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1.
Cell ; 186(2): 287-304.e26, 2023 01 19.
Article in English | MEDLINE | ID: mdl-36610399

ABSTRACT

Whether and how certain transposable elements with viral origins, such as endogenous retroviruses (ERVs) dormant in our genomes, can become awakened and contribute to the aging process is largely unknown. In human senescent cells, we found that HERVK (HML-2), the most recently integrated human ERVs, are unlocked to transcribe viral genes and produce retrovirus-like particles (RVLPs). These HERVK RVLPs constitute a transmissible message to elicit senescence phenotypes in young cells, which can be blocked by neutralizing antibodies. The activation of ERVs was also observed in organs of aged primates and mice as well as in human tissues and serum from the elderly. Their repression alleviates cellular senescence and tissue degeneration and, to some extent, organismal aging. These findings indicate that the resurrection of ERVs is a hallmark and driving force of cellular senescence and tissue aging.


Subject(s)
Aging , Endogenous Retroviruses , Aged , Animals , Humans , Mice , Aging/genetics , Aging/pathology , Cellular Senescence , Endogenous Retroviruses/genetics , Primates
2.
Nat Immunol ; 25(7): 1296-1305, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38806708

ABSTRACT

Inflammatory pain results from the heightened sensitivity and reduced threshold of nociceptor sensory neurons due to exposure to inflammatory mediators. However, the cellular and transcriptional diversity of immune cell and sensory neuron types makes it challenging to decipher the immune mechanisms underlying pain. Here we used single-cell transcriptomics to determine the immune gene signatures associated with pain development in three skin inflammatory pain models in mice: zymosan injection, skin incision and ultraviolet burn. We found that macrophage and neutrophil recruitment closely mirrored the kinetics of pain development and identified cell-type-specific transcriptional programs associated with pain and its resolution. Using a comprehensive list of potential interactions mediated by receptors, ligands, ion channels and metabolites to generate injury-specific neuroimmune interactomes, we also uncovered that thrombospondin-1 upregulated by immune cells upon injury inhibited nociceptor sensitization. This study lays the groundwork for identifying the neuroimmune axes that modulate pain in diverse disease contexts.


Subject(s)
Nociceptors , Pain , Animals , Mice , Pain/immunology , Pain/metabolism , Nociceptors/metabolism , Transcriptome , Mice, Inbred C57BL , Inflammation/immunology , Male , Macrophages/immunology , Macrophages/metabolism , Disease Models, Animal , Thrombospondin 1/metabolism , Thrombospondin 1/genetics , Skin/immunology , Skin/metabolism , Skin/pathology , Zymosan , Single-Cell Analysis , Neuroimmunomodulation , Gene Expression Profiling , Neutrophils/immunology , Neutrophils/metabolism
3.
Cell ; 180(3): 585-600.e19, 2020 02 06.
Article in English | MEDLINE | ID: mdl-32004457

ABSTRACT

Molecular mechanisms of ovarian aging and female age-related fertility decline remain unclear. We surveyed the single-cell transcriptomic landscape of ovaries from young and aged non-human primates (NHPs) and identified seven ovarian cell types with distinct gene-expression signatures, including oocyte and six types of ovarian somatic cells. In-depth dissection of gene-expression dynamics of oocytes revealed four subtypes at sequential and stepwise developmental stages. Further analysis of cell-type-specific aging-associated transcriptional changes uncovered the disturbance of antioxidant signaling specific to early-stage oocytes and granulosa cells, indicative of oxidative damage as a crucial factor in ovarian functional decline with age. Additionally, inactivated antioxidative pathways, increased reactive oxygen species, and apoptosis were observed in granulosa cells from aged women. This study provides a comprehensive understanding of the cell-type-specific mechanisms underlying primate ovarian aging at single-cell resolution, revealing new diagnostic biomarkers and potential therapeutic targets for age-related human ovarian disorders.


