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1.
Cell ; 185(24): 4654-4673.e28, 2022 11 23.
Article in English | MEDLINE | ID: mdl-36334589

ABSTRACT

Brown adipose tissue (BAT) regulates metabolic physiology. However, nearly all mechanistic studies of BAT protein function occur in a single inbred mouse strain, which has limited the understanding of generalizable mechanisms of BAT regulation over physiology. Here, we perform deep quantitative proteomics of BAT across a cohort of 163 genetically defined diversity outbred mice, a model that parallels the genetic and phenotypic variation found in humans. We leverage this diversity to define the functional architecture of the outbred BAT proteome, comprising 10,479 proteins. We assign co-operative functions to 2,578 proteins, enabling systematic discovery of regulators of BAT. We also identify 638 proteins that correlate with protection from, or sensitivity to, at least one parameter of metabolic disease. We use these findings to uncover SFXN5, LETMD1, and ATP1A2 as modulators of BAT thermogenesis or adiposity, and provide OPABAT as a resource for understanding the conserved mechanisms of BAT regulation over metabolic physiology.


Subject(s)
Adipose Tissue, Brown , Proteome , Humans , Mice , Animals , Adipose Tissue, Brown/metabolism , Proteome/metabolism , Thermogenesis/physiology , Adiposity , Obesity/metabolism , Mice, Inbred C57BL , Proto-Oncogene Proteins/metabolism
2.
Cell ; 184(11): 3022-3040.e28, 2021 05 27.
Article in English | MEDLINE | ID: mdl-33961781

ABSTRACT

Thousands of interactions assemble proteins into modules that impart spatial and functional organization to the cellular proteome. Through affinity-purification mass spectrometry, we have created two proteome-scale, cell-line-specific interaction networks. The first, BioPlex 3.0, results from affinity purification of 10,128 human proteins-half the proteome-in 293T cells and includes 118,162 interactions among 14,586 proteins. The second results from 5,522 immunoprecipitations in HCT116 cells. These networks model the interactome whose structure encodes protein function, localization, and complex membership. Comparison across cell lines validates thousands of interactions and reveals extensive customization. Whereas shared interactions reside in core complexes and involve essential proteins, cell-specific interactions link these complexes, "rewiring" subnetworks within each cell's interactome. Interactions covary among proteins of shared function as the proteome remodels to produce each cell's phenotype. Viewable interactively online through BioPlexExplorer, these networks define principles of proteome organization and enable unknown protein characterization.


Subject(s)
Protein Interaction Mapping/methods , Protein Interaction Maps/genetics , Proteome/genetics , Computational Biology/methods , HCT116 Cells/metabolism , HEK293 Cells/metabolism , Humans , Mass Spectrometry/methods , Protein Interaction Maps/physiology , Proteome/metabolism , Proteomics/methods
3.
Nature ; 631(8021): 635-644, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38961291

ABSTRACT

Innate immune pattern recognition receptors, such as the Toll-like receptors (TLRs), are key mediators of the immune response to infection and central to our understanding of health and disease1. After microbial detection, these receptors activate inflammatory signal transduction pathways that involve IκB kinases, mitogen-activated protein kinases, ubiquitin ligases and other adaptor proteins. The mechanisms that connect the proteins in the TLR pathways are poorly defined. To delineate TLR pathway activities, we engineered macrophages to enable microscopy and proteomic analysis of the endogenous myddosome constituent MyD88. We found that myddosomes form transient contacts with activated TLRs and that TLR-free myddosomes are dynamic in size, number and composition over the course of 24 h. Analysis using super-resolution microscopy revealed that, within most myddosomes, MyD88 forms barrel-like structures that function as scaffolds for effector protein recruitment. Proteomic analysis demonstrated that myddosomes contain proteins that act at all stages and regulate all effector responses of the TLR pathways, and genetic analysis defined the epistatic relationship between these effector modules. Myddosome assembly was evident in cells infected with Listeria monocytogenes, but these bacteria evaded myddosome assembly and TLR signalling during cell-to-cell spread. On the basis of these findings, we propose that the entire TLR signalling pathway is executed from within the myddosome.


