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1.
Cell ; 172(5): 1122-1131.e9, 2018 02 22.
Article in English | MEDLINE | ID: mdl-29474911

ABSTRACT

The implementation of clinical-decision support algorithms for medical imaging faces challenges with reliability and interpretability. Here, we establish a diagnostic tool based on a deep-learning framework for the screening of patients with common treatable blinding retinal diseases. Our framework utilizes transfer learning, which trains a neural network with a fraction of the data of conventional approaches. Applying this approach to a dataset of optical coherence tomography images, we demonstrate performance comparable to that of human experts in classifying age-related macular degeneration and diabetic macular edema. We also provide a more transparent and interpretable diagnosis by highlighting the regions recognized by the neural network. We further demonstrate the general applicability of our AI system for diagnosis of pediatric pneumonia using chest X-ray images. This tool may ultimately aid in expediting the diagnosis and referral of these treatable conditions, thereby facilitating earlier treatment, resulting in improved clinical outcomes. VIDEO ABSTRACT.


Subject(s)
Deep Learning , Diagnostic Imaging , Pneumonia/diagnosis , Child , Humans , Neural Networks, Computer , Pneumonia/diagnostic imaging , ROC Curve , Reproducibility of Results , Tomography, Optical Coherence
2.
Immunity ; 54(4): 648-659.e8, 2021 04 13.
Article in English | MEDLINE | ID: mdl-33667383

ABSTRACT

Loss of lymphocytes, particularly T cell apoptosis, is a central pathological event after severe tissue injury that is associated with increased susceptibility for life-threatening infections. The precise immunological mechanisms leading to T cell death after acute injury are largely unknown. Here, we identified a monocyte-T cell interaction driving bystander cell death of T cells in ischemic stroke and burn injury. Specifically, we found that stroke induced a FasL-expressing monocyte population, which led to extrinsic T cell apoptosis. This phenomenon was driven by AIM2 inflammasome-dependent interleukin-1ß (IL-1ß) secretion after sensing cell-free DNA. Pharmacological inhibition of this pathway improved T cell survival and reduced post-stroke bacterial infections. As such, this study describes inflammasome-dependent monocyte activation as a previously unstudied cause of T cell death after injury and challenges the current paradigms of post-injury lymphopenia.


Subject(s)
Coinfection/immunology , DNA-Binding Proteins/immunology , Immune Tolerance/immunology , Inflammasomes/immunology , Signal Transduction/immunology , Animals , Apoptosis/immunology , Bacterial Infections/immunology , Burns/immunology , Burns/microbiology , Coinfection/microbiology , Humans , Interleukin-1beta/immunology , Mice , Mice, Inbred C57BL , Monocytes/immunology , Stroke/immunology , Stroke/microbiology , T-Lymphocytes/immunology
3.
Proc Natl Acad Sci U S A ; 120(4): e2213727120, 2023 01 24.
Article in English | MEDLINE | ID: mdl-36656854

ABSTRACT

The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater Myoviridae cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology.


Subject(s)
Myoviridae , Virus Assembly , Bacteriophage T4/chemistry , Capsid , Capsid Proteins/chemistry , Cryoelectron Microscopy , Myoviridae/chemistry
4.
Crit Rev Immunol ; 44(4): 51-60, 2024.
Article in English | MEDLINE | ID: mdl-38505921

