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1.
Cell ; 186(19): 4235-4251.e20, 2023 09 14.
Article in English | MEDLINE | ID: mdl-37607536

ABSTRACT

Natural killer (NK) cells play indispensable roles in innate immune responses against tumor progression. To depict their phenotypic and functional diversities in the tumor microenvironment, we perform integrative single-cell RNA sequencing analyses on NK cells from 716 patients with cancer, covering 24 cancer types. We observed heterogeneity in NK cell composition in a tumor-type-specific manner. Notably, we have identified a group of tumor-associated NK cells that are enriched in tumors, show impaired anti-tumor functions, and are associated with unfavorable prognosis and resistance to immunotherapy. Specific myeloid cell subpopulations, in particular LAMP3+ dendritic cells, appear to mediate the regulation of NK cell anti-tumor immunity. Our study provides insights into NK-cell-based cancer immunity and highlights potential clinical utilities of NK cell subsets as therapeutic targets.


Subject(s)
Killer Cells, Natural , Neoplasms , Tumor Microenvironment , Humans , Immunity, Innate , Immunotherapy , Killer Cells, Natural/immunology , Myeloid Cells , Neoplasms/immunology , Dendritic Cells/immunology , Single-Cell Gene Expression Analysis
2.
Immunity ; 53(3): 685-696.e3, 2020 09 15.
Article in English | MEDLINE | ID: mdl-32783921

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic poses a current world-wide public health threat. However, little is known about its hallmarks compared to other infectious diseases. Here, we report the single-cell transcriptional landscape of longitudinally collected peripheral blood mononuclear cells (PBMCs) in both COVID-19- and influenza A virus (IAV)-infected patients. We observed increase of plasma cells in both COVID-19 and IAV patients and XIAP associated factor 1 (XAF1)-, tumor necrosis factor (TNF)-, and FAS-induced T cell apoptosis in COVID-19 patients. Further analyses revealed distinct signaling pathways activated in COVID-19 (STAT1 and IRF3) versus IAV (STAT3 and NFκB) patients and substantial differences in the expression of key factors. These factors include relatively increase of interleukin (IL)6R and IL6ST expression in COVID-19 patients but similarly increased IL-6 concentrations compared to IAV patients, supporting the clinical observations of increased proinflammatory cytokines in COVID-19 patients. Thus, we provide the landscape of PBMCs and unveil distinct immune response pathways in COVID-19 and IAV patients.


Subject(s)
Coronavirus Infections/immunology , Cytokines/immunology , Influenza, Human/immunology , Leukocytes, Mononuclear/immunology , Pneumonia, Viral/immunology , Signal Transduction/immunology , Betacoronavirus/immunology , COVID-19 , Humans , Influenza A Virus, H1N1 Subtype/immunology , Pandemics , SARS-CoV-2
3.
Crit Rev Immunol ; 41(1): 77-87, 2021.
Article in English | MEDLINE | ID: mdl-33822526

ABSTRACT

Immunotherapy has emerged as a potent and effective treatment for multiple cancer types. For example, the engineering of T cells through the expression of chimeric antigen receptor (CAR) against tumors has shown remarkable potential. This review outlines clinical applications of CAR-T cell therapy in hematological malignancies and solid tumors, with a focus on the main challenges related to the safety and efficacy of the current CAR-T cell therapy and the promising strategies to maximize antitumor efficacy while minimizing adverse events. Finally, we present the future outlook of CAR-T cell therapy for the treatment against malignancies. We believe that potential problems can be overcome by strategies to further facilitate effective clinical translation and improve the efficacy, especially through the combination of different approaches.