Subject(s)
Aging/genetics , Ovary/physiology , Single-Cell Analysis/methods , Transcriptome , Aged , Animals , Antioxidants/metabolism , Apoptosis/physiology , Atlases as Topic , Biomarkers , Cell Line, Tumor , Female , Granulosa Cells/metabolism , Humans , Macaca fascicularis , Oocytes/metabolism , Reactive Oxygen Species/metabolism , Signal Transduction/physiology
4.
Nature ; 2024 Sep 18.
Article in English | MEDLINE | ID: mdl-39294377

ABSTRACT

Micronuclear batteries harness energy from the radioactive decay of radioisotopes to generate electricity on a small scale, typically in the nanowatt or microwatt range1,2. Contrary to chemical batteries, the longevity of a micronuclear battery is tied to the half-life of the used radioisotope, enabling operational lifetimes that can span several decades3. Furthermore, the radioactive decay remains unaffected by environmental factors such as temperature, pressure and magnetic fields, making the micronuclear battery an enduring and reliable power source in scenarios in which conventional batteries prove impractical or challenging to replace4. Common radioisotopes of americium (241Am and 243Am) are α-decay emitters with half-lives longer than hundreds of years. Severe self-adsorption in traditional architectures of micronuclear batteries impedes high-efficiency α-decay energy conversion, making the development of α-radioisotope micronuclear batteries challenging5,6. Here we propose a micronuclear battery architecture that includes a coalescent energy transducer by incorporating 243Am into a luminescent lanthanide coordination polymer. This couples radioisotopes with energy transducers at the molecular level, resulting in an 8,000-fold enhancement in energy conversion efficiency from α decay energy to sustained autoluminescence compared with that of conventional architectures. When implemented in conjunction with a photovoltaic cell that translates autoluminescence into electricity, a new type of radiophotovoltaic micronuclear battery with a total power conversion efficiency of 0.889% and a power per activity of 139 microwatts per curie (µW Ci-1) is obtained.

5.
Nature ; 624(7992): 611-620, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37907096

ABSTRACT

Ageing is a critical factor in spinal-cord-associated disorders1, yet the ageing-specific mechanisms underlying this relationship remain poorly understood. Here, to address this knowledge gap, we combined single-nucleus RNA-sequencing analysis with behavioural and neurophysiological analysis in non-human primates (NHPs). We identified motor neuron senescence and neuroinflammation with microglial hyperactivation as intertwined hallmarks of spinal cord ageing. As an underlying mechanism, we identified a neurotoxic microglial state demarcated by elevated expression of CHIT1 (a secreted mammalian chitinase) specific to the aged spinal cords in NHP and human biopsies. In the aged spinal cord, CHIT1-positive microglia preferentially localize around motor neurons, and they have the ability to trigger senescence, partly by activating SMAD signalling. We further validated the driving role of secreted CHIT1 on MN senescence using multimodal experiments both in vivo, using the NHP spinal cord as a model, and in vitro, using a sophisticated system modelling the human motor-neuron-microenvironment interplay. Moreover, we demonstrated that ascorbic acid, a geroprotective compound, counteracted the pro-senescent effect of CHIT1 and mitigated motor neuron senescence in aged monkeys. Our findings provide the single-cell resolution cellular and molecular landscape of the aged primate spinal cord and identify a new biomarker and intervention target for spinal cord degeneration.


Subject(s)
Cellular Senescence , Chitinases , Microglia , Motor Neurons , Primates , Spinal Cord , Animals , Humans , Biomarkers/metabolism , Chitinases/metabolism , Microglia/enzymology , Microglia/metabolism , Microglia/pathology , Motor Neurons/metabolism , Neuroinflammatory Diseases/metabolism , Neuroinflammatory Diseases/pathology , Primates/metabolism , Reproducibility of Results , Single-Cell Gene Expression Analysis , Spinal Cord/metabolism , Spinal Cord/pathology
6.
Am J Hum Genet ; 111(8): 1544-1558, 2024 Aug 08.
Article in English | MEDLINE | ID: mdl-39079538