ABSTRACT

This study aimed to elucidate the role of microRNA-503 (miR-503) in pancreatic cancer (PC) progression and the underlying regulatory mechanisms. We acquired miR-503-3p and miR-503-5p expression data along with survival times of PC and normal samples from the UCSC Xena database. Using the t-test, we compared the expression of miR-503-3p and miR-503-5p between PC and normal samples, and evaluated their prognostic significance via Kaplan-Meier survival analysis. The expression of miR-503-5p in PC cells was detected by quantitative PCR. We subsequently overexpressed miR-503-5p in PC cells and examined cell viability, apoptosis, and migration through CCK8 assay, flow cytometry, and Transwell assay, respectively. Potential functional targets were identified using miRTarBase and validated by dual-luciferase reporter assay. Both miR-503-3p and miR-503-5p expression were found to be downregulated in PC; however, only miR-503-5p was linked to cancer prognosis based on public data. In vitro experiments demonstrated that overexpression of miR-503-5p substantially decreased cell viability, induced apoptosis, caused G0/G1 arrest, and inhibited cell migration. miR-503-5p was found to target cyclin E2 (CCNE2), and overexpression of CCNE2 could counteract the effects of miR-503-5p on PC cells. Conclusion: The downregulation of miR-503-5p enhances the progression of PC by targeting CCNE2. The detection of miR-503-5p expression may provide valuable insights for the prevention and prognostic evaluation of PC.


Subject(s)
MicroRNAs , Pancreatic Neoplasms , Humans , MicroRNAs/genetics , Down-Regulation , Cell Line, Tumor , Cell Proliferation/genetics , Cyclins/metabolism , Pancreatic Neoplasms/genetics , Gene Expression Regulation, Neoplastic
5.
Cell Mol Life Sci ; 81(1): 82, 2024 Feb 10.
Article in English | MEDLINE | ID: mdl-38340178

ABSTRACT

Interaction between programmed death-1 (PD-1) ligand 1 (PD-L1) on tumor cells and PD-1 on T cells allows tumor cells to evade T cell-mediated immune surveillance. Strategies targeting PD-1/PD-L1 have shown clinical benefits in a variety of cancers. However, limited response rates in hepatocellular carcinoma (HCC) have prompted us to investigate the molecular regulation of PD-L1. Here, we identify B cell lymphoma-2-associated transcription factor 1 (BCLAF1) as a key PD-L1 regulator in HCC. Specifically, BCLAF1 interacts with SPOP, an E3 ligase that mediates the ubiquitination and degradation of PD-L1, thereby competitively inhibiting SPOP-PD-L1 interaction and subsequent ubiquitination and degradation of PD-L1. Furthermore, we determined an SPOP-binding consensus (SBC) motif mediating the BCLAF1-SPOP interaction on BCLAF1 protein and mutation of BCLAF1-SBC motif disrupts the regulation of the SPOP-PD-L1 axis. In addition, BCLAF1 expression was positively correlated with PD-L1 expression and negatively correlated with biomarkers of T cell activation, including CD3 and CD8, as well as with the level of immune cell infiltration in HCC tissues. Besides, BCLAF1 depletion leads to a significant reduction of PD-L1 expression in vitro, and this reduction of PD-L1 promoted T cell-mediated cytotoxicity. Notably, overexpression of BCLAF1 sensitized tumor cells to checkpoint therapy in an in vitro HCC cells-Jurkat cells co-culture model, whereas BCLAF1-SBC mutant decreased tumor cell sensitivity to checkpoint therapy, suggesting that BCLAF1 and its SBC motif serve as a novel therapeutic target for enhancing anti-tumor immunity in HCC.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Humans , B7-H1 Antigen/genetics , B7-H1 Antigen/metabolism , Carcinoma, Hepatocellular/metabolism , Cell Line , Liver Neoplasms/metabolism , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Programmed Cell Death 1 Receptor , Repressor Proteins/genetics , Tumor Suppressor Proteins , Immune Evasion/genetics
6.
Drug Resist Updat ; 72: 101034, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38134561

ABSTRACT

Antibacterial drug resistance of gram-negative bacteria (GNB) results in high morbidity and mortality of GNB infection, seriously threaten human health globally. Developing new antibiotics has become the critical need for dealing with drug-resistant bacterial infections. Cefiderocol is an iron carrier cephalosporin that achieves drug accumulation through a unique "Trojan horse" strategy into the bacterial periplasm. It shows high antibacterial activity against multidrug-resistant (MDR) Enterobacteriaceae and MDR non-fermentative bacteria. The application of cefiderocol offers new hope for treating clinical drug-resistant bacterial infections. However, limited clinical data and uncertainties about its resistance mechanisms constrain the choice of its therapeutic use. This review aimed to summarize the clinical applications, drug resistance mechanisms, and co-administration of cefiderocol.