Subject(s)
Neoplasms , Receptors, Chimeric Antigen , Cell- and Tissue-Based Therapy , Humans , Immunotherapy , Immunotherapy, Adoptive , Neoplasms/therapy , Receptors, Chimeric Antigen/genetics , T-Lymphocytes
4.
Mol Microbiol ; 114(4): 641-652, 2020 10.
Article in English | MEDLINE | ID: mdl-32634279

ABSTRACT

Of the ~80 putative toxin-antitoxin (TA) modules encoded by the bacterial pathogen Mycobacterium tuberculosis (Mtb), three contain antitoxins essential for bacterial viability. One of these, Rv0060 (DNA ADP-ribosyl glycohydrolase, DarGMtb ), functions along with its cognate toxin Rv0059 (DNA ADP-ribosyl transferase, DarTMtb ), to mediate reversible DNA ADP-ribosylation (Jankevicius et al., 2016). We demonstrate that DarTMtb -DarGMtb form a functional TA pair and essentiality of darGMtb is dependent on the presence of darTMtb , but simultaneous deletion of both darTMtb -darGMtb does not alter viability of Mtb in vitro or in mice. The antitoxin, DarGMtb , forms a cytosolic complex with DNA-repair proteins that assembles independently of either DarTMtb or interaction with DNA. Depletion of DarGMtb alone is bactericidal, a phenotype that is rescued by expression of an orthologous antitoxin, DarGTaq , from Thermus aquaticus. Partial depletion of DarGMtb triggers a DNA-damage response and sensitizes Mtb to drugs targeting DNA metabolism and respiration. Induction of the DNA-damage response is essential for Mtb to survive partial DarGMtb -depletion and leads to a hypermutable phenotype.


Subject(s)
Mycobacterium tuberculosis/metabolism , Toxin-Antitoxin Systems/genetics , Toxin-Antitoxin Systems/physiology , Animals , Antitoxins/genetics , Bacterial Proteins/metabolism , Bacterial Toxins/metabolism , Cell Death , DNA/metabolism , Female , Mice , Mice, Inbred C57BL , Microbial Viability
5.
J Immunol ; 193(1): 130-8, 2014 Jul 01.
Article in English | MEDLINE | ID: mdl-24907345

ABSTRACT

The high temperature requirement A1 (HTRA1) is a potent protease involved in many diseases, including rheumatoid arthritis (RA). However, the regulatory mechanisms that control HTRA1 expression need to be determined. In this study, we demonstrated that IFN-γ significantly inhibited the basal and LPS-induced HTRA1 expression in fibroblasts and macrophages, which are two major cells for HTRA1 production in RA. Importantly, the inhibitory effect of IFN-γ on HTRA1 expression was evidenced in collagen-induced arthritis (CIA) mouse models and in human RA synovial cells. In parallel with the enhanced CIA incidence and pathological changes in IFN-γ-deficient mice, HTRA1 expression in the joint tissues was also increased as determined by real-time PCR and Western blots. IFN-γ deficiency increased the incidence of CIA and the pathological severity in mice. Neutralization of HTRA1 by Ab significantly reversed the enhanced CIA frequency and severity in IFN-γ-deficient mice. Mechanistically, IFN-γ negatively controls HTRA1 expression through activation of p38 MAPK/STAT1 pathway. Dual luciferase reporter assay and chromatin immunoprecipitation analysis showed that STAT1 could directly bind to HTRA1 promoter after IFN-γ stimulation. This study offers new insights into the molecular regulation of HTRA1 expression and its role in RA pathogenesis, which may have significant impact on clinical therapy for RA and possibly other HTRA1-related diseases, including osteoarthritis, age-related macular degeneration, and cancer.