Subject(s)
Macrophages , Signal Transduction , Toll-Like Receptors , Animals , Humans , Mice , Listeria monocytogenes/immunology , Listeriosis/immunology , Listeriosis/microbiology , Listeriosis/metabolism , Macrophages/immunology , Macrophages/metabolism , Macrophages/microbiology , Myeloid Differentiation Factor 88/metabolism , Proteomics , Toll-Like Receptors/metabolism , Microscopy , Immunity, Innate
4.
Nature ; 605(7909): 357-365, 2022 05.
Article in English | MEDLINE | ID: mdl-35508654

ABSTRACT

The entry of mammalian cells into the DNA synthesis phase (S phase) represents a key event in cell division1. According to current models of the cell cycle, the kinase CDC7 constitutes an essential and rate-limiting trigger of DNA replication, acting together with the cyclin-dependent kinase CDK2. Here we show that CDC7 is dispensable for cell division of many different cell types, as determined using chemical genetic systems that enable acute shutdown of CDC7 in cultured cells and in live mice. We demonstrate that another cell cycle kinase, CDK1, is also active during G1/S transition both in cycling cells and in cells exiting quiescence. We show that CDC7 and CDK1 perform functionally redundant roles during G1/S transition, and at least one of these kinases must be present to allow S-phase entry. These observations revise our understanding of cell cycle progression by demonstrating that CDK1 physiologically regulates two distinct transitions during cell division cycle, whereas CDC7 has a redundant function in DNA replication.


Subject(s)
Cell Cycle Proteins , G1 Phase , Protein Serine-Threonine Kinases , Proteolysis , S Phase , Animals , Cell Cycle Proteins/metabolism , DNA Replication , Mice , Protein Serine-Threonine Kinases/metabolism
5.
Mol Cell ; 80(5): 828-844.e6, 2020 12 03.
Article in English | MEDLINE | ID: mdl-33128871

ABSTRACT

Cancer-associated mutations that stabilize NRF2, an oxidant defense transcription factor, are predicted to promote tumor development. Here, utilizing 3D cancer spheroid models coupled with CRISPR-Cas9 screens, we investigate the molecular pathogenesis mediated by NRF2 hyperactivation. NRF2 hyperactivation was necessary for proliferation and survival in lung tumor spheroids. Antioxidant treatment rescued survival but not proliferation, suggesting the presence of distinct mechanisms. CRISPR screens revealed that spheroids are differentially dependent on the mammalian target of rapamycin (mTOR) for proliferation and the lipid peroxidase GPX4 for protection from ferroptosis of inner, matrix-deprived cells. Ferroptosis inhibitors blocked death from NRF2 downregulation, demonstrating a critical role of NRF2 in protecting matrix-deprived cells from ferroptosis. Interestingly, proteomics analyses show global enrichment of selenoproteins, including GPX4, by NRF2 downregulation, and targeting NRF2 and GPX4 killed spheroids overall. These results illustrate the value of spheroid culture in revealing environmental or spatial differential dependencies on NRF2 and reveal exploitable vulnerabilities of NRF2-hyperactivated tumors.


Subject(s)
CRISPR-Cas Systems , Cell Culture Techniques , Cell Proliferation , Ferroptosis , NF-E2-Related Factor 2/metabolism , Neoplasm Proteins/metabolism , Neoplasms/metabolism , Spheroids, Cellular/metabolism , A549 Cells , Humans , NF-E2-Related Factor 2/genetics , Neoplasm Proteins/genetics , Neoplasms/genetics , Neoplasms/pathology , Phospholipid Hydroperoxide Glutathione Peroxidase/genetics , Phospholipid Hydroperoxide Glutathione Peroxidase/metabolism , Spheroids, Cellular/pathology , TOR Serine-Threonine Kinases/genetics , TOR Serine-Threonine Kinases/metabolism
6.
Mol Cell ; 78(3): 459-476.e13, 2020 05 07.
Article in English | MEDLINE | ID: mdl-32240602

ABSTRACT

The cyclin-dependent kinase 1 (Cdk1) drives cell division. To uncover additional functions of Cdk1, we generated knockin mice expressing an analog-sensitive version of Cdk1 in place of wild-type Cdk1. In our study, we focused on embryonic stem cells (ESCs), because this cell type displays particularly high Cdk1 activity. We found that in ESCs, a large fraction of Cdk1 substrates is localized on chromatin. Cdk1 phosphorylates many proteins involved in epigenetic regulation, including writers and erasers of all major histone marks. Consistent with these findings, inhibition of Cdk1 altered histone-modification status of ESCs. High levels of Cdk1 in ESCs phosphorylate and partially inactivate Dot1l, the H3K79 methyltransferase responsible for placing activating marks on gene bodies. Decrease of Cdk1 activity during ESC differentiation de-represses Dot1l, thereby allowing coordinated expression of differentiation genes. These analyses indicate that Cdk1 functions to maintain the epigenetic identity of ESCs.


