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1.
Cell ; 184(9): 2471-2486.e20, 2021 04 29.
Article in English | MEDLINE | ID: mdl-33878291

ABSTRACT

Metastasis has been considered as the terminal step of tumor progression. However, recent genomic studies suggest that many metastases are initiated by further spread of other metastases. Nevertheless, the corresponding pre-clinical models are lacking, and underlying mechanisms are elusive. Using several approaches, including parabiosis and an evolving barcode system, we demonstrated that the bone microenvironment facilitates breast and prostate cancer cells to further metastasize and establish multi-organ secondary metastases. We uncovered that this metastasis-promoting effect is driven by epigenetic reprogramming that confers stem cell-like properties on cancer cells disseminated from bone lesions. Furthermore, we discovered that enhanced EZH2 activity mediates the increased stemness and metastasis capacity. The same findings also apply to single cell-derived populations, indicating mechanisms distinct from clonal selection. Taken together, our work revealed an unappreciated role of the bone microenvironment in metastasis evolution and elucidated an epigenomic reprogramming process driving terminal-stage, multi-organ metastases.


Subject(s)
Bone Neoplasms/secondary , Breast Neoplasms/pathology , Neoplasm Metastasis , Prostatic Neoplasms/pathology , Tumor Microenvironment , Animals , Apoptosis , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Bone Neoplasms/genetics , Bone Neoplasms/metabolism , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Cell Proliferation , Disease Progression , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Male , Mice , Mice, Inbred C57BL , Mice, Inbred NOD , Mice, Nude , Mice, SCID , Prostatic Neoplasms/genetics , Prostatic Neoplasms/metabolism , Tumor Cells, Cultured , Xenograft Model Antitumor Assays
2.
Mol Cell ; 83(7): 1180-1196.e8, 2023 04 06.
Article in English | MEDLINE | ID: mdl-37028415

ABSTRACT

Proper defense against microbial infection depends on the controlled activation of the immune system. This is particularly important for the RIG-I-like receptors (RLRs), which recognize viral dsRNA and initiate antiviral innate immune responses with the potential of triggering systemic inflammation and immunopathology. Here, we show that stress granules (SGs), molecular condensates that form in response to various stresses including viral dsRNA, play key roles in the controlled activation of RLR signaling. Without the SG nucleators G3BP1/2 and UBAP2L, dsRNA triggers excessive inflammation and immune-mediated apoptosis. In addition to exogenous dsRNA, host-derived dsRNA generated in response to ADAR1 deficiency is also controlled by SG biology. Intriguingly, SGs can function beyond immune control by suppressing viral replication independently of the RLR pathway. These observations thus highlight the multi-functional nature of SGs as cellular "shock absorbers" that converge on protecting cell homeostasis by dampening both toxic immune response and viral replication.


Subject(s)
DNA Helicases , RNA Helicases , Humans , DNA Helicases/metabolism , RNA Helicases/genetics , RNA Helicases/metabolism , Poly-ADP-Ribose Binding Proteins/metabolism , Stress Granules , RNA Recognition Motif Proteins/metabolism , Immunity, Innate , Inflammation/metabolism , Cytoplasmic Granules/metabolism , Carrier Proteins/metabolism
3.
Nature ; 630(8016): 346-352, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38811731

ABSTRACT

Vertical three-dimensional integration of two-dimensional (2D) semiconductors holds great promise, as it offers the possibility to scale up logic layers in the z axis1-3. Indeed, vertical complementary field-effect transistors (CFETs) built with such mixed-dimensional heterostructures4,5, as well as hetero-2D layers with different carrier types6-8, have been demonstrated recently. However, so far, the lack of a controllable doping scheme (especially p-doped WSe2 (refs. 9-17) and MoS2 (refs. 11,18-28)) in 2D semiconductors, preferably in a stable and non-destructive manner, has greatly impeded the bottom-up scaling of complementary logic circuitries. Here we show that, by bringing transition metal dichalcogenides, such as MoS2, atop a van der Waals (vdW) antiferromagnetic insulator chromium oxychloride (CrOCl), the carrier polarity in MoS2 can be readily reconfigured from n- to p-type via strong vdW interfacial coupling. The consequential band alignment yields transistors with room-temperature hole mobilities up to approximately 425 cm2 V-1 s-1, on/off ratios reaching 106 and air-stable performance for over one year. Based on this approach, vertically constructed complementary logic, including inverters with 6 vdW layers, NANDs with 14 vdW layers and SRAMs with 14 vdW layers, are further demonstrated. Our findings of polarity-engineered p- and n-type 2D semiconductor channels with and without vdW intercalation are robust and universal to various materials and thus may throw light on future three-dimensional vertically integrated circuits based on 2D logic gates.