Subject(s)
Arthritis, Rheumatoid/immunology , Gene Expression Regulation, Enzymologic/immunology , Interferon-gamma/immunology , Joints/immunology , Serine Endopeptidases/immunology , Animals , Arthritis, Rheumatoid/chemically induced , Arthritis, Rheumatoid/genetics , Arthritis, Rheumatoid/metabolism , Cell Line , Collagen/toxicity , Disease Models, Animal , Gene Expression Regulation, Enzymologic/drug effects , Gene Expression Regulation, Enzymologic/genetics , High-Temperature Requirement A Serine Peptidase 1 , Humans , Interferon-gamma/genetics , Interferon-gamma/metabolism , Joints/metabolism , Joints/pathology , Lipopolysaccharides/toxicity , Mice , Mice, Knockout , Promoter Regions, Genetic/immunology , STAT1 Transcription Factor/genetics , STAT1 Transcription Factor/immunology , STAT1 Transcription Factor/metabolism , Serine Endopeptidases/biosynthesis , Serine Endopeptidases/genetics , p38 Mitogen-Activated Protein Kinases/genetics , p38 Mitogen-Activated Protein Kinases/immunology , p38 Mitogen-Activated Protein Kinases/metabolism
6.
Inflamm Res ; 64(5): 303-11, 2015 May.
Article in English | MEDLINE | ID: mdl-25804385

ABSTRACT

OBJECTIVE AND DESIGN: Molecular mechanisms of microgravity-caused immunosuppression are not fully elucidated. In the present study, we investigated the effects of simulated microgravity on macrophage functions and tried to identify the related intracellular signal pathways. MATERIAL OR SUBJECTS: Primary mouse macrophages were used in the present study. The gene expression and function of IL-4-treated mouse macrophages were detected after simulated microgravity or 1 g control. METHODS: Freshly isolated primary mouse macrophages were cultured in a standard simulated microgravity situation using a rotary cell culture system (RCCS-1) and 1 g control conditions. Real-time PCR, western blots and flow cytometry were used to investigate the related intracellular signals and molecule expression. RESULTS: The arginase mRNA and protein levels in freshly isolated primary mouse macrophages under simulated microgravity using RCCS-1 were significantly higher than those under normal gravity. Meanwhile, simulated microgravity induced over-expression of C/EBPß, a transcription factor of arginase promoter, and activation of p38 MAPK, which could increase C/EBPß expression. Furthermore, up-regulation of Interleukin-6 (IL-6) and down-regulation of IL-12 p40 (IL-12B) in LPS-stimulated macrophages were also detected after simulated microgravity, which is regulated by C/EBPß. CONCLUSIONS: Simulated microgravity activates a p38 MAPK-C/EBPß pathway in macrophages to up-regulate arginase and IL-6 expression and down-regulate IL-12B expression. Both increased arginase expression and decreased IL-12B expression in macrophages during inflammation could result in immunosuppression under microgravity.


Subject(s)
Arginase/biosynthesis , CCAAT-Enhancer-Binding Protein-beta/physiology , Cytokines/biosynthesis , Inflammation/metabolism , Macrophages/metabolism , Signal Transduction/physiology , Weightlessness , p38 Mitogen-Activated Protein Kinases/physiology , Animals , CCAAT-Enhancer-Binding Protein-beta/metabolism , Enzyme Activation/physiology , Male , Mice , Mice, Inbred C57BL , Up-Regulation/physiology , p38 Mitogen-Activated Protein Kinases/metabolism
7.
Inflamm Res ; 63(1): 91-8, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24196691

ABSTRACT

OBJECTIVE AND DESIGN: Microgravity environments in space can cause major abnormalities in human physiology, including decreased immunity. The underlying mechanisms of microgravity-induced inflammatory defects in macrophages are unclear. MATERIAL OR SUBJECTS: RAW264.7 cells and primary mouse macrophages were used in the present study. Lipopolysaccharide (LPS)-induced cytokine expression in mouse macrophages was detected under either simulated microgravity or 1g control. METHODS: Freshly isolated primary mouse macrophages and RAW264.7 cells were cultured in a standard simulated microgravity situation using a rotary cell culture system (RCCS-1) and 1g control conditions. The cytokine expression was determined by real-time PCR and ELISA assays. Western blots were used to investigate the related intracellular signals. RESULTS: LPS-induced tumor necrosis factor-α (TNF-α) expression, but not interleukin-1ß expression, in mouse macrophages was significantly suppressed under simulated microgravity. The molecular mechanism studies showed that LPS-induced intracellular signal transduction including phosphorylation of IKK and JNK and nuclear translocation of NF-κB in macrophages was identical under normal gravity and simulated microgravity. Furthermore, TNF-α mRNA stability did not decrease under simulated microgravity. Finally, we found that heat shock factor-1 (HSF1), a known repressor of TNF-α promoter, was markedly activated under simulated microgravity. CONCLUSIONS: Short-term treatment with microgravity caused significantly decreased TNF-α production. Microgravity-activated HSF1 may contribute to the decreased TNF-α expression in macrophages directly caused by microgravity, while the LPS-induced NF-κB pathway is resistant to microgravity.