Subject(s)
CDC2 Protein Kinase/metabolism , Embryonic Stem Cells/physiology , Epigenesis, Genetic , Adenosine Triphosphate/analogs & derivatives , Adenosine Triphosphate/metabolism , Animals , CDC2 Protein Kinase/genetics , Cell Differentiation , Cells, Cultured , Chromatin Immunoprecipitation/methods , Female , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Humans , MCF-7 Cells , Male , Mice , Mice, Knockout , Phosphorylation , Saccharomyces cerevisiae Proteins/metabolism
7.
N Engl J Med ; 390(15): 1359-1371, 2024 Apr 18.
Article in English | MEDLINE | ID: mdl-38631003

ABSTRACT

BACKGROUND: Adjuvant pembrolizumab therapy after surgery for renal-cell carcinoma was approved on the basis of a significant improvement in disease-free survival in the KEYNOTE-564 trial. Whether the results regarding overall survival from the third prespecified interim analysis of the trial would also favor pembrolizumab was uncertain. METHODS: In this phase 3, double-blind, placebo-controlled trial, we randomly assigned (in a 1:1 ratio) participants with clear-cell renal-cell carcinoma who had an increased risk of recurrence after surgery to receive pembrolizumab (at a dose of 200 mg) or placebo every 3 weeks for up to 17 cycles (approximately 1 year) or until recurrence, the occurrence of unacceptable toxic effects, or withdrawal of consent. A significant improvement in disease-free survival according to investigator assessment (the primary end point) was shown previously. Overall survival was the key secondary end point. Safety was a secondary end point. RESULTS: A total of 496 participants were assigned to receive pembrolizumab and 498 to receive placebo. As of September 15, 2023, the median follow-up was 57.2 months. The disease-free survival benefit was consistent with that in previous analyses (hazard ratio for recurrence or death, 0.72; 95% confidence interval [CI], 0.59 to 0.87). A significant improvement in overall survival was observed with pembrolizumab as compared with placebo (hazard ratio for death, 0.62; 95% CI, 0.44 to 0.87; P = 0.005). The estimated overall survival at 48 months was 91.2% in the pembrolizumab group, as compared with 86.0% in the placebo group; the benefit was consistent across key subgroups. Pembrolizumab was associated with a higher incidence of serious adverse events of any cause (20.7%, vs. 11.5% with placebo) and of grade 3 or 4 adverse events related to pembrolizumab or placebo (18.6% vs. 1.2%). No deaths were attributed to pembrolizumab therapy. CONCLUSIONS: Adjuvant pembrolizumab was associated with a significant and clinically meaningful improvement in overall survival, as compared with placebo, among participants with clear-cell renal-cell carcinoma at increased risk for recurrence after surgery. (Funded by Merck Sharp and Dohme, a subsidiary of Merck; KEYNOTE-564 ClinicalTrials.gov number, NCT03142334.).


Subject(s)
Antineoplastic Agents, Immunological , Carcinoma, Renal Cell , Kidney Neoplasms , Humans , Adjuvants, Immunologic/administration & dosage , Adjuvants, Immunologic/adverse effects , Adjuvants, Immunologic/therapeutic use , Antibodies, Monoclonal, Humanized/administration & dosage , Antibodies, Monoclonal, Humanized/adverse effects , Antibodies, Monoclonal, Humanized/therapeutic use , Carcinoma, Renal Cell/drug therapy , Carcinoma, Renal Cell/mortality , Carcinoma, Renal Cell/surgery , Double-Blind Method , Kidney Neoplasms/drug therapy , Kidney Neoplasms/mortality , Kidney Neoplasms/surgery , Antineoplastic Agents, Immunological/administration & dosage , Antineoplastic Agents, Immunological/adverse effects , Antineoplastic Agents, Immunological/therapeutic use , Disease-Free Survival , Combined Modality Therapy , Survival Analysis
8.
Plant Cell ; 36(9): 3824-3837, 2024 Sep 03.
Article in English | MEDLINE | ID: mdl-39041486

