ABSTRACT
Low-grade gliomas almost invariably progress into secondary glioblastoma (sGBM) with limited therapeutic option and poorly understood mechanism. By studying the mutational landscape of 188 sGBMs, we find significant enrichment of TP53 mutations, somatic hypermutation, MET-exon-14-skipping (METex14), PTPRZ1-MET (ZM) fusions, and MET amplification. Strikingly, METex14 frequently co-occurs with ZM fusion and is present in â¼14% of cases with significantly worse prognosis. Subsequent studies show that METex14 promotes glioma progression by prolonging MET activity. Furthermore, we describe a MET kinase inhibitor, PLB-1001, that demonstrates remarkable potency in selectively inhibiting MET-altered tumor cells in preclinical models. Importantly, this compound also shows blood-brain barrier permeability and is subsequently applied in a phase I clinical trial that enrolls MET-altered chemo-resistant glioma patients. Encouragingly, PLB-1001 achieves partial response in at least two advanced sGBM patients with rarely significant side effects, underscoring the clinical potential for precisely treating gliomas using this therapy.
Subject(s)
Brain Neoplasms , Exons , Glioblastoma , Mutation , Protein Kinase Inhibitors , Proto-Oncogene Proteins c-met , Animals , Blood-Brain Barrier/metabolism , Blood-Brain Barrier/pathology , Brain Neoplasms/drug therapy , Brain Neoplasms/genetics , Brain Neoplasms/metabolism , Brain Neoplasms/pathology , Drug Delivery Systems , Female , Glioblastoma/drug therapy , Glioblastoma/genetics , Glioblastoma/metabolism , Humans , Male , Mice , Mice, Inbred BALB C , Mice, Nude , Protein Kinase Inhibitors/pharmacokinetics , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins c-met/antagonists & inhibitors , Proto-Oncogene Proteins c-met/genetics , Proto-Oncogene Proteins c-met/metabolism , Rats, Sprague-Dawley , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism , Xenograft Model Antitumor AssaysABSTRACT
Adoptively transferred T cells and agents designed to block the CD47-SIRPα axis are promising cancer therapeutics that activate distinct arms of the immune system1,2. Here we administered anti-CD47 antibodies in combination with adoptively transferred T cells with the goal of enhancing antitumour efficacy but observed abrogated therapeutic benefit due to rapid macrophage-mediated clearance of T cells expressing chimeric antigen receptors (CARs) or engineered T cell receptors. Anti-CD47-antibody-mediated CAR T cell clearance was potent and rapid enough to serve as an effective safety switch. To overcome this challenge, we engineered the CD47 variant CD47(Q31P) (47E), which engages SIRPα and provides a 'don't eat me' signal that is not blocked by anti-CD47 antibodies. TCR or CAR T cells expressing 47E are resistant to clearance by macrophages after treatment with anti-CD47 antibodies, and mediate substantial, sustained macrophage recruitment to the tumour microenvironment. Although many of the recruited macrophages manifested an M2-like profile3, the combined therapy synergistically enhanced antitumour efficacy. Our study identifies macrophages as major regulators of T cell persistence and illustrates the fundamental challenge of combining T-cell-directed therapeutics with those designed to activate macrophages. It delivers a therapeutic approach that is capable of simultaneously harnessing the antitumour effects of T cells and macrophages, offering enhanced potency against solid tumours.