Subject(s)
Cefiderocol , Gram-Negative Bacterial Infections , Humans , Siderophores/pharmacology , Siderophores/therapeutic use , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Cephalosporins/pharmacology , Cephalosporins/therapeutic use , Gram-Negative Bacterial Infections/drug therapy , Gram-Negative Bacterial Infections/microbiology , Gram-Negative Bacteria , Drug Resistance, Multiple, Bacterial , Microbial Sensitivity Tests
7.
Proc Natl Acad Sci U S A ; 119(45): e2214089119, 2022 Nov 08.
Article in English | MEDLINE | ID: mdl-36322768

ABSTRACT

Oxygen reduction reaction (ORR), an essential reaction in metal-air batteries and fuel cells, still faces many challenges, such as exploiting cost-effective nonprecious metal electrocatalysts and identifying their surface catalytic sites. Here we introduce bulk defects, Frank partial dislocations (FPDs), into metallic cobalt to construct a highly active and stable catalyst and demonstrate an atomic-level insight into its surface terminal catalysis. Through thermally dealloying bimetallic carbide (Co3ZnC), FPDs were in situ generated in the final dealloyed metallic cobalt. Both theoretical calculations and atomic characterizations uncovered that FPD-driven surface terminations create a distinctive type of surface catalytic site that combines concave geometry and compressive strain, and this two-in-one site intensively weakens oxygen binding. When being evaluated for the ORR, the catalyst exhibits onset and half-wave potentials of 1.02 and 0.90 V (versus the reversible hydrogen electrode), respectively, and negligible activity decay after 30,000 cycles. Furthermore, zinc-air batteries and H2-O2/air fuel cells built with this catalyst also achieve remarkable performance, making it a promising alternative to state-of-the-art Pt-based catalysts. Our findings pave the way for the use of bulk defects to upgrade the catalytic properties of nonprecious electrocatalysts.

8.
Proc Natl Acad Sci U S A ; 119(32): e2201899119, 2022 08 09.
Article in English | MEDLINE | ID: mdl-35914155

ABSTRACT

The cellular and molecular components required for the formation of premetastatic niche (PMN) to promote lung metastasis need to be further investigated. Lung epithelial cells have been reported to exhibit immunomodulatory roles in lung homeostasis and also to mediate immunosuppressive PMN formation in lung metastasis. Here, by single-cell sequencing, we identified a tumor-polarized subpopulation of alveolar type 2 (AT2) epithelial cells with increased expression of glutathione peroxidase 3 (GPX3) and high production of interleukin (IL)-10 in the PMN. IL-10-producing GPX3+ AT2 cells inhibited CD4+ T cell proliferation but enhanced regulatory T cell generation. Mechanistically, tumor exosome-inducing GPX3 expression is required for GPX3+ AT2 cells to preferentially produce IL-10 by stabilizing hypoxia-inducible factor 1 (HIF-1α) and promoting HIF-1α-induced IL-10 production. Accordingly, conditional knockout of GPX3 in AT2 cells suppressed lung metastasis in spontaneous metastatic models. Together, our findings reveal a role of tumor-polarized GPX3+ AT2 cells in promoting lung PMN formation, adding insights into immune evasion in lung metastasis and providing potential targets for the intervention of tumor metastasis.


Subject(s)
Alveolar Epithelial Cells , Interleukin-10 , Lung Neoplasms , Alveolar Epithelial Cells/cytology , CD4-Positive T-Lymphocytes/cytology , Glutathione Peroxidase/genetics , Glutathione Peroxidase/metabolism , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Interleukin-10/genetics , Interleukin-10/metabolism , Lung/cytology , Lung/pathology , Lung Neoplasms/pathology , Neoplasm Metastasis , Tumor Escape
9.
Proc Natl Acad Sci U S A ; 119(38): e2208337119, 2022 09 20.
Article in English | MEDLINE | ID: mdl-36103579