ABSTRACT

Recurrent copy-number variation represents one of the most well-established genetic drivers in neurodevelopmental disorders, including autism spectrum disorder. Duplication of 15q11-q13 (dup15q) is a well-described neurodevelopmental syndrome that increases the risk of autism more than 40-fold. However, the effects of this duplication on gene expression and chromatin accessibility in specific cell types in the human brain remain unknown. To identify the cell-type-specific transcriptional and epigenetic effects of dup15q in the human frontal cortex, we conducted single-nucleus RNA sequencing and multi-omic sequencing on dup15q-affected individuals (n = 6) as well as individuals with non-dup15q autism (n = 7) and neurotypical control individuals (n = 7). Cell-type-specific differential expression analysis identified significantly regulated genes, critical biological pathways, and differentially accessible genomic regions. Although there was overall increased gene expression across the duplicated genomic region, cellular identity represented an important factor mediating gene-expression changes. As compared to other cell types, neuronal subtypes showed greater upregulation of gene expression across a critical region within the duplication. Genes that fell within the duplicated region and had high baseline expression in control individuals showed only modest changes in dup15q, regardless of cell type. Of note, dup15q and autism had largely distinct signatures of chromatin accessibility but shared the majority of transcriptional regulatory motifs, suggesting convergent biological pathways. However, the transcriptional binding-factor motifs implicated in each condition implicated distinct biological mechanisms: neuronal JUN and FOS networks in autism vs. an inflammatory transcriptional network in dup15q microglia. This work provides a cell-type-specific analysis of how dup15q changes gene expression and chromatin accessibility in the human brain, and it finds evidence of marked cell-type-specific effects of this genetic driver. These findings have implications for guiding therapeutic development in dup15q syndrome, as well as understanding the functional effects of copy-number variants more broadly in neurodevelopmental disorders.


Subject(s)
Autistic Disorder , Brain , Chromosomes, Human, Pair 15 , DNA Copy Number Variations , Humans , Chromosomes, Human, Pair 15/genetics , Brain/metabolism , Brain/pathology , Male , Autistic Disorder/genetics , Female , Autism Spectrum Disorder/genetics , Chromosome Duplication/genetics , Chromatin/genetics , Chromatin/metabolism , Trisomy/genetics , Child , Neurons/metabolism , Neurons/pathology , Chromosome Aberrations , Intellectual Disability
7.
Development ; 150(19)2023 10 01.
Article in English | MEDLINE | ID: mdl-37796037

ABSTRACT

Inner ear development requires the coordination of cell types from distinct epithelial, mesenchymal and neuronal lineages. Although we have learned much from animal models, many details about human inner ear development remain elusive. We recently developed an in vitro model of human inner ear organogenesis using pluripotent stem cells in a 3D culture, fostering the growth of a sensorineural circuit, including hair cells and neurons. Despite previously characterizing some cell types, many remain undefined. This study aimed to chart the in vitro development timeline of the inner ear organoid to understand the mechanisms at play. Using single-cell RNA sequencing at ten stages during the first 36 days of differentiation, we tracked the evolution from pluripotency to various ear cell types after exposure to specific signaling modulators. Our findings showcase gene expression that influences differentiation, identifying a plethora of ectodermal and mesenchymal cell types. We also discern aspects of the organoid model consistent with in vivo development, while highlighting potential discrepancies. Our study establishes the Inner Ear Organoid Developmental Atlas (IODA), offering deeper insights into human biology and improving inner ear tissue differentiation.