Subject(s)
CD47 Antigen , Immunotherapy, Adoptive , Neoplasms , T-Lymphocytes , Animals , Female , Humans , Male , Mice , Antigens, Differentiation/immunology , Antigens, Differentiation/metabolism , CD47 Antigen/genetics , CD47 Antigen/immunology , CD47 Antigen/metabolism , Cell Line, Tumor , Immunotherapy, Adoptive/methods , Macrophages/cytology , Macrophages/immunology , Neoplasms/immunology , Neoplasms/metabolism , Neoplasms/therapy , Receptors, Antigen, T-Cell/genetics , Receptors, Antigen, T-Cell/immunology , Receptors, Antigen, T-Cell/metabolism , Receptors, Chimeric Antigen/genetics , Receptors, Chimeric Antigen/immunology , Receptors, Chimeric Antigen/metabolism , Receptors, Immunologic/immunology , Receptors, Immunologic/metabolism , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , T-Lymphocytes/transplantation , Tumor Microenvironment/immunology , Antibodies/immunology , Antibodies/therapeutic use , Macrophage ActivationABSTRACT
BACKGROUND: Pulmonary hypertension (PH) is a major complication linked to adverse outcomes in heart failure with preserved ejection fraction (HFpEF), yet no specific therapies exist for PH associated with HFpEF (PH-HFpEF). We have recently reported on the role of skeletal muscle SIRT3 (sirtuin-3) in modulation of PH-HFpEF, suggesting a novel endocrine signaling pathway for skeletal muscle modulation of pulmonary vascular remodeling. In this study, we attempted to define the processes by which skeletal muscle SIRT3 defects affect pulmonary vascular health in PH-HFpEF. METHODS AND RESULTS: Skeletal muscle-specific Sirt3 knockout mice (Sirt3skm-/-) exhibited reduced pulmonary vascular density accompanied by pulmonary vascular proliferative remodeling and elevated pulmonary pressures. Using mass spectrometry-based comparative secretome analysis, we demonstrated elevated secretion of LOXL2 (lysyl oxidase homolog 2) in SIRT3-deficient skeletal muscle cells. Elevated circulation and protein expression levels of LOXL2 were also observed in plasma and skeletal muscle of Sirt3skm-/- mice, a rat model of PH-HFpEF, and humans with PH-HFpEF. In addition, expression levels of CNPY2 (canopy fibroblast growth factor signaling regulator 2), a known proliferative and angiogenic factor, were increased in pulmonary artery endothelial cells and pulmonary artery smooth muscle cells of Sirt3skm-/- mice and animal models of PH-HFpEF. CNPY2 levels were also higher in pulmonary artery smooth muscle cells of subjects with obesity compared with nonobese subjects. Moreover, treatment with recombinant LOXL2 protein promoted pulmonary artery endothelial cell migration/proliferation and pulmonary artery smooth muscle cell proliferation through regulation of CNPY2-p53 signaling. Last, skeletal muscle-specific Loxl2 deletion decreased pulmonary artery endothelial cell and pulmonary artery smooth muscle cell expression of CNPY2 and improved pulmonary pressures in mice with high-fat diet-induced PH-HFpEF. CONCLUSIONS: This study demonstrates a systemic pathogenic impact of skeletal muscle SIRT3 deficiency in remote pulmonary vascular remodeling and PH-HFpEF. This study suggests a new endocrine signaling axis that links skeletal muscle health and SIRT3 deficiency to remote CNPY2 regulation in the pulmonary vasculature through myokine LOXL2. Our data also identify skeletal muscle SIRT3, myokine LOXL2, and CNPY2 as potential targets for the treatment of PH-HFpEF.
ABSTRACT
BACKGROUND: Pulmonary hypertension (PH) represents an important phenotype in heart failure with preserved ejection fraction (HFpEF). However, management of PH-HFpEF is challenging because mechanisms involved in the regulation of PH-HFpEF remain unclear. METHODS: We used a mass spectrometry-based comparative plasma proteomics approach as a sensitive and comprehensive hypothesis-generating discovery technique to profile proteins in patients with PH-HFpEF and control subjects. We then validated and investigated the role of one of the identified proteins using in vitro cell cultures, in vivo animal models, and independent cohort of human samples. RESULTS: Plasma proteomics identified high protein abundance levels of B2M (ß2-microglobulin) in patients with PH-HFpEF. Interestingly, both circulating and skeletal muscle levels of B2M were increased in mice with skeletal muscle SIRT3 (sirtuin-3) deficiency or high-fat diet-induced PH-HFpEF. Plasma and muscle biopsies from a validation cohort of PH-HFpEF patients were found to have increased B2M levels, which positively correlated with disease severity, especially pulmonary capillary wedge pressure and right atrial pressure at rest. Not only did the administration of exogenous B2M promote migration/proliferation in pulmonary arterial vascular endothelial cells but it also increased PCNA (proliferating cell nuclear antigen) expression and cell proliferation in pulmonary arterial vascular smooth muscle cells. Finally, B2m deletion improved glucose intolerance, reduced pulmonary vascular remodeling, lowered PH, and attenuated RV hypertrophy in mice with high-fat diet-induced PH-HFpEF. CONCLUSIONS: Patients with PH-HFpEF display higher circulating and skeletal muscle expression levels of B2M, the magnitude of which correlates with disease severity. Our findings also reveal a previously unknown pathogenic role of B2M in the regulation of pulmonary vascular proliferative remodeling and PH-HFpEF. These data suggest that circulating and skeletal muscle B2M can be promising targets for the management of PH-HFpEF.