4.
Cell ; 159(1): 134-147, 2014 Sep 25.
Article in English | MEDLINE | ID: mdl-25242744

ABSTRACT

Exon circularization has been identified from many loci in mammals, but the detailed mechanism of its biogenesis has remained elusive. By using genome-wide approaches and circular RNA recapitulation, we demonstrate that exon circularization is dependent on flanking intronic complementary sequences. Such sequences and their distribution exhibit rapid evolutionary changes, showing that exon circularization is evolutionarily dynamic. Strikingly, exon circularization efficiency can be regulated by competition between RNA pairing across flanking introns or within individual introns. Importantly, alternative formation of inverted repeated Alu pairs and the competition between them can lead to alternative circularization, resulting in multiple circular RNA transcripts produced from a single gene. Collectively, exon circularization mediated by complementary sequences in human introns and the potential to generate alternative circularization products extend the complexity of mammalian posttranscriptional regulation.


Subject(s)
Alternative Splicing , Exons , Genome, Human , Alu Elements , Animals , Base Sequence , Embryonic Stem Cells/metabolism , Evolution, Molecular , Humans , Introns , Mammals/genetics , Molecular Sequence Data , Nucleic Acid Conformation , Sequence Alignment
5.
Mol Cell ; 75(6): 1188-1202.e11, 2019 09 19.
Article in English | MEDLINE | ID: mdl-31399345

ABSTRACT

The maternal-to-zygotic transition (MZT) is a conserved and fundamental process during which the maternal environment is converted to an environment of embryonic-driven development through dramatic reprogramming. However, how maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein, through genome-wide profiling of RNA 5-methylcytosine (m5C) modification in zebrafish early embryos, we found that m5C-modified maternal mRNAs display higher stability than non-m5C-modified mRNAs during MZT. We discovered that Y-box binding protein 1 (Ybx1) preferentially recognizes m5C-modified mRNAs through π-π interactions with a key residue, Trp45, in Ybx1's cold shock domain (CSD), which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Together with the mRNA stabilizer Pabpc1a, Ybx1 promotes the stability of its target mRNAs in an m5C-dependent manner. Our study demonstrates an unexpected mechanism of RNA m5C-regulated maternal mRNA stabilization during zebrafish MZT, highlighting the critical role of m5C mRNA modification in early development.


Subject(s)
5-Methylcytosine/metabolism , Embryo, Nonmammalian/embryology , Embryonic Development/physiology , RNA Stability/physiology , RNA, Messenger, Stored/metabolism , Zebrafish/embryology , Animals , HeLa Cells , Humans , Mice , RNA, Messenger, Stored/genetics , Zebrafish/genetics
6.
Proc Natl Acad Sci U S A ; 121(26): e2319811121, 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38889146

ABSTRACT

Rational design of plant cis-regulatory DNA sequences without expert intervention or prior domain knowledge is still a daunting task. Here, we developed PhytoExpr, a deep learning framework capable of predicting both mRNA abundance and plant species using the proximal regulatory sequence as the sole input. PhytoExpr was trained over 17 species representative of major clades of the plant kingdom to enhance its generalizability. Via input perturbation, quantitative functional annotation of the input sequence was achieved at single-nucleotide resolution, revealing an abundance of predicted high-impact nucleotides in conserved noncoding sequences and transcription factor binding sites. Evaluation of maize HapMap3 single-nucleotide polymorphisms (SNPs) by PhytoExpr demonstrates an enrichment of predicted high-impact SNPs in cis-eQTL. Additionally, we provided two algorithms that harnessed the power of PhytoExpr in designing functional cis-regulatory variants, and de novo creation of species-specific cis-regulatory sequences through in silico evolution of random DNA sequences. Our model represents a general and robust approach for functional variant discovery in population genetics and rational design of regulatory sequences for genome editing and synthetic biology.