Subject(s)
Ear, Inner , Animals , Humans , Ear, Inner/metabolism , Hair Cells, Auditory , Organoids , Cells, Cultured , Cell Differentiation/genetics
8.
Proc Natl Acad Sci U S A ; 120(23): e2300052120, 2023 06 06.
Article in English | MEDLINE | ID: mdl-37252957

ABSTRACT

Short trinucleotide expansions at the FMR1 locus are associated with the late-onset condition fragile X-associated tremor/ataxia syndrome (FXTAS), which shows very different clinical and pathological features from fragile X syndrome (associated with longer expansions), with no clear molecular explanation for these marked differences. One prevailing theory posits that the shorter, premutation expansion uniquely causes extreme neurotoxic increases in FMR1 mRNA (i.e., four to eightfold increases), but evidence to support this hypothesis is largely derived from analysis of peripheral blood. We applied single-nucleus RNA sequencing to postmortem frontal cortex and cerebellum from 7 individuals with premutation and matched controls (n = 6) to assess cell type-specific molecular neuropathology. We found only modest upregulation (~1.3-fold) of FMR1 in some glial populations associated with premutation expansions. In premutation cases, we also identified decreased astrocyte proportions in the cortex. Differential expression and gene ontology analysis demonstrated altered neuroregulatory roles of glia. Using network analyses, we identified cell type-specific and region-specific patterns of FMR1 protein target gene dysregulation unique to premutation cases, with notable network dysregulation in the cortical oligodendrocyte lineage. We used pseudotime trajectory analysis to determine how oligodendrocyte development was altered and identified differences in early gene expression in oligodendrocyte trajectories in premutation cases specifically, implicating early cortical glial developmental perturbations. These findings challenge dogma regarding extremely elevated FMR1 increases in FXTAS and implicate glial dysregulation as a critical facet of premutation pathophysiology, representing potential unique therapeutic targets directly derived from the human condition.


Subject(s)
Fragile X Syndrome , Humans , Fragile X Syndrome/pathology , Tremor/genetics , Trinucleotide Repeat Expansion , Fragile X Mental Retardation Protein/genetics , Fragile X Mental Retardation Protein/metabolism , Ataxia/genetics , Ataxia/pathology , Brain/metabolism , Astrocytes/metabolism
9.
PLoS Genet ; 19(2): e1010640, 2023 02.
Article in English | MEDLINE | ID: mdl-36802400

ABSTRACT

The molecular mechanism of tumor metastasis, especially how metastatic tumor cells colonize in a distant site, remains poorly understood. Here we reported that ARHGAP15, a Rho GTPase activating protein, enhanced gastric cancer (GC) metastatic colonization, which was quite different from its reported role as a tumor suppressor gene in other cancers. It was upregulated in metastatic lymph nodes and significantly associated with a poor prognosis. Ectopic expression of ARHGAP15 promoted metastatic colonization of gastric cancer cells in murine lungs and lymph nodes in vivo or protected cells from oxidative-related death in vitro. However, genetic downregulation of ARHGAP15 had the opposite effect. Mechanistically, ARHGAP15 inactivated RAC1 and then decreased intracellular accumulation of reactive oxygen species (ROS), thus enhancing the antioxidant capacity of colonizing tumor cells under oxidative stress. This phenotype could be phenocopied by inhibition of RAC1 or rescued by the introduction of constitutively active RAC1 into cells. Taken together, these findings suggested a novel role of ARHGAP15 in promoting gastric cancer metastasis by quenching ROS through inhibiting RAC1 and its potential value for prognosis estimation and targeted therapy.


Subject(s)
Stomach Neoplasms , Mice , Animals , Reactive Oxygen Species/metabolism , Stomach Neoplasms/genetics , Down-Regulation , Oxidative Stress , rac1 GTP-Binding Protein/genetics , Cell Line, Tumor
10.
Proc Natl Acad Sci U S A ; 120(8): e2206878120, 2023 02 21.
Article in English | MEDLINE | ID: mdl-36791099