Subject(s)
Macrophages/immunology , Tumor Necrosis Factor-alpha/immunology , Weightlessness , Animals , Cell Line, Tumor , Cells, Cultured , DNA-Binding Proteins/immunology , Heat Shock Transcription Factors , Heat-Shock Proteins/immunology , Lipopolysaccharides , Male , Mice , Mice, Inbred C57BL , NF-kappa B/immunology , RNA, Messenger/metabolism , Transcription Factors/immunology , Tumor Necrosis Factor-alpha/genetics
8.
Arthritis Rheum ; 65(11): 2835-46, 2013 Nov.
Article in English | MEDLINE | ID: mdl-23982886

ABSTRACT

OBJECTIVE: The protease HTRA-1 is closely associated with rheumatoid arthritis (RA). The molecular mechanisms that control HTRA-1 expression are currently unknown. This study was undertaken to determine the regulatory role of Toll-like receptors (TLRs) on HTRA-1 expression in mice with collagen-induced arthritis (CIA) and in synovial cells from RA patients. METHODS: HTRA-1 messenger RNA and protein production in mouse fibroblasts, mouse macrophages, and freshly isolated RA patient synovial cells treated with TLR ligands were detected by real-time polymerase chain reaction and enzyme-linked immunosorbent assay, respectively. Arthritis incidence and severity were determined using clinical scores and histopathologic analysis. Involvement of HTRA-1 in lipopolysaccharide (LPS)-increased arthritis incidence and severity in mice was determined using anti-HTRA-1 monoclonal antibody. The signal pathways involved in HTRA-1 expression were accessed by specific inhibitors, RNA interference, dual-luciferase reporter, and chromatin immunoprecipitation methods. RESULTS: LPS and tenascin-C, but not the other TLR ligands tested, strongly induced HTRA-1 expression. LPS significantly increased HTRA-1 expression in the joint tissue as well as arthritis incidence and severity in mice with CIA. Blocking HTRA-1 by antibody significantly decreased LPS-promoted CIA severity. Inhibiting NF-κB significantly decreased LPS-induced HTRA-1 expression in mouse and human cells. Dual-luciferase reporter assay and ChIP analysis showed that p65 directly binds to HTRA-1 promoter (amino acid 347). CONCLUSION: Our findings indicate that TLR-4 activation increases HTRA-1 expression through the NF-κB pathway in fibroblasts and macrophages. HTRA-1 expression is involved in the enhancing effects of LPS on CIA. This study offers new insights into the regulation of HTRA-1 expression via LPS/TLR-4 and the role of HTRA-1 in RA pathogenesis.


Subject(s)
Arthritis, Experimental/genetics , Arthritis, Experimental/metabolism , Lipopolysaccharides/pharmacology , Serine Endopeptidases/genetics , Serine Endopeptidases/metabolism , Animals , Arthritis, Experimental/immunology , Disease Models, Animal , Fibroblasts/drug effects , Fibroblasts/physiology , Gene Expression Regulation, Enzymologic/drug effects , Gene Expression Regulation, Enzymologic/immunology , High-Temperature Requirement A Serine Peptidase 1 , Humans , Incidence , Macrophages/drug effects , Macrophages/physiology , Mice , Mice, Inbred C57BL , NF-kappa B/metabolism , RNA, Messenger/metabolism , Synovial Membrane/cytology , Synovial Membrane/physiology , Toll-Like Receptor 4/metabolism
9.
mBio ; 14(4): e0034023, 2023 08 31.
Article in English | MEDLINE | ID: mdl-37350592