ABSTRACT

Germline fate determination is a critical event in sexual reproduction. Unlike animals, plants specify the germline by reprogramming somatic cells at the late stages of their development. However, the genetic basis of germline fate determination and how it evolved during the land plant evolution are still poorly understood. Here, we report that the plant homeodomain finger protein GERMLINE IDENTITY DETERMINANT (GLID) is a key regulator of the germline specification in liverwort, Marchantia polymorpha. Loss of the MpGLID function causes failure of germline initiation, leading to the absence of sperm and egg cells. Remarkably, the overexpression of MpGLID in M. polymorpha induces the ectopic formation of cells with male germline cell features exclusively in male thalli. We further show that MpBONOBO (BNB), with an evolutionarily conserved function, can induce the formation of male germ cell-like cells through the activation of MpGLID by directly binding to its promoter. The Arabidopsis (Arabidopsis thaliana) MpGLID ortholog, MALE STERILITY1 (AtMS1), fails to replace the germline specification function of MpGLID in M. polymorpha, demonstrating that a derived function of MpGLID orthologs has been restricted to tapetum development in flowering plants. Collectively, our findings suggest the presence of the BNB-GLID module in complex ancestral land plants that has been retained in bryophytes, but rewired in flowering plants for male germline fate determination.


Subject(s)
Gene Expression Regulation, Plant , Marchantia , Plant Proteins , Marchantia/genetics , Plant Proteins/genetics , Plant Proteins/metabolism , Germ Cells, Plant/metabolism , Arabidopsis/genetics , Plants, Genetically Modified
9.
Nature ; 600(7889): 536-542, 2021 12.
Article in English | MEDLINE | ID: mdl-34819669

ABSTRACT

The cell is a multi-scale structure with modular organization across at least four orders of magnitude1. Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are typically treated separately2,3. Here we integrate immunofluorescence images in the Human Protein Atlas4 with affinity purifications in BioPlex5 to create a unified hierarchical map of human cell architecture. Integration is achieved by configuring each approach as a general measure of protein distance, then calibrating the two measures using machine learning. The map, known as the multi-scale integrated cell (MuSIC 1.0), resolves 69 subcellular systems, of which approximately half are to our knowledge undocumented. Accordingly, we perform 134 additional affinity purifications and validate subunit associations for the majority of systems. The map reveals a pre-ribosomal RNA processing assembly and accessory factors, which we show govern rRNA maturation, and functional roles for SRRM1 and FAM120C in chromatin and RPS3A in splicing. By integration across scales, MuSIC increases the resolution of imaging while giving protein interactions a spatial dimension, paving the way to incorporate diverse types of data in proteome-wide cell maps.


Subject(s)
Chromosomes , Proteome , Antigens, Nuclear/genetics , Antigens, Nuclear/metabolism , Chromatin/genetics , Chromosomes/metabolism , Humans , Nuclear Matrix-Associated Proteins/metabolism , Proteome/metabolism , RNA, Ribosomal , RNA-Binding Proteins/genetics
10.
Proc Natl Acad Sci U S A ; 121(3): e2319335121, 2024 Jan 16.
Article in English | MEDLINE | ID: mdl-38198526

ABSTRACT

The phytohormone cytokinin has various roles in plant development, including meristem maintenance, vascular differentiation, leaf senescence, and regeneration. Prior investigations have revealed that cytokinin acts via a phosphorelay similar to the two-component system by which bacteria sense and respond to external stimuli. The eventual targets of this phosphorelay are type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs), containing the conserved N-terminal receiver domain (RD), middle DNA binding domain (DBD), and C-terminal transactivation domain. While it has been established for two decades that the phosphoryl transfer from a specific histidyl residue in ARABIDOPSIS HIS PHOSPHOTRANSFER PROTEINS (AHPs) to an aspartyl residue in the RD of B-ARRs results in a rapid transcriptional response to cytokinin, the underlying molecular basis remains unclear. In this work, we determine the crystal structures of the RD-DBD of ARR1 (ARR1RD-DBD) as well as the ARR1DBD-DNA complex from Arabidopsis. Analyses of the ARR1DBD-DNA complex have revealed the structural basis for sequence-specific recognition of the GAT trinucleotide by ARR1. In particular, comparing the ARR1RD-DBD and ARR1DBD-DNA structures reveals that unphosphorylated ARR1RD-DBD exists in a closed conformation with extensive contacts between the RD and DBD. In vitro and vivo functional assays have further suggested that phosphorylation of the RD weakens its interaction with DBD, subsequently permits the DNA binding capacity of DBD, and promotes the transcriptional activity of ARR1. Our findings thus provide mechanistic insights into phosphorelay activation of gene transcription in response to cytokinin.