Subject(s)
Polymorphism, Single Nucleotide , Regulatory Sequences, Nucleic Acid , Zea mays , Regulatory Sequences, Nucleic Acid/genetics , Zea mays/genetics , Quantitative Trait Loci , Algorithms , Gene Expression Regulation, Plant , Deep Learning , Plants/genetics , Transcription Factors/genetics , Transcription Factors/metabolism , Models, Genetic , Genes, Plant , Binding Sites/genetics
7.
Proc Natl Acad Sci U S A ; 121(21): e2313797121, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38709948

ABSTRACT

During 2010 to 2020, Northeast Pacific (NEP) sea surface temperature (SST) experienced the warmest decade ever recorded, manifested in several extreme marine heatwaves, referred to as "warm blob" events, which severely affect marine ecosystems and extreme weather along the west coast of North America. While year-to-year internal climate variability has been suggested as a cause of individual events, the causes of the continuous dramatic NEP SST warming remain elusive. Here, we show that other than the greenhouse gas (GHG) forcing, rapid aerosol abatement in China over the period likely plays an important role. Anomalous tropospheric warming induced by declining aerosols in China generated atmospheric teleconnections from East Asia to the NEP, featuring an intensified and southward-shifted Aleutian Low. The associated atmospheric circulation anomaly weakens the climatological westerlies in the NEP and warms the SST there by suppressing the evaporative cooling. The aerosol-induced mean warming of the NEP SST, along with internal climate variability and the GHG-induced warming, made the warm blob events more frequent and intense during 2010 to 2020. As anthropogenic aerosol emissions continue to decrease, there is likely to be an increase in NEP warm blob events, disproportionately large beyond the direct radiative effects.

8.
Blood ; 143(26): 2722-2734, 2024 Jun 27.
Article in English | MEDLINE | ID: mdl-38635762

ABSTRACT

ABSTRACT: Axicabtagene ciloleucel (axi-cel) is an autologous anti-CD19 chimeric antigen receptor (CAR) T-cell therapy approved for relapsed/refractory (R/R) large B-cell lymphoma (LBCL). Despite extensive data supporting its use, outcomes stratified by race and ethnicity groups are limited. Here, we report clinical outcomes with axi-cel in patients with R/R LBCL by race and ethnicity in both real-world and clinical trial settings. In the real-world setting, 1290 patients who received axi-cel between 2017 and 2020 were identified from the Center for International Blood and Marrow Transplant Research database; 106 and 169 patients were included from the ZUMA-1 and ZUMA-7 trials, respectively. Overall survival was consistent across race/ethnicity groups. However, non-Hispanic (NH) Black patients had lower overall response rate (OR, 0.37; 95% CI, 0.22-0.63) and lower complete response rate (OR, 0.57; 95% CI, 0.33-0.97) than NH White patients. NH Black patients also had a shorter progression-free survival vs NH White (HR, 1.41; 95% CI, 1.04-1.90) and NH Asian patients (HR, 1.67; 95% CI, 1.08-2.59). NH Asian patients had a longer duration of response than NH White (HR, 0.56; 95% CI, 0.33-0.94) and Hispanic patients (HR, 0.54; 95% CI, 0.30-0.97). There was no difference in cytokine release syndrome by race/ethnicity; however, higher rates of any-grade immune effector cell-associated neurotoxicity syndrome were observed in NH White patients than in other patients. These results provide important context when treating patients with R/R LBCL with CAR T-cell therapy across different racial and ethnic groups. ZUMA-1 and ZUMA-7 (ClinicalTrials.gov identifiers: #NCT02348216 and #NCT03391466, respectively) are registered on ClinicalTrials.gov.