ABSTRACT

Synchronous release at neuronal synapses is accomplished by a machinery that senses calcium influx and fuses the synaptic vesicle and plasma membranes to release neurotransmitters. Previous studies suggested the calcium sensor synaptotagmin (Syt) is a facilitator of vesicle docking and both a facilitator and inhibitor of fusion. On phospholipid monolayers, the Syt C2AB domain spontaneously oligomerized into rings that are disassembled by Ca2+, suggesting Syt rings may clamp fusion as membrane-separating "washers" until Ca2+-mediated disassembly triggers fusion and release [J. Wang et al., Proc. Natl. Acad. Sci. U.S.A. 111, 13966-13971 (2014)].). Here, we combined mathematical modeling with experiment to measure the mechanical properties of Syt rings and to test this mechanism. Consistent with experimental results, the model quantitatively recapitulates observed Syt ring-induced dome and volcano shapes on phospholipid monolayers and predicts rings are stabilized by anionic phospholipid bilayers or bulk solution with ATP. The selected ring conformation is highly sensitive to membrane composition and bulk ATP levels, a property that may regulate vesicle docking and fusion in ATP-rich synaptic terminals. We find the Syt molecules hosted by a synaptic vesicle oligomerize into a halo, unbound from the vesicle, but in proximity to sufficiently phosphatidylinositol 4,5-bisphosphate (PIP2)-rich plasma membrane (PM) domains, the PM-bound trans Syt ring conformation is preferred. Thus, the Syt halo serves as landing gear for spatially directed docking at PIP2-rich sites that define the active zones of exocytotic release, positioning the Syt ring to clamp fusion and await calcium. Our results suggest the Syt ring is both a Ca2+-sensitive fusion clamp and a high-fidelity sensor for directed docking.


Subject(s)
Synaptic Vesicles , Synaptotagmin I , Adenosine Triphosphate/metabolism , Calcium/metabolism , Phosphatidylinositol 4,5-Diphosphate/chemistry , Synaptic Vesicles/metabolism , Synaptotagmin I/chemistry
10.
J Cell Mol Med ; 28(6): e18147, 2024 03.
Article in English | MEDLINE | ID: mdl-38429901

ABSTRACT

HCC is a globally high-incidence malignant tumour, and its pathogenesis is still unclear. Recently, STRN3 has been found to be elevated in various tumours, but its expression and biological functions in HCC have not been studied. In the study, clinical correlation analysis was performed on 371 liver cancer patients from TCGA database and liver cancer tissues and normal tissues from the GEO database. qRT-PCR and western blotting were used to detect relevant proteins in cells, and CCK8 and colony formation experiments were performed to analyse cell proliferation ability. Transwell and wound healing experiments were performed to detect cell invasion ability, and flow cytometry was used to detect cell apoptosis. Single-cell sequencing data and multiple immunofluorescence were analysed for the expression abundance and distribution of certain proteins. Immunohistochemistry was used to assess the expression of STRN3 in patients' tumour and adjacent non-cancerous tissues. The results indicated STRN3 was highly expressed in liver tumour tissues and was closely associated with poor prognosis. Knockdown of STRN3 could significantly inhibit cell proliferation and migration ability. At the same time, we found that STRN3 could inhibit the Hippo pathway and promote the entry of YAP protein into the nucleus. Our study first found that STRN3 could promote tumour growth by inhibiting the Hippo pathway. The study of STRN3 can promote the understanding and treatment of the occurrence and development of HCC.


Subject(s)
Carcinoma, Hepatocellular , Hippo Signaling Pathway , Liver Neoplasms , Humans , Autoantigens , Calmodulin-Binding Proteins/metabolism , Carcinoma, Hepatocellular/metabolism , Carcinoma, Hepatocellular/pathology , Cell Line, Tumor , Cell Movement/genetics , Cell Proliferation/genetics , Gene Expression Regulation, Neoplastic , Hippo Signaling Pathway/genetics , Liver Neoplasms/pathology , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Signal Transduction
11.
J Biol Chem ; 299(4): 103057, 2023 04.
Article in English | MEDLINE | ID: mdl-36822331