Subject(s)
Arabidopsis , Cytokinins , Transcriptional Activation , Arabidopsis/genetics , Plant Growth Regulators , DNA
11.
Plant Cell ; 35(5): 1386-1407, 2023 04 20.
Article in English | MEDLINE | ID: mdl-36748203

ABSTRACT

Plants undergo extended morphogenesis. The shoot apical meristem (SAM) allows for reiterative development and the formation of new structures throughout the life of the plant. Intriguingly, the SAM produces morphologically different leaves in an age-dependent manner, a phenomenon known as heteroblasty. In Arabidopsis thaliana, the SAM produces small orbicular leaves in the juvenile phase, but gives rise to large elliptical leaves in the adult phase. Previous studies have established that a developmental decline of microRNA156 (miR156) is necessary and sufficient to trigger this leaf shape switch, although the underlying mechanism is poorly understood. Here we show that the gradual increase in miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE transcription factors with age promotes cell growth anisotropy in the abaxial epidermis at the base of the leaf blade, evident by the formation of elongated giant cells. Time-lapse imaging and developmental genetics further revealed that the establishment of adult leaf shape is tightly associated with the longitudinal cell expansion of giant cells, accompanied by a prolonged cell proliferation phase in their vicinity. Our results thus provide a plausible cellular mechanism for heteroblasty in Arabidopsis, and contribute to our understanding of anisotropic growth in plants.


Subject(s)
Arabidopsis Proteins , Arabidopsis , MicroRNAs , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Transcription Factors/metabolism , Plant Leaves/metabolism , Meristem/genetics , Meristem/metabolism , Cell Proliferation/genetics , Gene Expression Regulation, Plant/genetics , MicroRNAs/genetics , MicroRNAs/metabolism
12.
Circ Res ; 134(2): 165-185, 2024 01 19.
Article in English | MEDLINE | ID: mdl-38166463

ABSTRACT

BACKGROUND: Atherosclerosis is a globally prevalent chronic inflammatory disease with high morbidity and mortality. The development of atherosclerotic lesions is determined by macrophages. This study aimed to investigate the specific role of myeloid-derived CD147 (cluster of differentiation 147) in atherosclerosis and its translational significance. METHODS AND RESULTS: We generated mice with a myeloid-specific knockout of CD147 and mice with restricted CD147 overexpression, both in an apoE-deficient (ApoE-/-) background. Here, the myeloid-specific deletion of CD147 ameliorated atherosclerosis and inflammation. Consistent with our in vivo data, macrophages isolated from myeloid-specific CD147 knockout mice exhibited a phenotype shift from proinflammatory to anti-inflammatory macrophage polarization in response to lipopolysaccharide/IFN (interferon)-γ. These macrophages demonstrated a weakened proinflammatory macrophage phenotype, characterized by reduced production of NO and reactive nitrogen species derived from iNOS (inducible NO synthase). Mechanistically, the TRAF6 (tumor necrosis factor receptor-associated factor 6)-IKK (inhibitor of κB kinase)-IRF5 (IFN regulatory factor 5) signaling pathway was essential for the effect of CD147 on proinflammatory responses. Consistent with the reduced size of the necrotic core, myeloid-specific CD147 deficiency diminished the susceptibility of iNOS-mediated late apoptosis, accompanied by enhanced efferocytotic capacity mediated by increased secretion of GAS6 (growth arrest-specific 6) in proinflammatory macrophages. These findings were consistent in a mouse model with myeloid-restricted overexpression of CD147. Furthermore, we developed a new atherosclerosis model in ApoE-/- mice with humanized CD147 transgenic expression and demonstrated that the administration of an anti-human CD147 antibody effectively suppressed atherosclerosis by targeting inflammation and efferocytosis. CONCLUSIONS: Myeloid CD147 plays a crucial role in the growth of plaques by promoting inflammation in a TRAF6-IKK-IRF5-dependent manner and inhibiting efferocytosis by suppressing GAS6 during proinflammatory conditions. Consequently, the use of anti-human CD147 antibodies presents a complementary therapeutic approach to the existing lipid-lowering strategies for treating atherosclerotic diseases.