ABSTRACT

SET is a multifunctional histone-binding oncoprotein that regulates transcription by an unclear mechanism. Here we show that SET enhances estrogen-dependent transcription. SET knockdown abrogates transcription of estrogen-responsive genes and their enhancer RNAs. In response to 17ß-estradiol (E2), SET binds to the estrogen receptor α (ERα) and is recruited to ERα-bound enhancers and promoters at estrogen response elements (EREs). SET functions as a histone H2 chaperone that dynamically associates with H2A.Z via its acidic C-terminal domain and promotes H2A.Z incorporation, ERα, MLL1, and KDM3A loading and modulates histone methylation at EREs. SET depletion diminishes recruitment of condensin complexes to EREs and impairs E2-dependent enhancer-promoter looping. Thus, SET boosts E2-induced gene expression by establishing an active chromatin structure at ERα-bound enhancers and promoters, which is essential for transcriptional activation.


Subject(s)
Chromatin , Histones , Chromatin/genetics , Histones/genetics , Histones/metabolism , Estrogen Receptor alpha/genetics , Estrogen Receptor alpha/metabolism , Cell Line, Tumor , Estrogens/metabolism , Estradiol/pharmacology , Oncogene Proteins/metabolism , Transcription, Genetic
11.
J Biol Chem ; : 107785, 2024 Sep 19.
Article in English | MEDLINE | ID: mdl-39305961

ABSTRACT

Cancer cells undergo metabolic reprogramming that is intricately linked to malignancy. Protein acylations are especially responsive to metabolic changes, influencing signal transduction pathways and fostering cell proliferation. However, as a novel type of acylations, the involvement of malonylation in cancer remains poorly understood. In this study, we observed a significant reduction in malonyl-CoA levels in hepatocellular carcinoma (HCC), which correlated with a global decrease in malonylation. Subsequent nuclear malonylome analysis unveiled nucleolin (NCL) malonylation, which was notably enhanced in HCC biopsies. we demonstrated that NCL undergoes malonylation at lysine residues 124 and 398. This modification triggers the translocation of NCL from the nucleolus to nucleoplasm and cytoplasm, binding to AKT mRNA, and promoting AKT translation in HCC. Silencing AKT expression markedly attenuated HCC cell proliferation driven by NCL malonylation. These findings collectively highlight nuclear signaling in modulating AKT expression, suggesting NCL malonylation as a novel mechanism through which cancer cells drive cell proliferation.

12.
Mol Biol Evol ; 41(4)2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38415839

ABSTRACT

Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determine the extant distribution of yeast enterobactin producers and cheaters.


Subject(s)
Enterobactin , Evolution, Molecular , Operon , Phylogeny , Enterobactin/metabolism , Enterobactin/genetics , Siderophores/metabolism , Siderophores/genetics , Genes, Fungal , Saccharomycetales/genetics , Saccharomycetales/metabolism , Gene Transfer, Horizontal
13.
Circ Res ; 133(1): e1-e16, 2023 06 23.
Article in English | MEDLINE | ID: mdl-37154033