ABSTRACT

CLEC16A is an E3 ubiquitin ligase that regulates mitochondrial quality control through mitophagy and is associated with over 20 human diseases. CLEC16A forms a complex with another E3 ligase, RNF41, and a ubiquitin-specific peptidase, USP8; however, regions that regulate CLEC16A activity or the assembly of the tripartite mitophagy regulatory complex are unknown. Here, we report that CLEC16A contains an internal intrinsically disordered protein region (IDPR) that is crucial for CLEC16A function and turnover. IDPRs lack a fixed secondary structure and possess emerging yet still equivocal roles in protein stability, interactions, and enzymatic activity. We find that the internal IDPR of CLEC16A is crucial for its degradation. CLEC16A turnover was promoted by RNF41, which binds and acts upon the internal IDPR to destabilize CLEC16A. Loss of this internal IDPR also destabilized the ubiquitin-dependent tripartite CLEC16A-RNF41-USP8 complex. Finally, the presence of an internal IDPR within CLEC16A was confirmed using NMR and CD spectroscopy. Together, our studies reveal that an IDPR is essential to control the reciprocal regulatory balance between CLEC16A and RNF41, which could be targeted to improve mitochondrial health in disease.


Subject(s)
Intrinsically Disordered Proteins , Mitophagy , Humans , Intrinsically Disordered Proteins/genetics , Intrinsically Disordered Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism , Ubiquitin/metabolism , Monosaccharide Transport Proteins/metabolism , Lectins, C-Type/metabolism
12.
J Am Chem Soc ; 146(18): 12691-12701, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38676653

ABSTRACT

Aliphatic strained rings have been increasingly applied in medicinal chemistry due to their beneficial physicochemical and pharmacokinetic properties. However, the divergent synthesis of enantioenriched cyclobutane derivatives with various structural patterns continues to be a significant challenge. Here, we disclose a palladium-catalyzed enantioselective desymmetrization of cyclobutenes, resulting in a series of hydroarylation and 1,2- and 1,3-diarylation products via the interceptions of a common Heck intermediate. Mechanistic investigations provide valuable insights into understanding the catalytic mode of the palladium catalysts and the observed variations in the deuterium-responsive behavior during reactions. Furthermore, the synthetic utility is demonstrated in the syntheses of deuterated drug candidate belaperidone skeletons and pseudosymmetrical truxinic acid-type derivatives.

13.
Cancer Sci ; 115(4): 1141-1153, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38287724

ABSTRACT

The indigenous microbial milieu within tumorous tissues exerts a pivotal influence on the genesis and advancement of gastric cancer (GC). This investigation scrutinizes the functions and molecular mechanisms attributed to Prevotella intermedia in the malignant evolution of GC. Isolation of P. intermedia from paired GC tissues was undertaken. Quantification of P. intermedia abundance in 102 tissues was accomplished using quantitative real-time PCR (qRT-PCR). Assessment of the biological effects of P. intermedia on GC cells was observed using culture medium supernatant. Furthermore, the protein profile of GC cells treated with tumor-derived P. intermedia was examined through label-free protein analysis. The functionality of perilipin 3 (PLIN3) was subsequently confirmed using shRNA. Our investigation revealed that the relative abundance of P. intermedia in tumor tissues significantly surpassed that of corresponding healthy tissues. The abundance of P. intermedia exhibited correlations with tumor differentiation (p = 0.006), perineural invasion (p = 0.004), omentum majus invasion (p = 0.040), and the survival duration of GC patients (p = 0.042). The supernatant derived from tumor-associated P. intermedia bolstered the proliferation, clone formation, migration, and invasion of GC cells. After indirect co-cultivation with tumor-derived P. intermedia, dysregulation of 34 proteins, including PLIN3, was discerned in GC cells. Knockdown of PLIN3 mitigated the malignancy instigated by P. intermedia in GC cells. Our findings posit that P. intermedia from the tumor microenvironment plays a substantial role in the malignant progression of GC via the modulation of PLIN3 expression. Moreover, the relative abundance of P. intermedia might serve as a potential biomarker for the diagnosis and prognosis of GC.