Subject(s)
Biological Products , Immunotherapy, Adoptive , Lymphoma, Large B-Cell, Diffuse , Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Antigens, CD19/immunology , Antigens, CD19/therapeutic use , Biological Products/therapeutic use , Ethnicity , Lymphoma, Large B-Cell, Diffuse/therapy , Treatment Outcome , Black or African American , White , Asian , Clinical Trials as Topic
9.
Proc Natl Acad Sci U S A ; 120(23): e2301981120, 2023 Jun 06.
Article in English | MEDLINE | ID: mdl-37253001

ABSTRACT

Understanding nanodiamond structures is of great scientific and practical interest. It has been a long-standing challenge to unravel the complexity underlying nanodiamond structures and to resolve the controversies surrounding their polymorphic forms. Here, we use transmission electron microscopy with high-resolution imaging, electron diffraction, multislice simulations, and other supplementary techniques to study the impacts of small sizes and defects on cubic diamond nanostructures. The experimental results show that common cubic diamond nanoparticles display the (200) forbidden reflections in their electron diffraction patterns, which makes them indistinguishable from new diamond (n-diamond). The multislice simulations demonstrate that cubic nanodiamonds smaller than 5 nm can present the d-spacing at 1.78 Å corresponding to the (200) forbidden reflections, and the relative intensity of these reflections increases as the particle size decreases. Our simulation results also reveal that defects, such as surface distortions, internal dislocations, and grain boundaries can also make the (200) forbidden reflections visible. These findings provide valuable insights into the diamond structural complexity at nanoscale, the impact of defects on nanodiamond structures, and the discovery of novel diamond structures.

10.
Proc Natl Acad Sci U S A ; 120(45): e2304179120, 2023 Nov 07.
Article in English | MEDLINE | ID: mdl-37903265

ABSTRACT

The unexpected discovery of hot Jupiters challenged the classical theory of planet formation inspired by our solar system. Until now, the origin and evolution of hot Jupiters are still uncertain. Determining their age distribution and temporal evolution can provide more clues into the mechanism of their formation and subsequent evolution. Using a sample of 383 giant planets around Sun-like stars collected from the kinematic catalogs of the Planets Across Space and Time project, we find that hot Jupiters are preferentially hosted by relatively younger stars in the Galactic thin disk. We subsequently find that the frequency of hot Jupiters declines with age as [Formula: see text]. In contrast, the frequency of warm/cold Jupiters shows no significant dependence on age. Such a trend is expected from the tidal evolution of hot Jupiters' orbits, and our result offers supporting evidence using a large sample. We also perform a joint analysis on the planet frequencies in the stellar age-metallicity plane. The result suggests that the frequencies of hot Jupiters and warm/cold Jupiters, after removing the age dependence are both correlated with stellar metallicities as [Formula: see text] and [Formula: see text], respectively. Moreover, we show that the above correlations can explain the bulk of the discrepancy in hot Jupiter frequencies inferred from the transit and radial velocity (RV) surveys, given that RV targets tend to be more metal-rich and younger than transits.

11.
Brief Bioinform ; 24(1)2023 01 19.
Article in English | MEDLINE | ID: mdl-36592058

ABSTRACT

The progress of single-cell RNA sequencing (scRNA-seq) has led to a large number of scRNA-seq data, which are widely used in biomedical research. The noise in the raw data and tens of thousands of genes pose a challenge to capture the real structure and effective information of scRNA-seq data. Most of the existing single-cell analysis methods assume that the low-dimensional embedding of the raw data belongs to a Gaussian distribution or a low-dimensional nonlinear space without any prior information, which limits the flexibility and controllability of the model to a great extent. In addition, many existing methods need high computational cost, which makes them difficult to be used to deal with large-scale datasets. Here, we design and develop a depth generation model named Gaussian mixture adversarial autoencoders (scGMAAE), assuming that the low-dimensional embedding of different types of cells follows different Gaussian distributions, integrating Bayesian variational inference and adversarial training, as to give the interpretable latent representation of complex data and discover the statistical distribution of different types of cells. The scGMAAE is provided with good controllability, interpretability and scalability. Therefore, it can process large-scale datasets in a short time and give competitive results. scGMAAE outperforms existing methods in several ways, including dimensionality reduction visualization, cell clustering, differential expression analysis and batch effect removal. Importantly, compared with most deep learning methods, scGMAAE requires less iterations to generate the best results.