ABSTRACT

BACKGROUND: Atrial fibrillation (AF), the most common arrhythmia, is associated with the downregulation of FKBP5 (encoding FKBP5 [FK506 binding protein 5]). However, the function of FKBP5 in the heart remains unknown. Here, we elucidate the consequences of cardiomyocyte-restricted loss of FKBP5 on cardiac function and AF development and study the underlying mechanisms. METHODS: Right atrial samples from patients with AF were used to assess the protein levels of FKBP5. A cardiomyocyte-specific FKBP5 knockdown mouse model was established by crossbreeding Fkbp5flox/flox mice with Myh6MerCreMer/+ mice. Cardiac function and AF inducibility were assessed by echocardiography and programmed intracardiac stimulation. Histology, optical mapping, cellular electrophysiology, and biochemistry were employed to elucidate the proarrhythmic mechanisms due to loss of cardiomyocyte FKBP5. RESULTS: FKBP5 protein levels were lower in the atrial lysates of patients with paroxysmal AF or long-lasting persistent (chronic) AF. Cardiomyocyte-specific knockdown mice exhibited increased AF inducibility and duration compared with control mice. Enhanced AF susceptibility in cardiomyocyte-specific knockdown mice was associated with the development of action potential alternans and spontaneous Ca2+ waves, and increased protein levels and activity of the NCX1 (Na+/Ca2+-exchanger 1), mimicking the cellular phenotype of chronic AF patients. FKBP5-deficiency enhanced transcription of Slc8a1 (encoding NCX1) via transcription factor hypoxia-inducible factor 1α. In vitro studies revealed that FKBP5 negatively modulated the protein levels of hypoxia-inducible factor 1α by competitively interacting with heat-shock protein 90. Injections of the heat-shock protein 90 inhibitor 17-AAG normalized protein levels of hypoxia-inducible factor 1α and NCX1 and reduced AF susceptibility in cardiomyocyte-specific knockdown mice. Furthermore, the atrial cardiomyocyte-selective knockdown of FKBP5 was sufficient to enhance AF arrhythmogenesis. CONCLUSIONS: This is the first study to demonstrate a role for the FKBP5-deficiency in atrial arrhythmogenesis and to establish FKBP5 as a negative regulator of hypoxia-inducible factor 1α in cardiomyocytes. Our results identify a potential molecular mechanism for the proarrhythmic NCX1 upregulation in chronic AF patients.


Subject(s)
Atrial Fibrillation , Mice , Animals , Atrial Fibrillation/metabolism , Down-Regulation , Myocytes, Cardiac/metabolism , Hypoxia/metabolism , Heat-Shock Proteins/metabolism
14.
J Am Chem Soc ; 146(20): 14318-14327, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38718345

ABSTRACT

Multiband convergence has attracted significant interest due to its positive effects on further improving thermoelectric performance. However, the current research mainly focuses on two- or three-band convergence in lead chalcogenides through doping and alloying. Therefore, exploring a new strategy to facilitate more-band convergence has instructive significance and practical value in thermoelectric research. Herein, we first propose a high-entropy strategy to achieve four-band convergence for optimizing thermoelectric performance. Taking high-entropy AgSbPbSnGeTe5 as an example, we found that the emergence of more-band convergence occurs as the configuration entropy increases; in particular, the four-band convergence occurs in high-entropy AgSbPbSnGeTe5. The overlap of multiatom orbitals in the high-entropy sample contributes to the convergence of four valence bands, promoting the improvement of electrical performance. Meanwhile, due to large lattice distortion and disordered atoms, the phonon mean free path is effectively compressed, resulting in low lattice thermal conductivity of high-entropy AgSbPbSnGeTe5. Consequently, AgSbPbSnGeTe5 achieved an intrinsically high ZT value of 1.22 at 673 K, providing a cornerstone for further optimizing thermoelectric performance. For example, by generally optimizing the carrier concentration, a peak ZT value of ∼1.75 at 723 K is achieved. These insights offer a comprehensive understanding of the band structure affected by unique structures of high-entropy materials and also shed useful light on innovation mechanisms and functionalities for future improvement of thermoelectric performance.

15.
J Am Chem Soc ; 146(1): 892-900, 2024 Jan 10.
Article in English | MEDLINE | ID: mdl-38151507

ABSTRACT

Layered compounds characterized by van der Waals gaps are often associated with relatively weak interlayer particle interactions. However, in specific scenarios, these seemingly feeble forces can exert an impact on interlayer interactions through subtle energy fluctuations, which can give rise to a diverse range of physical and chemical properties, particularly intriguing in the context of thermal transport. In this study, taking a natural superlattice composed of alternately stacked PbS and SnS2 sublayers as a model, we proposed that in a superlattice, there is strong hybridization between acoustic phonons of heavy sublayers and optical phonons of light sublayers. We identified newly generated vibration modes in the superlattice, such as interlayer shear and breathing, which exhibit lower sound velocity and contribute less to heat transport compared to their parent materials, which significantly alters the thermal behaviors of the superlattice compared to its bulk counterparts. Our findings on the behavior of interlayer phonons in superlattices not only can shed light on developing functional materials with enhanced thermal dissipation capabilities but also contribute to the broader field of condensed matter physics, offering insights into various fields, including thermoelectrics and phononic devices, and may pave the way for technological advancements in these areas.