Subject(s)
Stomach Neoplasms , Humans , Cell Differentiation , Cell Line, Tumor , Cell Movement/genetics , Cell Proliferation/genetics , Perilipin-3 , Prevotella intermedia , Prognosis , Stomach Neoplasms/pathology , Tumor Microenvironment
14.
Apoptosis ; 2024 Jun 17.
Article in English | MEDLINE | ID: mdl-38886312

ABSTRACT

With global warming, extreme environmental heat is becoming a social issue of concern, which can cause adverse health results including heatstroke (HS). Severe heat stress is characterized by cell death of direct heat damage, excessive inflammatory responses, and coagulation disorders that can lead to multiple organ dysfunction (MODS) and even death. However, the significant pathophysiological mechanism and treatment of HS are still not fully clear. Various modes of cell death, including apoptosis, pyroptosis, ferroptosis, necroptosis and PANoptosis are involved in MODS induced by heatstroke. In this review, we summarized molecular mechanism, key transcriptional regulation as for HSF1, NRF2, NF-κB and PARP-1, and potential therapies of cell death resulting in CNS, liver, intestine, reproductive system and kidney injury induced by heat stress. Understanding the mechanism of cell death provides new targets to protect multi-organ function in HS.

15.
J Neuroinflammation ; 21(1): 5, 2024 Jan 04.
Article in English | MEDLINE | ID: mdl-38178136

ABSTRACT

A key pathological factor of Alzheimer's disease (AD), the most prevalent form of age-related dementia in the world, is excessive ß-amyloid protein (Aß) in extracellular aggregation in the brain. And in the peripheral blood, a large amount of Aß is derived from platelets. So far, the causality between the levels of peripheral blood Aß and its aggregation in the brain, particularly the role of the peripheral blood Aß in the pathology of AD, is still unclear. And the relation between the peripheral blood Aß and tau tangles of brain, another crucial pathologic factor contributing to the pathogenesis of AD, is also ambiguous. More recently, the anti-Aß monoclonal antibodies are approved for treatment of AD patients through declining the peripheral blood Aß mechanism of action to enhance plasma and central nervous system (CNS) Aß clearance, leading to a decrease Aß burden in brain and improving cognitive function, which clearly indicates that the levels of the peripheral blood Aß impacted on the Aß burden in brain and involved in the pathogenesis of AD. In addition, the role of peripheral innate immune cells in AD remains mostly unknown and the results obtained were controversial. In the present review, we summarize recent studies on the roles of peripheral blood Aß and the peripheral innate immune cells in the pathogenesis of AD. Finally, based on the published data and our own work, we believe that peripheral blood Aß plays an important role in the development and progression of AD by impacting on the peripheral innate immune cells.


Subject(s)
Alzheimer Disease , Humans , Alzheimer Disease/pathology , Amyloid beta-Peptides/metabolism , Brain/metabolism , Cognition , Immunity, Innate
16.
J Virol ; 97(11): e0132223, 2023 Nov 30.
Article in English | MEDLINE | ID: mdl-37882519

ABSTRACT

IMPORTANCE: Chickens immunized with the infectious laryngotracheitis chicken embryo origin (CEO) vaccine (Medivac, PT Medion Farma Jaya) experience adverse reactions, hindering its safety and effective use in poultry flocks. To improve the effect of the vaccine, we sought to find a strategy to alleviate the respiratory reactions associated with the vaccine. Here, we confirmed that co-administering the CEO vaccine with chIL-2 by oral delivery led to significant alleviation of the vaccine reactions in chickens after immunization. Furthermore, we found that the co-administration of chIL-2 with the CEO vaccine reduced the clinical signs of the CEO vaccine while enhancing natural killer cells and cytotoxic T lymphocyte response to decrease viral loads in their tissues, particularly in the trachea and conjunctiva. Importantly, we demonstrated that the chIL-2 treatment can ameliorate the replication of the CEO vaccine without compromising its effectiveness. This study provides new insights into further applications of chIL-2 and a promising strategy for alleviating the adverse reaction of vaccines.