Subject(s)
Disease Models, Animal , Heart Failure , Hypertension, Pulmonary , Proteomics , Stroke Volume , beta 2-Microglobulin , Adult , Aged , Animals , Humans , Male , Mice , Middle Aged , beta 2-Microglobulin/genetics , beta 2-Microglobulin/blood , beta 2-Microglobulin/metabolism , Biomarkers/blood , Case-Control Studies , Cell Movement , Cell Proliferation , Cells, Cultured , Endothelial Cells/metabolism , Endothelial Cells/pathology , Heart Failure/physiopathology , Heart Failure/metabolism , Heart Failure/blood , Heart Failure/genetics , Hypertension, Pulmonary/physiopathology , Hypertension, Pulmonary/metabolism , Hypertension, Pulmonary/blood , Hypertension, Pulmonary/etiology , Hypertension, Pulmonary/genetics , Mice, Inbred C57BL , Mice, Knockout , Muscle, Skeletal/metabolism , Proteomics/methods , Pulmonary Artery/physiopathology , Pulmonary Artery/metabolism , Sirtuin 3/genetics , Sirtuin 3/metabolism , Vascular Remodeling , Ventricular Function, LeftABSTRACT
Testicular nuclear receptor 4 (TR4) modulates the transcriptional activation of genes and plays important roles in many diseases. The regulation of TR4 on target genes involves direct interactions with DNA molecules via the DNA-binding domain (DBD) and recruitment of coregulators by the ligand-binding domain (LBD). However, their regulatory mechanisms are unclear. Here, we report high-resolution crystal structures of TR4DBD, TR4DBD-DNA complexes and the TR4LBD-JAZF1 complex. For DNA recognition, multiple factors come into play, and a specific mutual selectivity between TR4 and target genes is found. The coactivators SRC-1 and CREBBP can bind at the interface of TR4 originally occupied by the TR4 activation function region 2 (AF-2); however, JAZF1 suppresses the binding through a novel mechanism. JAZF1 binds to an unidentified surface of TR4 and stabilizes an α13 helix never reported in the nuclear receptor family. Moreover, the cancer-associated mutations affect the interactions and the transcriptional activation of TR4 in vitro and in vivo, respectively. Overall, our results highlight the crucial role of DNA recognition and a novel mechanism of how JAZF1 reinforces the autorepressed conformation and influences the transcriptional activation of TR4, laying out important structural bases for drug design for a variety of diseases, including diabetes and cancers.
Subject(s)
Co-Repressor Proteins , Gene Expression Regulation , Receptors, Steroid , Humans , Carrier Proteins/genetics , Co-Repressor Proteins/metabolism , DNA , DNA-Binding Proteins/genetics , Receptors, Steroid/chemistry , Receptors, Steroid/metabolism , Transcriptional ActivationABSTRACT
Cerebral cavernous malformations (CCMs) are vascular disorders that affect up to 0.5% of the total population. About 20% of CCMs are inherited because of familial mutations in CCM genes, including CCM1/KRIT1, CCM2/MGC4607, and CCM3/PDCD10, whereas the etiology of a majority of simplex CCM-affected individuals remains unclear. Here, we report somatic mutations of MAP3K3, PIK3CA, MAP2K7, and CCM genes in CCM lesions. In particular, somatic hotspot mutations of PIK3CA are found in 11 of 38 individuals with CCMs, and a MAP3K3 somatic mutation (c.1323C>G [p.Ile441Met]) is detected in 37.0% (34 of 92) of the simplex CCM-affected individuals. Strikingly, the MAP3K3 c.1323C>G mutation presents in 95.7% (22 of 23) of the popcorn-like lesions but only 2.5% (1 of 40) of the subacute-bleeding or multifocal lesions that are predominantly attributed to mutations in the CCM1/2/3 signaling complex. Leveraging mini-bulk sequencing, we demonstrate the enrichment of MAP3K3 c.1323C>G mutation in CCM endothelium. Mechanistically, beyond the activation of CCM1/2/3-inhibited ERK5 signaling, MEKK3 p.Ile441Met (MAP3K3 encodes MEKK3) also activates ERK1/2, JNK, and p38 pathways because of mutation-induced MEKK3 kinase activity enhancement. Collectively, we identified several somatic activating mutations in CCM endothelium, and the MAP3K3 c.1323C>G mutation defines a primary CCM subtype with distinct characteristics in signaling activation and magnetic resonance imaging appearance.