16.
Apoptosis ; 29(5-6): 799-815, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38347337

ABSTRACT

PANoptosis is a form of inflammatory programmed cell death that is regulated by the PANoptosome. This PANoptosis possesses key characteristics of pyroptosis, apoptosis, and necroptosis, yet cannot be fully explained by any of these cell death modes. The unique nature of this cell death mechanism has garnered significant interest. However, the specific role of PANoptosis-associated features in gastric cancer (GC) is still uncertain. Patients were categorized into different PAN subtypes based on the expression of genes related to the PANoptosome. We conducted a systematic analysis to investigate the variations in prognosis and tumor microenvironment (TME) among these subtypes. Furthermore, we developed a risk score, called PANoptosis-related risk score (PANS), which is constructed from genes associated with the PANoptosis. We comprehensively analyzed the correlation between PANS and GC prognosis, TME, immunotherapy efficacy and chemotherapeutic drug sensitivity. Additionally, we performed in vitro experiments to validate the impact of Keratin 7 (KRT7) on GC. We identified two PAN subtypes (PANcluster A and B). PANoptosome genes were highly expressed in PANcluster A. PANcluster A has the characteristics of favorable prognosis, abundant infiltration of anti-tumor lymphocytes, and sensitivity to immunotherapy, thus it was categorized as an immune-inflammatory type. Meanwhile, our constructed PANS can effectively predict the prognosis and immune efficacy of GC. Patients with low PANS have a good prognosis, and have the characteristics of high tumor mutation load (TMB), high microsatellite instability (MSI), low tumor purity and sensitivity to immunotherapy. In addition, PANS can also identify suitable populations for different chemotherapy drugs. Finally, we confirmed that KRT7 is highly expressed in GC. Knocking down the expression of KRT7 significantly weakens the proliferation and migration abilities of GC cells. The models based on PANoptosis signature help to identify the TME features of GC and can effectively predict the prognosis and immune efficacy of GC. Furthermore, the experimental verification results of KRT7 provide theoretical support for anti-tumor treatment.


Subject(s)
Immunotherapy , Stomach Neoplasms , Tumor Microenvironment , Stomach Neoplasms/genetics , Stomach Neoplasms/immunology , Stomach Neoplasms/pathology , Stomach Neoplasms/drug therapy , Stomach Neoplasms/diagnosis , Humans , Prognosis , Tumor Microenvironment/immunology , Tumor Microenvironment/genetics , Cell Line, Tumor , Gene Expression Regulation, Neoplastic , Keratin-7/genetics , Keratin-7/metabolism , Apoptosis/genetics
17.
Biochem Cell Biol ; 102(2): 179-193, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38086039

ABSTRACT

Mitochondria play a critical role in nerve regeneration, yet the impact of gene expression changes related to mitochondria in facial nerve regeneration remains unknown. To address this knowledge gap, we analyzed the expression profile of the facial motor nucleus (FMN) using data obtained from the Gene Expression Omnibus (GEO) database (GSE162977). By comparing different time points in the data, we identified differentially expressed genes (DEGs). Additionally, we collected mitochondria-related genes from the Gene Ontology (GO) database and intersected them with the DEGs, resulting in the identification of mitochondria-related DEGs (MIT-DEGs). To gain further insights, we performed functional enrichment and pathway analysis of the MIT-DEGs. To explore the interactions among these MIT-DEGs, we constructed a protein-protein interaction (PPI) network using the STRING database and identified hub genes using the Degree algorithm of Cytoscape software. To validate the relevance of these genes to nerve regeneration, we established a rat facial nerve injury (FNI) model and conducted a series of experiments. Through these experiments, we confirmed three MIT-DEGs (Myc, Lyn, and Cdk1) associated with facial nerve regeneration. Our findings provide valuable insights into the transcriptional changes of mitochondria-related genes in the FMN following FNI, which can contribute to the development of new treatment strategies for FNI.