Subject(s)
Gene Expression Profiling , Single-Cell Gene Expression Analysis , Gene Expression Profiling/methods , Sequence Analysis, RNA/methods , Normal Distribution , Bayes Theorem , Single-Cell Analysis/methods , Cluster Analysis
12.
Nat Mater ; 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38849556

ABSTRACT

Surface terminations profoundly influence the intrinsic properties of MXenes, but existing terminations are limited to monoatomic layers or simple groups, showing disordered arrangements and inferior stability. Here we present the synthesis of MXenes with triatomic-layer borate polyanion terminations (OBO terminations) through a flux-assisted eutectic molten etching approach. During the synthesis, Lewis acidic salts act as the etching agent to obtain the MXene backbone, while borax generates BO2- species, which cap the MXene surface with an O-B-O configuration. In contrast to conventional chlorine/oxygen-terminated Nb2C with localized charge transport, OBO-terminated Nb2C features band transport described by the Drude model, exhibiting a 15-fold increase in electrical conductivity and a 10-fold improvement in charge mobility at the d.c. limit. This transition is attributed to surface ordering that effectively mitigates charge carrier backscattering and trapping. Additionally, OBO terminations provide Ti3C2 MXene with substantially enriched Li+-hosting sites and thereby a large charge-storage capacity of 420 mAh g-1. Our findings illustrate the potential of intricate termination configurations in MXenes and their applications for (opto)electronics and energy storage.

13.
PLoS Pathog ; 19(5): e1011411, 2023 May.
Article in English | MEDLINE | ID: mdl-37253057

ABSTRACT

Seneca virus A (SVA) is an emerging novel picornavirus that has recently been identified as the causative agent of many cases of porcine vesicular diseases in multiple countries. In addition to cleavage of viral polyprotein, the viral 3C protease (3Cpro) plays an important role in the regulation of several physiological processes involved in cellular antiviral responses by cleaving critical cellular proteins. Through a combination of crystallography, untargeted lipidomics, and immunoblotting, we identified the association of SVA 3Cpro with an endogenous phospholipid molecule, which binds to a unique region neighboring the proteolytic site of SVA 3Cpro. Our lipid-binding assays showed that SVA 3Cpro displayed preferred binding to cardiolipin (CL), followed by phosphoinositol-4-phosphate (PI4P) and sulfatide. Importantly, we found that the proteolytic activity of SVA 3Cpro was activated in the presence of the phospholipid, and the enzymatic activity is inhibited when the phospholipid-binding capacity decreased. Interestingly, in the wild-type SVA 3Cpro-substrate peptide structure, the cleavage residue cannot form a covalent binding to the catalytic cysteine residue to form the acyl-enzyme intermediate observed in several picornaviral 3Cpro structures. We observed a decrease in infectivity titers of SVA mutants harboring mutations that impaired the lipid-binding ability of 3Cpro, indicating a positive regulation of SVA infection capacity mediated by phospholipids. Our findings reveal a mutual regulation between the proteolytic activity and phospholipid-binding capacity in SVA 3Cpro, suggesting that endogenous phospholipid may function as an allosteric activator that regulate the enzyme's proteolytic activity during infection.


Subject(s)
Cysteine Endopeptidases , Picornaviridae , Animals , Swine , Cysteine Endopeptidases/metabolism , 3C Viral Proteases/metabolism , Peptide Hydrolases/metabolism , Allosteric Regulation , Phospholipids , Viral Proteins/metabolism
14.
PLoS Pathog ; 19(5): e1011384, 2023 05.
Article in English | MEDLINE | ID: mdl-37196026