Subject(s)
Hemangioma, Cavernous, Central Nervous System/genetics , MAP Kinase Kinase Kinase 3/genetics , Mutation , Amino Acid Sequence , Class I Phosphatidylinositol 3-Kinases/genetics , Endothelial Cells/metabolism , Germ-Line Mutation , Hemangioma, Cavernous, Central Nervous System/pathology , Human Umbilical Vein Endothelial Cells , Humans , MAP Kinase Kinase Kinase 3/metabolism , MAP Kinase Signaling System , Models, MolecularABSTRACT
N6-methyladenine (6mA) of DNA is an emerging epigenetic mark in the genomes of Chlamydomonas, Caenorhabditis elegans, and mammals recently. Levels of 6mA undergo drastic fluctuation and thus affect fertility during meiosis and early embryogenesis. Here, we showed three complex structures of 6mA demethylase C. elegans NMAD-1A, a canonical isoform of NMAD-1 (F09F7.7). Biochemical results revealed that NMAD-1A prefers 6mA Bubble or Bulge DNAs. Structural studies of NMAD-1A revealed an unexpected "stretch-out" conformation of its Flip2 region, a conserved element that is usually bent over the catalytic center to facilitate substrate base flipping in other DNA demethylases. Moreover, the wide channel between the Flip1 and Flip2 of the NMAD-1A explained the observed preference of NMAD-1A for unpairing substrates, of which the flipped 6mA was primed for catalysis. Structural analysis and mutagenesis studies confirmed that key elements such as carboxy-terminal domain (CTD) and hypothetical zinc finger domain (ZFD) critically contributed to structural integrity, catalytic activity, and nucleosome binding. Collectively, our biochemical and structural studies suggest that NMAD-1A prefers to regulate 6mA in the unpairing regions and is thus possibly associated with dynamic chromosome regulation and meiosis regulation.
Subject(s)
Nucleic Acids , Animals , Caenorhabditis elegans/genetics , Meiosis , DNA , Demethylation , MammalsABSTRACT
Boronate rearrangements, such as the Matteson and Petasis reactions, are valuable metal-free reactions for the transfer of the carbo group on boron to intramolecular electrophilic sites. However, only highly reactive electrophiles are suitable, and ketones are too inactive for those boronate rearrangements due to the high energy barriers. We disclose here the 1,3-boronate rearrangement to ketones, for which a high energy barrier (44.9â kcal/mol) is prohibitory for thermal reactions in the ground state. The reaction is enabled by the key keto-enol-boronate bidentate complex formation in situ, which absorbs visible light to reach the excited state for the chemoselective 1,3-boronate rearrangement to ketones. Experimental and computational investigations exclude free radical intermediates from organoboronates. The aryl, alkenyl, and alkyl boronic acids react with various 1,3-diketones driven by visible light irradiation to construct structurally diverse ß-keto tertiary alcohols under metal-free conditions. The reaction demonstrates substrate diversity with 58 examples, yields up to 98 %, and it is suitable for gram-scale synthesis.
ABSTRACT
Metal-free synthesis of heterocycles is highly sought after in the pharmaceutical industry and has garnered widespread attention due to its environmental sustainability and cost-effectiveness. We report a radical 6-endo addition method for pyridine synthesis from cyclopropylamides and alkynes under metal-free conditions. Various terminal and substituted alkynes are inserted as C2 units into cyclopropylamides to synthesize versatile pyridines with more than 51 examples. Mechanistic investigations and computational studies indicate the unprecedented 6-endo-trig addition of vinyl radicals to the imine nitrogen atom rather than the conventional 5-exo-trig addition to the imine carbon atom, in which the hypervalent iodine(III) plays a critical role. This reaction easily scales up with excellent functional group compatibility and suits the late-stage pyridine installation on complex molecules.