Subject(s)
Atherosclerosis , Plaque, Atherosclerotic , Mice , Animals , Efferocytosis , TNF Receptor-Associated Factor 6/metabolism , Atherosclerosis/metabolism , Inflammation/genetics , Mice, Knockout , Phenotype , Apolipoproteins E , Interferon Regulatory Factors/genetics , Mice, Inbred C57BL
13.
Plant Physiol ; 2024 Sep 12.
Article in English | MEDLINE | ID: mdl-39268875

ABSTRACT

Dwarf or semi-dwarf plant structures are well-suited for intensive farming, maximizing yield, and minimizing labor costs. Watermelon (Citrullus lanatus) is classified as an annual vine plant with elongated internodes, yet the mechanism governing watermelon dwarfing remains unclear. In this study, a compact watermelon mutant dwarf, induced by the insertion of T-DNA, was discovered. Through re-sequencing, a gene named domain of unknown function 21 (ClDUF21), located downstream of the T-DNA insertion site, was identified as the candidate gene for the dwarf mutant, and its functionality was subsequently confirmed. Watermelon mutants generated through CRISPR/Cas9-mediated knockout of ClDUF21 revealed that homozygous mutants displayed a pronounced dwarfing phenotype, and protein-protein interaction analysis confirmed the direct interaction between ClDUF21 and ClDWF1. Subsequently, we employed CRISPR/Cas9 technology to precisely modify the homologous gene CsDUF21 in cucumber (Cucumis sativus) and performed protein interaction validation between CsDUF21 and CsDWF1, thereby demonstrating that the CsDUF21 gene also exhibits analogous functionality in plant dwarfing. These findings demonstrate that ClDUF21 governs plant dwarfism by modulating the brassinosteroid synthesis pathway via ClDWF1.

14.
Nucleic Acids Res ; 51(7): 3150-3165, 2023 04 24.
Article in English | MEDLINE | ID: mdl-36869674

ABSTRACT

DNA double-strand breaks (DSBs) are functionally linked to genomic instability in spermatocytes and to male infertility. The heavy metal cadmium (Cd) is known to induce DNA damage in spermatocytes by unknown mechanisms. Here, we showed that Cd ions impaired the canonical non-homologous end-joining (NHEJ) repair pathway, but not the homologous recombination (HR) repair pathway, through stimulation of Ser2056 and Thr2609 phosphorylation of DNA-PKcs at DSB sites. Hyper-phosphorylation of DNA-PKcs led to its premature dissociation from DNA ends and the Ku complex, preventing recruitment of processing enzymes and further ligation of DNA ends. Specifically, this cascade was initiated by the loss of PP5 phosphatase activity, which results from the dissociation of PP5 from its activating ions (Mn), that is antagonized by Cd ions through a competitive mechanism. In accordance, in a mouse model Cd-induced genomic instability and consequential male reproductive dysfunction were effectively reversed by a high dosage of Mn ions. Together, our findings corroborate a protein phosphorylation-mediated genomic instability pathway in spermatocytes that is triggered by exchange of heavy metal ions.


Subject(s)
Cadmium , Genomic Instability , Infertility, Male , Spermatocytes , Animals , Humans , Male , Mice , Cadmium/toxicity , DNA/metabolism , DNA End-Joining Repair , DNA Repair , Genomic Instability/drug effects , Infertility, Male/genetics , Infertility, Male/metabolism , Ions/metabolism , Phosphorylation , Recombinational DNA Repair , Spermatocytes/drug effects
15.
Nano Lett ; 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38857313