ABSTRACT

Nicotinamide adenine dinucleotide (NAD) and its phosphorylated derivative (NADP) are essential cofactors that participate in hundreds of biochemical reactions and have emerged as therapeutic targets in cancer, metabolic disorders, neurodegenerative diseases, and infections, including tuberculosis. The biological basis for the essentiality of NAD(P) in most settings, however, remains experimentally unexplained. Here, we report that inactivation of the terminal enzyme of NAD synthesis, NAD synthetase (NadE), elicits markedly different metabolic and microbiologic effects than those of the terminal enzyme of NADP biosynthesis, NAD kinase (PpnK), in Mycobacterium tuberculosis (Mtb). Inactivation of NadE led to parallel reductions of both NAD and NADP pools and Mtb viability, while inactivation of PpnK selectively depleted NADP pools but only arrested growth. Inactivation of each enzyme was accompanied by metabolic changes that were specific for the affected enzyme and associated microbiological phenotype. Bacteriostatic levels of NAD depletion caused a compensatory remodeling of NAD-dependent metabolic pathways in the absence of an impact on NADH/NAD ratios, while bactericidal levels of NAD depletion resulted in a disruption of NADH/NAD ratios and inhibition of oxygen respiration. These findings reveal a previously unrecognized physiologic specificity associated with the essentiality of two evolutionarily ubiquitous cofactors. IMPORTANCE The current course for cure of Mycobacterium tuberculosis (Mtb)-the etiologic agent of tuberculosis (TB)-infections is lengthy and requires multiple antibiotics. The development of shorter, simpler treatment regimens is, therefore, critical to the goal of eradicating TB. NadE, an enzyme required for the synthesis of the ubiquitous cofactor NAD, is essential for survival of Mtb and regarded as a promising drug target. However, the basis of this essentiality was not clear due to its role in the synthesis of both NAD and NADP. Here, we resolve this ambiguity through a combination of gene silencing and metabolomics. We specifically show that NADP deficiency is bacteriostatic, while NAD deficiency is bactericidal due to its role in Mtb's respiratory capacity. These results argue for a prioritization of NAD biosynthesis inhibitors in anti-TB drug development.


Subject(s)
Mycobacterium tuberculosis , Tuberculosis , Humans , NAD/metabolism , NADP/metabolism , Ligases/metabolism
10.
Front Cell Dev Biol ; 11: 1209320, 2023.
Article in English | MEDLINE | ID: mdl-38020907

ABSTRACT

Background: Currently, the mechanism(s) underlying corticogenesis is still under characterization. Methods: We curated the most comprehensive single-cell RNA-seq (scRNA-seq) datasets from mouse and human fetal cortexes for data analysis and confirmed the findings with co-immunostaining experiments. Results: By analyzing the developmental trajectories with scRNA-seq datasets in mice, we identified a specific developmental sub-path contributed by a cell-population expressing both deep- and upper-layer neurons (DLNs and ULNs) specific markers, which occurred on E13.5 but was absent in adults. In this cell-population, the percentages of cells expressing DLN and ULN markers decreased and increased, respectively, during the development suggesting direct neuronal transition (namely D-T-U). Whilst genes significantly highly/uniquely expressed in D-T-U cell population were significantly enriched in PTN/MDK signaling pathways related to cell migration. Both findings were further confirmed by co-immunostaining with DLNs, ULNs and D-T-U specific markers across different timepoints. Furthermore, six genes (co-expressed with D-T-U specific markers in mice) showing a potential opposite temporal expression between human and mouse during fetal cortical development were associated with neuronal migration and cognitive functions. In adult prefrontal cortexes (PFC), D-T-U specific genes were expressed in neurons from different layers between humans and mice. Conclusion: Our study characterizes a specific cell population D-T-U showing direct DLNs to ULNs neuronal transition and migration during fetal cortical development in mice. It is potentially associated with the difference of cortical development in humans and mice.