ABSTRACT
Environmental cues such as nutrients alter cellular behaviors by acting on a wide array of molecular sensors inside cells. Of emerging interest is the link observed between effects of dietary sugars on cancer proliferation. Here, we identify the requirements of hexosamine biosynthetic pathway (HBP) and O-GlcNAc transferase (OGT) for Drosophila homeodomain-interacting protein kinase (Hipk)-induced growth abnormalities in response to a high sugar diet. On a normal diet, OGT is both necessary and sufficient for inducing Hipk-mediated tumor-like growth. We further show that OGT maintains Hipk protein stability by blocking its proteasomal degradation and that Hipk is O-GlcNAcylated by OGT. In mammalian cells, human HIPK2 proteins accumulate posttranscriptionally upon OGT overexpression. Mass spectrometry analyses reveal that HIPK2 is at least O-GlcNAc modified at S852, T1009, and S1147 residues. Mutations of these residues reduce HIPK2 O-GlcNAcylation and stability. Together, our data demonstrate a conserved role of OGT in positively regulating the protein stability of HIPKs (fly Hipk and human HIPK2), which likely permits the nutritional responsiveness of HIPKs.
Subject(s)
Carcinogenesis/pathology , Carrier Proteins/metabolism , Drosophila Proteins/metabolism , Drosophila melanogaster/growth & development , Glucose/pharmacology , N-Acetylglucosaminyltransferases/metabolism , Protein Kinases/metabolism , Protein Serine-Threonine Kinases/metabolism , Acetylglucosamine/metabolism , Animals , Carcinogenesis/chemically induced , Carcinogenesis/metabolism , Carrier Proteins/genetics , Cell Proliferation , Cells, Cultured , Drosophila Proteins/genetics , Drosophila melanogaster/drug effects , Drosophila melanogaster/metabolism , Fibroblasts/drug effects , Fibroblasts/metabolism , Fibroblasts/pathology , HEK293 Cells , Humans , MCF-7 Cells , Mice , N-Acetylglucosaminyltransferases/genetics , Phosphorylation , Protein Kinases/genetics , Protein Serine-Threonine Kinases/genetics , Protein Stability , Sweetening Agents/pharmacologyABSTRACT
The aldehydes installation by radical formylation constitutes an attractive synthetic strategy. However, the generation of formyl radicals for organic synthesis applications remains unknown. Herein we report the first formyl radical generation from α-chloro N-methoxyphthalimides, which selectively synthesize aldehydes by alkene hydroformylation under mild photoredox conditions. The aldehydes can be installed on acrylates, acrylamides, vinyl sulfones, vinyl ketones, and complex steroids by radical hydroformylation in excellent chemoselectivity and regioselectivity. The concerted hydrochloride elimination for the formyl radical generation from α-chloro methoxy radicals is established by experimental and computational approaches.
Subject(s)
Aldehydes , Ketones , Alkenes , Hydrochloric AcidABSTRACT
Sphingosines are antimicrobial lipids that form part of the innate barrier to skin colonization by microbes. Sphingosine deficiencies can result in increased epithelial infections by bacteria including Staphylococcus aureus. Recent studies have focused on the potential use of sphingosine resistance or its potential mechanisms. We used RNA-Seq to identify the common d-sphingosine transcriptomic response of the transient skin colonizer S. aureus and the dominant skin coloniser S. epidermidis. A common d-sphingosine stimulon was identified that included downregulation of the SaeSR two-component system (TCS) regulon and upregulation of both the VraSR TCS and CtsR stress regulons. We show that the PstSCAB phosphate transporter, and VraSR offer intrinsic resistance to d-sphingosine. Further, we demonstrate increased sphingosine resistance in these staphylococci evolves readily through mutations in genes encoding the FarE-FarR efflux/regulator proteins. The ease of selecting mutants with resistance to sphingosine may impact upon staphylococcal colonization of skin where the lipid is present and have implications with topical therapeutic applications.