ABSTRACT

Malayan pangolin SARS-CoV-2-related coronavirus (SARSr-CoV-2) is closely related to SARS-CoV-2. However, little is known about its pathogenicity in pangolins. Using CT scans we show that SARSr-CoV-2 positive Malayan pangolins are characterized by bilateral ground-glass opacities in lungs in a similar manner to COVID-19 patients. Histological examination and blood gas tests are indicative of dyspnea. SARSr-CoV-2 infected multiple organs in pangolins, with the lungs the major target, and histological expression data revealed that ACE2 and TMPRSS2 were co-expressed with viral RNA. Transcriptome analysis indicated that virus-positive pangolins were likely to have inadequate interferon responses, with relative greater cytokine and chemokine activity in the lung and spleen. Notably, both viral RNA and viral proteins were detected in three pangolin fetuses, providing initial evidence for vertical virus transmission. In sum, our study outlines the biological framework of SARSr-CoV-2 in pangolins, revealing striking similarities to COVID-19 in humans.


Subject(s)
COVID-19 , Chiroptera , Animals , Humans , Pangolins/genetics , SARS-CoV-2/genetics , Virulence , Phylogeny , RNA, Viral , Tropism
15.
Acc Chem Res ; 57(13): 1851-1869, 2024 Jul 02.
Article in English | MEDLINE | ID: mdl-38902854

ABSTRACT

ConspectusThe directed synthesis and functionalization of porous crystalline materials pose significant challenges for chemists. The synergistic integration of different functionalities within an ordered molecular material holds great significance for expanding its applications as functional materials. The presence of coordination bonds connected by inorganic and organic components in molecular materials can not only increase the structural diversity of materials but also modulate the electronic structure and band gap, which further regulates the physical and chemical properties of molecular materials. In fact, porous crystalline materials with coordination bonds, which inherit the merits of both organic and inorganic materials, already showcase their superior advantages in optical, electrical, and magnetic applications. In addition to the inorganic components that provide structural rigidity, organic ligands of various types serve as crucial connectors in the construction of functional porous crystalline materials. In addition, redox activity can endow organic linkers with electrochemical activity, thereby making them a perfect platform for the study of charge transfer with atom-resolved single-crystal structures, and they can additionally serve as stimuli-responsive sites in sensor devices and smart materials.In this Account, we introduce the synthesis, structural characteristics, and applications of porous crystalline materials based on the famous redox-active units, tetrathiafulvalene (TTF) and its analogues, by primarily focusing on metal-organic frameworks (MOFs) and covalent organic frameworks (COFs). TTF, a sulfur-rich conjugated molecule with two reversible and easily accessible oxidation states (i.e., radical TTF•+ cation and TTF2+ dication), and its analogues boast special electrical characteristics that enable them to display switchable redox activity and stimuli-responsive properties. These inherent properties contribute to the enhancement of the optical, electrical, and magnetic characteristics of the resultant porous crystalline materials. Moreover, delving into the charge transfer phenomena, which is key for the electrochemical process within these materials, uncovers a myriad of potential functional applications. The Account is organized into five main sections that correspond to the different properties and applications of these materials: optical, electrical, and magnetic functionalities; energy storage and conversion; and catalysis. Each section provides detailed discussions of synthetic methods, structural characteristics, the physical and chemical properties, and the functional performances of highlighted examples. The Account also discusses future directions by emphasizing the exploration of novel organic units, the transformation between radical cation TTF•+ and dication TTF2+, and the integration of multifunctionalities within these frameworks to foster the development of smart materials for enhanced performance across diverse applications. Through this Account, we aim to highlight the massive potential of TTF and its analogues-based porous crystals in chemistry and material science.

16.
Plant Cell ; 34(5): 1890-1911, 2022 04 26.
Article in English | MEDLINE | ID: mdl-35166333

ABSTRACT

The unique morphology of grass stomata enables rapid responses to environmental changes. Deciphering the basis for these responses is critical for improving food security. We have developed a planta platform of single-nucleus RNA-sequencing by combined fluorescence-activated nuclei flow sorting, and used it to identify cell types in mature and developing stomata from 33,098 nuclei of the maize epidermis-enriched tissues. Guard cells (GCs) and subsidiary cells (SCs) displayed differential expression of genes, besides those encoding transporters, involved in the abscisic acid, CO2, Ca2+, starch metabolism, and blue light signaling pathways, implicating coordinated signal integration in speedy stomatal responses, and of genes affecting cell wall plasticity, implying a more sophisticated relationship between GCs and SCs in stomatal development and dumbbell-shaped guard cell formation. The trajectory of stomatal development identified in young tissues, and by comparison to the bulk RNA-seq data of the MUTE defective mutant in stomatal development, confirmed known features, and shed light on key participants in stomatal development. Our study provides a valuable, comprehensive, and fundamental foundation for further insights into grass stomatal function.


