting labels, identification platforms, intelligent displays, and others are briefly reviewed. Finally, the challenges and opportunities in this emerging field are discussed. This review serves as a useful resource for manipulating SRP-based anti-counterfeiting materials and creating cutting-edge information security and encryption systems.

20.
J Biol Chem ; 299(4): 103025, 2023 04.
Article in English | MEDLINE | ID: mdl-36805336

ABSTRACT

Gastric cancer is one of the cancers with high morbidity and mortality worldwide. The aryl sulfonamide indisulam inhibits the proliferation of several types of cancer cells through its function as a molecular glue to promote the ubiquitination and degradation of RNA-binding motif protein 39 (RBM39). However, it is unknown whether and how indisulam regulates the migration of cancer cells. In this work, using label-free quantitative proteomics, we discover that indisulam significantly attenuates N-cadherin, a marker for epithelial to mesenchymal transition and migration of cancer cells. Our bioinformatics analysis and biochemical experiments reveal that indisulam promotes the interaction between the zinc finger E-box-binding homeobox 1 (ZEB1), a transcription factor of N-cadherin, and DCAF15, a substrate receptor of CRL4 E3 ubiquitin ligase, and enhances ZEB1 ubiquitination and proteasomal degradation. In addition, our cell line-based experiments demonstrate that indisulam inhibits the migration of gastric cancer cells in a ZEB1-dependent manner. Analyses of patient samples and datasets in public databases reveal that tumor tissues from patients with gastric cancer express high ZEB1 mRNA and this high expression reduces patient survival rate. Finally, we show that treatment of gastric tumor samples with indisulam significantly reduces ZEB1 protein levels. Therefore, this work discloses a new mechanism by which indisulam inhibits the migration of gastric cancer cells, indicating that indisulam exhibits different biological functions through distinct signaling molecules.


Subject(s)
Stomach Neoplasms , Humans , Stomach Neoplasms/drug therapy , Stomach Neoplasms/genetics , Stomach Neoplasms/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Cell Line, Tumor , Epithelial-Mesenchymal Transition/genetics , Ubiquitination , Sulfonamides/pharmacology , Zinc Finger E-box-Binding Homeobox 1/genetics , Zinc Finger E-box-Binding Homeobox 1/metabolism , Cell Movement , Cadherins/genetics , Cadherins/metabolism
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