Subject(s)
Staphylococcal Infections , Staphylococcus aureus , Anti-Bacterial Agents/metabolism , Anti-Bacterial Agents/pharmacology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Humans , Lipids , Sphingosine , Staphylococcal Infections/drug therapy , Staphylococcal Infections/microbiology , Staphylococcus/genetics , Staphylococcus aureus/genetics , Staphylococcus aureus/metabolism , Transcriptome/geneticsABSTRACT
Protein modulation by light illumination enables the investigation of biological function in high spatiotemporal precision. Compared to genetic methods, the small molecule approach is uniquely suited for modulating endogenous proteins. Endogenous protein modulation in live cells with small molecules and light has recently advanced on three distinctive frontiers: i) the infrared-light-induced or localized decaging of small molecules by photolysis, ii) the visible-light-induced photocatalytic releasing of small molecules, and iii) the small-molecule-ligand-directed caging for photomodulation of proteins. Together, these methods provide powerful chemical biology tool kits for spatiotemporal modulation of endogenous proteins with potential therapeutic applications. This Concept article aims to inspire organic chemists and chemical biologists to delve into this burgeoning endogenous protein modulation field for new biological discoveries.
Subject(s)
Light , Proteins , Photolysis , LigandsABSTRACT
BACKGROUND AND AIMS: We aimed to develop and validate a deep learning-based system that covers various aspects of early gastric cancer (EGC) diagnosis, including detecting gastric neoplasm, identifying EGC, and predicting EGC invasion depth and differentiation status. Herein, we provide a state-of-the-art comparison of the system with endoscopists using real-time videos in a nationwide human-machine competition. METHODS: This multicenter, prospective, real-time, competitive comparative, diagnostic study enrolled consecutive patients who received magnifying narrow-band imaging endoscopy at the Peking University Cancer Hospital from June 9, 2020 to November 17, 2020. The offline competition was conducted in Wuhan, China, and the endoscopists and the system simultaneously read patients' videos and made diagnoses. The primary outcomes were sensitivity in detecting neoplasms and diagnosing EGCs. RESULTS: One hundred videos, including 37 EGCs and 63 noncancerous lesions, were enrolled; 46 endoscopists from 44 hospitals in 19 provinces in China participated in the competition. The sensitivity rates of the system for detecting neoplasms and diagnosing EGCs were 87.81% and 100%, respectively, significantly higher than those of endoscopists (83.51% [95% confidence interval [CI], 81.23-85.79] and 87.13% [95% CI, 83.75-90.51], respectively). Accuracy rates of the system for predicting EGC invasion depth and differentiation status were 78.57% and 71.43%, respectively, slightly higher than those of endoscopists (63.75% [95% CI, 61.12-66.39] and 64.41% [95% CI, 60.65-68.16], respectively). CONCLUSIONS: The system outperformed endoscopists in identifying EGCs and was comparable with endoscopists in predicting EGC invasion depth and differentiation status in videos. This deep learning-based system could be a powerful tool to assist endoscopists in EGC diagnosis in clinical practice.
Subject(s)
Deep Learning , Stomach Neoplasms , Endoscopy, Gastrointestinal , Humans , Narrow Band Imaging , Prospective Studies , Stomach Neoplasms/diagnostic imagingABSTRACT
The control of endogenous protein activity with light inside live cells is helpful for the high spatiotemporal probing of their dynamic roles. Herein, we report the first small-molecule-ligand-directed caging approach to control the endogenous human O6 -alkylguanine-DNA alkyltransferase (AGT) activity with light, and the caged AGT is constructed from the native intracellular AGT. The photo-responsive O6 -benzylguanine derivative O6 -NBG3 is developed to site-specifically cage the AGT's catalytic cysteine residue, and the light irradiation on-demand restores AGT's activity in vitro, in bacteria, and in mammalian cells. With O6 -NBG3, the alkylated AGT is dealkylated for the first time to recover the DNA repair activity in breast cancer MCF-7 cells by the dose-dependent light irradiation. This decaging strategy enables the localized modulation of endogenous AGT activity with high temporal precision without genetic engineering, which holds great potential for therapeutic applications.