Subject(s)
Plant Stomata , Zea mays , Humans , Plant Leaves/metabolism , Plant Stomata/metabolism , Poaceae/genetics , Transcriptome/genetics , Zea mays/genetics
17.
FASEB J ; 38(8): e23613, 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38661048

ABSTRACT

The unpredictable survival rate of autologous fat grafting (AFG) seriously affects its clinical application. Improving the survival rate of AFG has become an unresolved issue in plastic surgery. Peroxisome proliferator-activated receptor-γ (PPAR-γ) regulates the adipogenic differentiation of adipocytes, but the functional mechanism in AFG remains unclear. In this study, we established an animal model of AFG and demonstrated the superior therapeutic effect of PPAR-γ regulation in the process of AFG. From day 3 after fat grafting, the PPAR-γ agonist rosiglitazone group consistently showed better adipose integrity, fewer oil cysts, and fibrosis. Massive macrophage infiltration was observed after 7 days. At the same time, M2 macrophages begin to appear. At day 14, M2 macrophages gradually became the dominant cell population, which suppressed inflammation and promoted revascularization and fat regeneration. In addition, transcriptome sequencing showed that the differentially expressed genes in the Rosiglitazone group were associated with the pathways of adipose regeneration, differentiation, and angiogenesis; these results provide new ideas for clinical treatment.


Subject(s)
Adipose Tissue , Macrophages , PPAR gamma , Rosiglitazone , Transplantation, Autologous , Animals , PPAR gamma/metabolism , PPAR gamma/genetics , Macrophages/metabolism , Adipose Tissue/metabolism , Adipose Tissue/cytology , Rosiglitazone/pharmacology , Male , Cell Differentiation , Adipogenesis , Adipocytes/metabolism , Mice , Rats
18.
FASEB J ; 38(1): e23354, 2024 01.
Article in English | MEDLINE | ID: mdl-38085162

ABSTRACT

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide, and the development of novel therapeutic strategies for HNSCC requires a profound understanding of tumor cells and the tumor microenvironment (TME). Additionally, HNSCC has a poor prognosis, necessitating the use of genetic markers for predicting clinical outcomes in HNSCC. In this study, we performed single-cell sequencing analysis on tumor tissues from seven HNSCC patients, along with one adjacent normal tissue. Firstly, the analysis of epithelial cell clusters revealed two clusters of malignant epithelial cells, characterized by unique gene expression patterns and dysregulated signaling pathways compared to normal epithelial cells. Secondly, the examination of the TME unveiled extensive crosstalk between fibroblasts and malignant epithelial cells, potentially mediated through ligand-receptor interactions such as COL1A1-SDC1, COL1A1-CD44, and COL1A2-SDC1. Furthermore, transcriptional heterogeneity was observed in immune cells present in the TME, including macrophages and dendritic cells. Finally, leveraging the gene expression profiles of malignant epithelial cells, we developed a prognostic model comprising six genes, which we validated using two independent datasets. These findings shed light on the heterogeneity within HNSCC tumors and the intricate interplay between malignant cells and the TME. Importantly, the developed prognostic model demonstrates high efficacy in predicting the survival outcomes of HNSCC patients.