ABSTRACT

The quantum yield of reactive oxygen species is of central importance for the development of organic photosensitizers and photodynamic therapy (PDT). A common molecular design approach for optimizing organic photosensitizers involves the incorporation of heavy atoms into their backbones. However, this raises concerns regarding heightened dark cytotoxicity and a shortened triplet-state lifetime. Herein, we demonstrate a heavy-atom-free (HAF) photosensitizer design strategy founded on the singlet fission (SF) mechanism for cancer PDT. Through the "single-atom surgery" approach to deleting oxygen atoms in pyrazino[2,3-g]quinoxaline skeleton photosensitizers, photosensitizers PhPQ and TriPhPQ are produced with Huckel's aromaticity and Baird's aromaticity in the ground state and triplet state, respectively, enabling the generation of two triplet excitons through SF. The SF process endows photosensitizer PhPQ with an ultrahigh triplet-state quantum yield (186%) and an outstanding 1O2 quantum yield (177%). Notably, HAF photosensitizers PhPQ and TriPhPQ enhanced PDT efficacy and potentiated αPD-L1 immune check blockade therapy in vivo, which show their promise for translational oncology treatment.

16.
Nano Lett ; 24(1): 202-208, 2024 Jan 10.
Article in English | MEDLINE | ID: mdl-38126308

ABSTRACT

This work presents a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas-nanopipette nano-electrochemistry (Cas = CRISPR-associated proteins) capable of ultrasensitive microRNA detection. Nanoconfinement of the CRISPR/Cas13a within a nanopipette leads to a high catalytic efficacy of ca. 169 times higher than that in bulk electrolyte, contributing to the amplified electrochemical responses. CRISPR/Cas13a-enabled detection of representative microRNA-25 achieves a low limit of detection down to 10 aM. Practical application of this method is further demonstrated for single-cell and real human serum detection. Its general applicability is validated by addressing microRNA-141 and the SARS-CoV-2 RNA gene fragment. This work introduces a new CRISPR/Cas-empowered nanotechnology for ultrasensitive nano-electrochemistry and bioanalysis.


Subject(s)
MicroRNAs , Nanopores , Humans , MicroRNAs/genetics , MicroRNAs/analysis , CRISPR-Cas Systems/genetics , RNA, Viral
17.
J Cell Mol Med ; 28(7): e18174, 2024 04.
Article in English | MEDLINE | ID: mdl-38494839

ABSTRACT

This study investigates genetic mutations and immune cell dynamics in stomach adenocarcinoma (STAD), focusing on identifying prognostic markers and therapeutic targets. Analysis of TCGA-STAD samples revealed C > A as the most common single nucleotide variant (SNV) in both high and low-risk groups. Key mutated driver genes included TTN, TP53 and MUC16, with frame-shift mutations more prevalent in the low-risk group and missense mutations in the high-risk group. Interaction analysis of hub genes such as C1QA and CD68 showed significant correlations, impacting immune cell infiltration patterns. Using ssGSEA, we found higher immune cell infiltration (B cells, CD4+ T cells, CD8+ T cells, DC cells, NK cells) in the high-risk group, correlated with increased risk scores. xCell algorithm results indicated distinct immune infiltration levels between the groups. The study's risk scoring model proved effective in prognosis prediction and immunotherapy efficacy assessment. Key molecules like CD28, CD27 and SLAMF7 correlated significantly with risk scores, suggesting potential targets for high-risk STAD patients. Drug sensitivity analysis showed a negative correlation between risk scores and sensitivity to certain treatments, indicating potential therapeutic options for high-risk STAD patients. We also validated the carcinogenic role of RPL14 in gastric cancer through phenotypic experiments, demonstrating its influence on cancer cell proliferation, invasion and migration. Overall, this research provides crucial insights into the genetic and immune aspects of STAD, highlighting the importance of a risk scoring model for personalized treatment strategies and clinical decision-making in gastric cancer management.


Subject(s)
Adenocarcinoma , Stomach Neoplasms , Humans , Stomach Neoplasms/genetics , Stomach Neoplasms/therapy , CD8-Positive T-Lymphocytes , Immunotherapy , Mutation/genetics
18.
Plant J ; 115(3): 678-689, 2023 08.
Article in English | MEDLINE | ID: mdl-37092342