Subject(s)
Alkyl and Aryl Transferases , Guanine , Animals , Guanine/chemistry , Humans , Ligands , Mammals/metabolism , O(6)-Methylguanine-DNA Methyltransferase/chemistryABSTRACT
While China experienced a peak and decline in coronavirus disease 2019 (COVID-19) cases at the start of 2020, regional outbreaks continuously emerged in subsequent months. Resurgences of COVID-19 have also been observed in many other countries. In Guangzhou, China, a small outbreak, involving less than 100 residents, emerged in March and April 2020, and comprehensive and near-real-time genomic surveillance of SARS-CoV-2 was conducted. When the numbers of confirmed cases among overseas travelers increased, public health measures were enhanced by shifting from self-quarantine to central quarantine and SARS-CoV-2 testing for all overseas travelers. In an analysis of 109 imported cases, we found diverse viral variants distributed in the global viral phylogeny, which were frequently shared within households but not among passengers on the same flight. In contrast to the viral diversity of imported cases, local transmission was predominately attributed to two specific variants imported from Africa, including local cases that reported no direct or indirect contact with imported cases. The introduction events of the virus were identified or deduced before the enhanced measures were taken. These results show the interventions were effective in containing the spread of SARS-CoV-2, and they rule out the possibility of cryptic transmission of viral variants from the first wave in January and February 2020. Our study provides evidence and emphasizes the importance of controls for overseas travelers in the context of the pandemic and exemplifies how viral genomic data can facilitate COVID-19 surveillance and inform public health mitigation strategies.
Subject(s)
COVID-19 , SARS-CoV-2 , Africa , COVID-19 Testing , China/epidemiology , Genomics , HumansABSTRACT
BACKGROUND AND AIMS: Rupture of gastroesophageal varices is the most common fatal adverse event of cirrhosis. EGD is considered the criterion standard for diagnosis and risk stratification of gastroesophageal variceal bleeding. The aim of this study was to train and validate a real-time deep convolutional neural network (DCNN) system, named ENDOANGEL, for diagnosing gastroesophageal varices and predicting the risk of rupture. METHODS: After training with 8566 images of endoscopic gastroesophageal varices from 3021 patients and 6152 images of normal esophagus/stomach from 3168 patients, ENDOANGEL was also tested with independent images and videos. It was also compared with endoscopists in several aspects. RESULTS: ENDOANGEL, in contrast with endoscopists, displayed higher accuracy of 97.00% and 92.00% in terms of detecting esophageal varices (EVs) and gastric varices (GVs) in an image contest (97.00% vs 93.94% , P < .01; 92.00% vs 84.43%, P < .05). It also surpassed endoscopists for red color signs of EVs and red spots of GVs (84.21% vs 73.45%, P < .01; 85.26% vs 77.52%, P < .05). Moreover, ENDOANGEL achieved comparable performance in the determination of size, form, color, and bleeding signs. ENDOANGEL also had good performance in making treatment suggestions. With regard to predicting risk factors in multicenter videos, ENDOANGEL showed great stability. CONCLUSIONS: Our data suggest that DCNNs were precise in detecting both EVs and GVs and performed excellently in uncovering the endoscopic risk factors of gastroesophageal variceal bleeding. Thus, the application of DCNNs will assist endoscopists in evaluating gastroesophageal varices more objectively and precisely. (Clinical trial registration number: ChiCTR1900023970.).