Subject(s)
Carcinoma , Head and Neck Neoplasms , Humans , Squamous Cell Carcinoma of Head and Neck/genetics , Prognosis , Head and Neck Neoplasms/genetics , Epithelial Cells , Tumor Microenvironment/genetics
19.
Mol Cell ; 66(5): 581-596.e6, 2017 Jun 01.
Article in English | MEDLINE | ID: mdl-28552615

ABSTRACT

The action of DNA topoisomerase II (Top2) creates transient DNA breaks that are normally concealed inside Top2-DNA covalent complexes. Top2 poisons, including ubiquitously present natural compounds and clinically used anti-cancer drugs, trap Top2-DNA complexes. Here, we show that cells actively prevent Top2 degradation to avoid the exposure of concealed DNA breaks. A genome-wide screen revealed that fission yeast cells lacking Rrp2, an Snf2-family DNA translocase, are strongly sensitive to Top2 poisons. Loss of Rrp2 enhances SUMOylation-dependent ubiquitination and degradation of Top2, which in turn increases DNA damage at sites where Top2-DNA complexes are trapped. Rrp2 possesses SUMO-binding ability and prevents excessive Top2 degradation by competing against the SUMO-targeted ubiquitin ligase (STUbL) for SUMO chain binding and by displacing SUMOylated Top2 from DNA. The budding yeast homolog of Rrp2, Uls1, plays a similar role, indicating that this genome protection mechanism is widely employed, a finding with implications for cancer treatment.


Subject(s)
DNA Damage , DNA Topoisomerases, Type II/metabolism , DNA, Fungal/metabolism , DNA-Binding Proteins/metabolism , Genome, Fungal , Genomic Instability , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/enzymology , Sumoylation , DNA Damage/drug effects , DNA Helicases/genetics , DNA Helicases/metabolism , DNA Topoisomerases, Type II/genetics , DNA, Fungal/drug effects , DNA, Fungal/genetics , DNA-Binding Proteins/genetics , Drug Resistance , Etoposide/pharmacology , Genome, Fungal/drug effects , Genomic Instability/drug effects , Mutation , Protein Binding , Protein Interaction Domains and Motifs , Proteolysis , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Schizosaccharomyces/drug effects , Schizosaccharomyces/genetics , Schizosaccharomyces pombe Proteins/genetics , Topoisomerase II Inhibitors/pharmacology , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitination
20.
Mol Cell ; 65(6): 1096-1108.e6, 2017 Mar 16.
Article in English | MEDLINE | ID: mdl-28306505

ABSTRACT

Protein aggregation is associated with age-related neurodegenerative disorders, such as Alzheimer's and polyglutamine diseases. As a causal relationship between protein aggregation and neurodegeneration remains elusive, understanding the cellular mechanisms regulating protein aggregation will help develop future treatments. To identify such mechanisms, we conducted a forward genetic screen in a C. elegans model of polyglutamine aggregation and identified the protein MOAG-2/LIR-3 as a driver of protein aggregation. In the absence of polyglutamine, MOAG-2/LIR-3 regulates the RNA polymerase III-associated transcription of small non-coding RNAs. This regulation is lost in the presence of polyglutamine, which mislocalizes MOAG-2/LIR-3 from the nucleus to the cytosol. We then show biochemically that MOAG-2/LIR-3 can also catalyze the aggregation of polyglutamine-expanded huntingtin. These results suggest that polyglutamine can induce an aggregation-promoting activity of MOAG-2/LIR-3 in the cytosol. The concept that certain aggregation-prone proteins can convert other endogenous proteins into drivers of aggregation and toxicity adds to the understanding of how cellular homeostasis can be deteriorated in protein misfolding diseases.


Subject(s)
Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans/enzymology , Neurodegenerative Diseases/enzymology , Peptides/metabolism , Protein Aggregates , Protein Aggregation, Pathological , RNA Polymerase III/metabolism , Transcription Factors/metabolism , Active Transport, Cell Nucleus , Animals , Animals, Genetically Modified , Binding Sites , Caenorhabditis elegans/genetics , Caenorhabditis elegans Proteins/genetics , Cell Nucleus/enzymology , Cytosol/enzymology , Disease Models, Animal , Neurodegenerative Diseases/genetics , Neurodegenerative Diseases/pathology , Promoter Regions, Genetic , Protein Binding , RNA Interference , RNA Polymerase III/genetics , RNA, Small Untranslated/genetics , RNA, Small Untranslated/metabolism , Transcription Factors/genetics , Transcription, Genetic
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