ABSTRACT

The presence or absence of spines is an important economic trait of cucumber fruit. Spines are believed to be a type of specialized trichome on the fruit surface, and all the identified cucumber trichome-less mutants lack fruit spines. However, genes that specifically regulate fruit spine initiation remain to be identified. Here, we found that knocking out cucumber TARGET OF EAT3 homolog (CsTOE3), belonging to the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) family, affected flower development and, more interestingly, inhibited cucumber fruit spine initiation. On analyzing expression patterns by quantitative reverse transcriptase-polymerase chain reaction and in situ hybridization assay, CsTOE3 was found to be highly expressed in male and female flowers, and its mRNA accumulated in the tips of sepal and petal primordia and in the cells of fruit spines and peels. Biochemical analyses indicated that CsTOE3 directly interacts with GLABRA1 (CsGL1) and TRANSPARENT TESTA GLABRA1 (CsTTG1), which are positive regulators of trichome formation. In addition, RNA-seq showed that the transcription levels of eight ERFs were significantly upregulated in CsTOE3 knockout lines. Phytohormone content analysis also revealed a significant increase in the amount of ethylene released by CsTOE3 knockout line, and treatment with the ethylene synthesis inhibitor aminoethoxyvinyl-glycine partly restored the spineless phenotype. Our results suggest that CsTOE3 specifically regulates fruit spine initiation but does not affect the formation of trichomes on other organs in cucumber. Our findings may have a far-reaching significance for cucumber germplasm improvement and quality breeding using fruit spines as the target trait.


Subject(s)
Cucumis sativus , Fruit/metabolism , Plant Proteins/metabolism , Plant Breeding , Ethylenes/metabolism
19.
Neuroimage ; 298: 120785, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39154869

ABSTRACT

Working memory (WM) is an essential cognitive function that underpins various higher-order cognitive processes. Improving WM capacity through targeted training interventions has emergered as a potential approach for enhancing cognitive abilities. The present study employed an 8-week regimen of computerized WM training (WMT) to investigate its effect on neuroplasticity in healthy individuals, utilizing neuroimaging data gathered both before and after the training. The key metrics assessed included the amplitude of low-frequency fluctuations (ALFF), voxel-based morphometry (VBM), and the spatial distribution correlations of neurotransmitter. The results indicated that post-training, compared to baseline, there was a reduction in ALFF in the medial superior frontal gyrus and an elevation in ALFF in the left middle occipital gyrus within the training group. In comparison to the control group, the training group also exhibited decreased ALFF in the anterior cingulate cortex, angular gyrus, and superior parietal lobule, along with increased ALFF in the postcentral gyrus post-training. VBM analysis revealed a significant increase in gray matter volume (GMV) in the right dorsal superior frontal gyrus after the training period, compared to the initial baseline measurement. Furthermore, the training group showed GMV increases in the dorsal superior frontal gyrus, Rolandic operculum, precentral gyrus, and postcentral gyrus when compared to the control group. In addition, significant associations were identifed between neuroimaging measurements (AFLL and VBM) and the spatial patterns of neurotransmitters such as serotonin (5-HT), dopamine (DA), and N-methyl-D-aspartate (NMDA), providing insights into the underlying neurochemical processes. These findings clarify the neuroplastic changes caused by WMT, offering a deeper understanding of brain plasticity and highlighting the potential advantages of cognitive training interventions.


Subject(s)
Magnetic Resonance Imaging , Memory, Short-Term , Neuronal Plasticity , Humans , Neuronal Plasticity/physiology , Male , Memory, Short-Term/physiology , Female , Adult , Young Adult , Brain/physiology , Brain/diagnostic imaging , Neurotransmitter Agents/metabolism , Neuroimaging/methods , Cognitive Training
20.
J Am Chem Soc ; 146(38): 25912-25917, 2024 Sep 25.
Article in English | MEDLINE | ID: mdl-39270209

ABSTRACT

We report the first bottleable enantiopure P-chiral secondary phosphines from the rhodium-catalyzed asymmetric hydrogenation of phosphaalkenes. Catalytic asymmetric hydrogenation, a reaction of broad academic and industrial importance for C═C, N═C, and O═C bonds, has not previously been reported for the P═C bond. The hydrogenation of ArP═CR2 (Ar = Mes, m-Xyl and TMOP; R = Ph, 4-C6H4F) affords four unprecedented P-stereogenic secondary phosphines in 76%-90% isolated yields with 91%-97% enantiomeric excess (ee). These isolable P-chiral secondary phosphines are configurationally stable indefinitely in the solid state and show only modest loss in ee when kept in solution for over a month at room temperature.

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