Subject(s)
Esophageal and Gastric Varices , Varicose Veins , Endoscopy, Digestive System , Esophageal and Gastric Varices/diagnosis , Gastrointestinal Hemorrhage/diagnosis , Gastrointestinal Hemorrhage/etiology , Humans , Liver Cirrhosis/complications , Neural Networks, Computer , Retrospective StudiesABSTRACT
BACKGROUND : Accurate identification of the differentiation status and margins for early gastric cancer (EGC) is critical for determining the surgical strategy and achieving curative resection in EGC patients. The aim of this study was to develop a real-time system to accurately identify differentiation status and delineate the margins of EGC on magnifying narrow-band imaging (ME-NBI) endoscopy. METHODS : 2217 images from 145 EGC patients and 1870 images from 139 EGC patients were retrospectively collected to train and test the first convolutional neural network (CNN1) to identify EGC differentiation status. The performance of CNN1 was then compared with that of experts using 882 images from 58 EGC patients. Finally, 928 images from 132 EGC patients and 742 images from 87 EGC patients were used to train and test CNN2 to delineate the EGC margins. RESULTS : The system correctly predicted the differentiation status of EGCs with an accuracy of 83.3â% (95â% confidence interval [CI] 81.5â%â-â84.9â%) in the testing dataset. In the manâ-âmachine contest, CNN1 performed significantly better than the five experts (86.2â%, 95â%CI 75.1â%â-â92.8â% vs. 69.7â%, 95â%CI 64.1â%â-â74.7â%). For delineating EGC margins, the system achieved an accuracy of 82.7â% (95â%CI 78.6â%â-â86.1â%) in differentiated EGC and 88.1â% (95â%CI 84.2â%â-â91.1â%) in undifferentiated EGC under an overlap ratio of 0.80.âIn unprocessed EGC videos, the system achieved real-time diagnosis of EGC differentiation status and EGC margin delineation in ME-NBI endoscopy. CONCLUSION : We developed a deep learning-based system to accurately identify differentiation status and delineate the margins of EGC in ME-NBI endoscopy. This system achieved superior performance when compared with experts and was successfully tested in real EGC videos.
Subject(s)
Deep Learning , Stomach Neoplasms , Gastroscopy , Humans , Narrow Band Imaging , Retrospective Studies , Stomach Neoplasms/diagnostic imagingABSTRACT
BACKGROUND: This study retrospectively reviewed the recurrence rate and survival time of primary hepatocellular carcinoma (HCC) patients after treatment with Erzhu Qinggan Jiedu Recipe (ESQJR), explored the impact of Chinese medicine in reducing tumour recurrence and prolonging survival time, and explored an effective prevention treatment for the recurrence of HCC. AIM: To explore the impact of Chinese medicine in reducing tumor recurrence and prolonging survival time, and explore an effective prevention treatment for the recurrence of HCC. METHODS: A total of 137 patients who underwent HCC resection from May 2004 to January 2018 was included in this retrospective study. The patients were divided into two groups, with 68 patients in the Western medicine group and 69 patients in the Western medicine plus ESQJR group. The relapse rate, overall survival period, and disease-free survival period before and after treatment were analysed. Indices including alpha-fetoprotein, alanine aminotransferase, aspartate aminotransferase and Karnofsky performance score were obtained for analysis and comparison. RESULTS: There was no significant difference among patient clinical parameters between the two groups. Compared with the Western medicine group, the Western medicine plus ESQJR group had a reduced cumulative recurrence rate, prolonged overall survival time and disease-free survival time and improved clinical symptoms, including quality of life and liver function. CONCLUSION: ESQJR effectively improved long-term survival in resected HCC patients. ESQJR has the potential to be used as an adjuvant therapy with significant beneficial effects for treating HCC.
Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Carcinoma, Hepatocellular/drug therapy , Carcinoma, Hepatocellular/surgery , Case-Control Studies , Disease-Free Survival , Humans , Liver Neoplasms/drug therapy , Liver Neoplasms/surgery , Neoplasm Recurrence, Local/drug therapy , Quality of Life , Retrospective Studies , Treatment OutcomeABSTRACT
During this global pandemic, cryo-EM has made a great impact on the structure determination of COVID-19 proteins. However, nearly all high-resolution results are based on data acquired on state-of-the-art microscopes where their availability is restricted to a number of centers across the globe with the studies on infectious viruses being further regulated or forbidden. One potential remedy is to employ multipurpose microscopes. Here, we investigated the capability of 200 kV multipurpose microscopes equipped with a direct electron camera in determining the structures of infectious particles. We used 30 nm particles of the grouper nerve necrosis virus as a test sample and obtained the cryo-EM structure with a resolution as high as â¼2.7 Å from a setting that used electron counting. For comparison, we tested a high-end cryo-EM (Talos Arctica) using a similar virus (Macrobrachium rosenbergii nodavirus) to obtain virtually the same resolution. Those results revealed that the resolution is ultimately limited by the depth of field. Our work updates the density maps of these viruses at the sub-3Å level to allow for building accurate atomic models from de novo to provide structural insights into the assembly of the capsids. Importantly, this study demonstrated that multipurpose TEMs are capable of the high-resolution cryo-EM structure determination of infectious particles and is thus germane to the research on pandemics.