Subject(s)
Gene Expression Profiling , Gene Regulatory Networks , Animals , Rats , Gene Expression Profiling/methods , Protein Interaction Maps/genetics , Software , Computational Biology/methods , Gene Ontology
18.
Small ; : e2407299, 2024 Sep 18.
Article in English | MEDLINE | ID: mdl-39291893

ABSTRACT

Polymer dielectrics are the key materials for pulsed energy storage systems, but their low energy densities greatly restrict the applications in integrated electronic devices. Herein, a unique bumpy granular interlayer consisting of gold nanoparticles (Au NPs) and polymethyksesquioxane (PMSQ) microspheres is introduced into a poly(vinylidene fluoride) (PVDF) film, forming trilayered PVDF-Au/PMSQ-PVDF films. Interestingly, the Au/PMSQ interlayer arouses a dielectric enhancement of 47% and an ultrahigh breakdown strength of 704 MV m-1, which reaches 153% of pure PVDF. It is revealed that the greatly enhanced breakdown strength originated from the Coulomb-blockade effect of Au NPs and the excellent insulating properties of PMSQ microspheres with a special molecular-scale organic-inorganic hybrid structure. Benefiting from the concurrently enhanced dielectric and breakdown performances, an outstanding energy density of 22.42 J cm-3 with an efficiency of 67.1%, which reaches 249% of that of the pure PVDF, is achieved. It is further confirmed that this design strategy is also applicable to linear dielectric polymer polyethyleneimine. The composites exhibit an energy density of 8.91 J cm-3 with a high efficiency of ≈95%. This work offers a novel and efficient strategy for concurrently enhancing the dielectric and breakdown performances of polymers toward pulsed power applications.

19.
Plant Cell Environ ; 2024 Sep 09.
Article in English | MEDLINE | ID: mdl-39248638

ABSTRACT

Drought is one of the most severe environmental factors limiting plant growth and crop yield, necessitating the identification of genes that enhance drought resistance for crop improvement. Through screening an ethyl methyl sulfonate-mutagenized rice mutant library, we isolated the PEG tolerance mutant 97-1 (ptm97-1), which displays enhanced resistance to osmotic and drought stress, and increased yield under drought conditions. A point mutation in OsMATE6 was identified as being associated with the drought-resistant phenotype of ptm97-1. The role of OsMATE6 in conferring drought resistance was confirmed by additional OsMATE6 knockout mutants. OsMATE6 is expressed in guard cells, shoots and roots and the OsMATE6-GFP fusion protein predominantly localizes to the plasma membrane. Our ABA efflux assays suggest that OsMATE6 functions as an ABA efflux transporter; mutant protoplasts exhibited a slower ABA release rate compared to the wild type. We hypothesize that OsMATE6 regulates ABA levels in guard cells, influencing stomatal closure and enhancing drought resistance. Notably, OsMATE6 knockout mutants demonstrated greater yields under field drought conditions compared to wild-type plants, highlighting OsMATE6 as a promising candidate for improving crop drought resistance.

20.
Phys Rev Lett ; 132(11): 110204, 2024 Mar 15.
Article in English | MEDLINE | ID: mdl-38563922

ABSTRACT

We present an approach to estimate the operational distinguishability between an entangled state and any separable state directly from measuring an entanglement witness. We show that this estimation also implies bounds on a variety of other well-known entanglement quantifiers. This approach for entanglement estimation is then extended to both the measurement-device-independent scenario and the fully device-independent scenario, where we obtain nontrivial but suboptimal bounds. The procedure requires no numerical optimization and is easy to compute. It offers ways for experimenters to not only detect, but also quantify, entanglement from the standard entanglement witness procedure.

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