Subject(s)
Chickens , Herpesviridae Infections , Herpesvirus 1, Gallid , Interleukin-2 , Killer Cells, Natural , T-Lymphocytes, Cytotoxic , Viral Vaccines , Animals , Administration, Oral , Chickens/immunology , Chickens/virology , Conjunctiva/virology , Herpesviridae Infections/immunology , Herpesviridae Infections/prevention & control , Herpesviridae Infections/veterinary , Herpesviridae Infections/virology , Herpesvirus 1, Gallid/immunology , Interleukin-2/administration & dosage , Interleukin-2/immunology , Killer Cells, Natural/immunology , Poultry Diseases/immunology , Poultry Diseases/prevention & control , Poultry Diseases/virology , Respiratory Tract Diseases/immunology , Respiratory Tract Diseases/prevention & control , Respiratory Tract Diseases/veterinary , Respiratory Tract Diseases/virology , T-Lymphocytes, Cytotoxic/immunology , Trachea/virology , Viral Load , Viral Vaccines/administration & dosage , Viral Vaccines/adverse effects , Viral Vaccines/biosynthesis , Viral Vaccines/immunology
17.
Brief Bioinform ; 23(5)2022 09 20.
Article in English | MEDLINE | ID: mdl-36088543

ABSTRACT

Ensemble learning is a kind of machine learning method which can integrate multiple basic learners together and achieve higher accuracy. Recently, single machine learning methods have been established to predict survival for patients with cancer. However, it still lacked a robust ensemble learning model with high accuracy to pick out patients with high risks. To achieve this, we proposed a novel genetic algorithm-aided three-stage ensemble learning method (3S score) for survival prediction. During the process of constructing the 3S score, double training sets were used to avoid over-fitting; the gene-pairing method was applied to reduce batch effect; a genetic algorithm was employed to select the best basic learner combination. When used to predict the survival state of glioma patients, this model achieved the highest C-index (0.697) as well as area under the receiver operating characteristic curve (ROC-AUCs) (first year = 0.705, third year = 0.825 and fifth year = 0.839) in the combined test set (n = 1191), compared with 12 other baseline models. Furthermore, the 3S score can distinguish survival significantly in eight cohorts among the total of nine independent test cohorts (P < 0.05), achieving significant improvement of ROC-AUCs. Notably, ablation experiments demonstrated that the gene-pairing method, double training sets and genetic algorithm make sure the robustness and effectiveness of the 3S score. The performance exploration on pan-cancer showed that the 3S score has excellent ability on survival prediction in five kinds of cancers, which was verified by Cox regression, survival curves and ROC curves together. To enable its clinical adoption, we implemented the 3S score and other two clinical factors as an easy-to-use web tool for risk scoring and therapy stratification in glioma patients.


Subject(s)
Glioma , Machine Learning , Glioma/genetics , Humans , ROC Curve , Risk Factors
18.
J Transl Med ; 22(1): 563, 2024 Jun 12.
Article in English | MEDLINE | ID: mdl-38867230

ABSTRACT

In recent years, single-cell analyses have revealed the heterogeneity of the tumour microenvironment (TME) at the genomic, transcriptomic, and proteomic levels, further improving our understanding of the mechanisms of tumour development. Single-cell RNA sequencing (scRNA-seq) technology allow analysis of the transcriptome at the single-cell level and have unprecedented potential for exploration of the characteristics involved in tumour development and progression. These techniques allow analysis of transcript sequences at higher resolution, thereby increasing our understanding of the diversity of cells found in the tumour microenvironment and how these cells interact in complex tumour tissue. Although scRNA-seq has emerged as an important tool for studying the tumour microenvironment in recent years, it cannot be used to analyse spatial information for cells. In this regard, spatial transcriptomics (ST) approaches allow researchers to understand the functions of individual cells in complex multicellular organisms by understanding their physical location in tissue sections. In particular, in related research on tumour heterogeneity, ST is an excellent complementary approach to scRNA-seq, constituting a new method for further exploration of tumour heterogeneity, and this approach can also provide unprecedented insight into the development of treatments for pancreatic cancer (PC). In this review, based on the methods of scRNA-seq and ST analyses, research progress on the tumour microenvironment and treatment of pancreatic cancer is further explained.