11.
Front Immunol ; 13: 939940, 2022.
Article in English | MEDLINE | ID: mdl-35928827

ABSTRACT

T cell receptor-engineered T cells (TCR-Ts) have emerged as potent cancer immunotherapies. While most research focused on classical cytotoxic CD8+ T cells, the application of CD4+ T cells in adoptive T cell therapy has gained much interest recently. However, the cytotoxic mechanisms of CD4+ TCR-Ts have not been fully revealed. In this study, we obtained an MHC class I-restricted MART-127-35-specific TCR sequence based on the single-cell V(D)J sequencing technology, and constructed MART-127-35-specific CD4+ TCR-Ts and CD8+ TCR-Ts. The antitumor effects of CD4+ TCR-Ts were comparable to those of CD8+ TCR-Ts in vitro and in vivo. To delineate the killing mechanisms of cytotoxic CD4+ TCR-Ts, we performed single-cell RNA sequencing and found that classical granule-dependent and independent cytolytic pathways were commonly used in CD4+ and CD8+ TCR-Ts, while high expression of LTA and various costimulatory receptors were unique features for cytotoxic CD4+ TCR-Ts. Further signaling pathway analysis revealed that transcription factors Runx3 and Blimp1/Tbx21 were crucial for the development and killing function of cytotoxic CD4+ T cells. Taken together, we report the antitumor effects and multifaceted killing mechanisms of CD4+ TCR-Ts, and also indicate that MHC class I-restricted CD4+ TCR-Ts could serve as potential adoptive T cell therapies.


Subject(s)
CD8-Positive T-Lymphocytes , Receptors, Antigen, T-Cell , CD4-Positive T-Lymphocytes/metabolism , CD8-Positive T-Lymphocytes/metabolism , Receptors, Antigen, T-Cell/genetics , Receptors, Antigen, T-Cell/metabolism , T-Lymphocytes, Cytotoxic/metabolism , Transcriptome
12.
Theranostics ; 11(10): 4957-4974, 2021.
Article in English | MEDLINE | ID: mdl-33754038

ABSTRACT

Rationale: TCR-T cell therapy plays a critical role in the treatment of malignant cancers. However, it is unclear how TCR-T cells are affected by PD-L1 molecule in the tumor environment. We performed an in-depth evaluation on how differential expressions of tumor PD-L1 can affect the functionality of T cells. Methods: We used MART-1-specific TCR-T cells (TCR-TMART-1), stimulated with MART-127-35 peptide-loaded MEL-526 tumor cells, expressing different proportions of PD-L1, to perform cellular assays and high-throughput single-cell RNA sequencing. Results: Different clusters of activated or cytotoxic TCR-TMART-1 responded divergently when stimulated with tumor cells expressing different percentages of PD-L1 expression. Compared to control T cells, TCR-TMART-1 were more sensitive to exhaustion, and secreted not only pro-inflammatory cytokines but also anti-inflammatory cytokines with increasing proportions of PD-L1+ tumor cells. The gene profiles of chemokines were modified by increased expression of tumor PD-L1, which concurrently downregulated pro-inflammatory and anti-inflammatory transcription factors. Furthermore, increased expression of tumor PD-L1 showed distinct effects on different inhibitory checkpoint molecules (ICMs). In addition, there was a limited correlation between the enrichment of cell death signaling in tumor cells and T cells and increased tumor PD-L1 expression. Conclusion: Overall, though the effector functionality of TCR-T cells was suppressed by increased expression percentages of tumor PD-L1 in vitro, scRNA-seq profiles revealed that both the anti-inflammatory and pro-inflammatory responses were triggered by a higher expression of tumor PD-L1. This suggests that the sole blockade of tumor PD-L1 might inhibit not only the anti-inflammatory response but also the pro-inflammatory response in the complicated tumor microenvironment. Thus, the outcome of PD-L1 intervention may depend on the final balance among the highly dynamic and heterogeneous immune regulatory circuits.