Subject(s)
Pancreatic Neoplasms , Sequence Analysis, RNA , Single-Cell Analysis , Transcriptome , Tumor Microenvironment , Tumor Microenvironment/genetics , Humans , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/pathology , Transcriptome/genetics , Gene Expression Profiling , Animals
19.
Ann Surg Oncol ; 31(6): 3803-3812, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38280959

ABSTRACT

BACKGROUND: Neoadjuvant chemoradiotherapy (NCRT) has shown promise in improving the prognosis of individuals with locally advanced esophageal squamous cell carcinoma (LA-ESCC). However, the factors influencing tumor response and long-term survival in these patients remain unknown. The optimal timing for surgery after the completion of radiotherapy in LA-ESCC remains controversial. Therefore, this study was designed to identify biomarkers and to determine the optimal post-NCRT time-to-surgery (TTS) for patients with LA-ESCC. METHODS: This retrospective study included patients with resectable LA-ESCC who underwent NCRT between May 2017 and June 2021. The tumor shrinkage rate was calculated as the difference between the pre- and post-primary gross tumor volume (GTVp) divided by the pre-GTVp. Univariate and multivariate Cox regression analyses and Kaplan-Meier curves were used to calculate overall survival (OS) and progression-free survival (PFS). RESULTS: We collected data from 248 patients with resectable LA-ESCC who underwent computed tomography (CT) scans before the initiation of treatment. The median follow-up time was 37.7 months. The optimal cutoff of tumor shrinkage was 45%. In the univariate and multivariate analyses, we found a significant association between the tumor shrinkage rate and PFS (p = 0.001). Among the subgroup of patients who responded to treatment, extending the TTS was associated with improved OS (p = 0.037) and PFS (p = 0.028). CONCLUSIONS: For patients with resectable LA-ESCC, the tumor shrinkage rate is an independent prognostic factor for PFS. Thus, for responders, prolonging TTS is recommended to obtain a better OS.


Subject(s)
Esophageal Neoplasms , Esophagectomy , Neoadjuvant Therapy , Time-to-Treatment , Tumor Burden , Humans , Esophageal Neoplasms/pathology , Esophageal Neoplasms/therapy , Esophageal Neoplasms/mortality , Male , Retrospective Studies , Female , Neoadjuvant Therapy/mortality , Middle Aged , Survival Rate , Aged , Follow-Up Studies , Prognosis , Chemoradiotherapy/mortality , Esophageal Squamous Cell Carcinoma/therapy , Esophageal Squamous Cell Carcinoma/pathology , Adult , Chemoradiotherapy, Adjuvant
20.
Opt Lett ; 49(10): 2765-2768, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38748156

ABSTRACT

In this Letter, a quasi-distributed quartz enhanced photoacoustic spectroscopy (QEPAS) gas sensing system based on hollow waveguide micropores (HWGMP) was reported for the first time, to the best of our knowledge. Three micropores were developed on the HWG to achieve distributed detection units. Three self-designed quartz tuning forks (QTFs) with low resonant frequency of 8.7 kHz were selected as the acoustic wave transducer to improve the detection performance. Compared with micro-nano fiber evanescent wave (FEW) QEPAS, the HWGMP-QEPAS sensor has advantages such as strong anti-interference ability, low loss, and low cost. Acetylene (C2H2) was selected as the target gas to verify the characteristics of the reported sensor. The experimental results showed that the three QTFs almost had the same sensing ability and possessed an excellent linear concentration response to C2H2. The minimum detection limits (MDLs) for the three QTFs were determined as 68.90, 68.31, and 66.62 ppm, respectively. Allan deviation analysis indicated that the system had good long-term stability, and the MDL can be improved below 3 ppm in an average time of 1000 s.

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