Subject(s)
B7-H1 Antigen/immunology , T-Lymphocytes/immunology , Tumor Microenvironment/immunology , B7-H1 Antigen/genetics , Cell Line, Tumor , Chemokines/genetics , Chemokines/immunology , Cytokines/genetics , Cytokines/immunology , Cytotoxicity Tests, Immunologic , Gene Expression Profiling , HEK293 Cells , Humans , Immunotherapy, Adoptive , Inflammation/genetics , Inflammation/immunology , MART-1 Antigen/immunology , Melanoma/immunology , RNA-Seq , Receptors, Antigen, T-Cell/genetics , Receptors, Antigen, T-Cell/immunology , Single-Cell Analysis , Skin Neoplasms/immunology , T-Cell Antigen Receptor Specificity/immunology , T-Lymphocytes/metabolism , Tumor Microenvironment/genetics
13.
Intensive Care Med Exp ; 9(1): 13, 2021 Mar 15.
Article in English | MEDLINE | ID: mdl-33721144

ABSTRACT

PURPOSE: Critically ill COVID-19 patients have significantly increased risk of death. Although several circulating biomarkers are thought to be related to COVID-19 severity, few studies have focused on the characteristics of critically ill patients with different outcomes. The objective of this study was to perform a longitudinal investigation of the potential mechanisms affecting the prognosis of critically ill COVID-19 patients. METHODS: In addition to clinical data, 113 whole blood samples and 85 serum samples were collected from 33 severe and critical COVID-19 patients without selected comorbidities. Multi-omics analysis was then performed using longitudinal samples. RESULTS: Obvious transcriptional transitions were more frequent in critical survivors than in critical non-survivors, indicating that phase transition may be related to survival. Based on analysis of differentially expressed genes during transition, the erythrocyte differentiation pathway was significantly enriched. Furthermore, clinical data indicated that red blood cell counts showed greater fluctuation in survivors than in non-survivors. Moreover, declining red blood cell counts and hemoglobin levels were validated as prognostic markers of poor outcome in an independent cohort of 114 critical COVID-19 patients. Protein-metabolite-lipid network analysis indicated that tryptophan metabolism and melatonin may contribute to molecular transitions in critical COVID-19 patients with different outcomes. CONCLUSIONS: This study systematically and comprehensively depicted the longitudinal hallmarks of critical COVID-19 patients and indicated that multi-omics transition may impact the prognosis. TAKE HOME MESSAGE: Frequent transcriptional phase transitions may contribute to outcome in critically ill COVID-19 patients. Furthermore, fluctuation in red blood cell and hemoglobin levels may relate to poor prognosis. The biological function of melatonin was suppressed in COVID-19 non-survivors, which may provide a potential theoretical basis for clinical administration.

14.
Nat Commun ; 12(1): 7083, 2021 12 06.
Article in English | MEDLINE | ID: mdl-34873160

ABSTRACT

The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening of animal cells could reveal the expression patterns of viral entry genes in different hosts. However, such exploration for SARS-CoV-2 remains limited. Here, we perform single-nucleus RNA sequencing for 11 non-model species, including pets (cat, dog, hamster, and lizard), livestock (goat and rabbit), poultry (duck and pigeon), and wildlife (pangolin, tiger, and deer), and investigated the co-expression of ACE2 and TMPRSS2. Furthermore, cross-species analysis of the lung cell atlas of the studied mammals, reptiles, and birds reveals core developmental programs, critical connectomes, and conserved regulatory circuits among these evolutionarily distant species. Overall, our work provides a compendium of gene expression profiles for non-model animals, which could be employed to identify potential SARS-CoV-2 target cells and putative zoonotic reservoirs.


Subject(s)
Atlases as Topic , Single-Cell Analysis/veterinary , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/metabolism , Animals , Birds , Cell Communication , Evolution, Molecular , Gene Regulatory Networks , Host-Pathogen Interactions , Lung/cytology , Lung/metabolism , Lung/virology , Mammals , Receptors, Virus/genetics , Receptors, Virus/metabolism , Reptiles , SARS-CoV-2/metabolism , Serine Endopeptidases/genetics , Serine Endopeptidases/metabolism , Transcriptome , Viral Tropism , Virus Internalization
15.
J Immunol Methods ; 484-485: 112831, 2020.
Article in English | MEDLINE | ID: mdl-32758496

ABSTRACT

Neoantigen-based cancer immunotherapies hold the promise of being a truly personalized, effective treatment for diverse cancer types. ELISPOT assays, as a powerful experimental technique, can verify the existence of antigen specific T cells to support basic clinical research and monitor clinical trials. However, despite the high sensitivity of ELISPOT assays, detecting immune responses of neoantigen specific T cells in a patient or healthy donor's PBMCs is still extremely difficult, since the frequency of these T cells can be very low. We developed a novel experimental method, by co-stimulation of T cells with anti-CD28 and IL-2 at the beginning of ELISPOT, to further increase the sensitivity of ELISPOT and mitigate the challenge introduced by low frequency T cells. Under the optimal concentration of 1 µg/ml for anti-CD28 and 1 U/ml for IL-2, an 11.7-fold increase of T cell response against CMV peptide was observed by using our method, and it outperforms other cytokine stimulation alternatives (5-10 folds). We also showed that this method can be effectively applied to detect neoantigen-specific T cells in healthy donors' and a melanoma patient's PBMCs. To the best of our knowledge, this is the first report that the co-stimulation of anti-CD28 and IL-2 is able to significantly improve the sensitivity of ELISPOT assays, indicating that anti-CD28 and IL-2 signaling can act in synergy to lower the T cell activation threshold and trigger more neoantigen-specific T cells.


Subject(s)
Antibodies/pharmacology , Antigens, Neoplasm/immunology , CD28 Antigens/immunology , Enzyme-Linked Immunospot Assay , Interferon-gamma Release Tests , Interleukin-2/pharmacology , Lymphocyte Activation/drug effects , Neoplasms/immunology , T-Lymphocytes/drug effects , Antigens, Neoplasm/genetics , Antigens, Neoplasm/metabolism , Cells, Cultured , Drug Synergism , Humans , Interferon-gamma/immunology , Interferon-gamma/metabolism , MART-1 Antigen/immunology , Mutation , Neoplasms/genetics , Neoplasms/metabolism , Peptide Fragments/immunology , Reproducibility of Results , Signal Transduction , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , Viral Matrix Proteins/immunology
16.
PeerJ ; 7: e6861, 2019.
Article in English | MEDLINE | ID: mdl-31110924

ABSTRACT

AIM: In this study, we used a series of diallelic genetic marker insertion/deletion polymorphism (indel) to investigate three populations of Yao, Kelao, and Zhuang groups in the Guangxi region of China and to evaluate their efficiency in forensic application. RESULT: No deviations for all 30 loci were observed from the Hardy-Weinberg equilibrium after Bonferroni correction (p > 0.05/30 = 0.0017). The allele frequencies of the short allele (DIP-) for the above three populations were in the range of 0.0520-0.9480, 0.0950-0.8780, and 0.0850-0.915, respectively. The observed heterozygosity of the 30 loci for the three populations was in the ranges 0.0802-0.5802, 0.1908-0.6053, and 0.1400-0.5600, respectively. The cumulative power of exclusion and combined discrimination power for Yao, Kelao, and Zhuang groups were (0.9843 and 0.9999999999433), (0.9972 and 0.9999999999184), and (0.9845 and 0.9999999999608), respectively. The DA distance, principal component analysis, and cluster analysis indicated a clear regional distribution. In addition, Zhuang groups had close genetic relationships with the Yao and Kelao populations in the Guangxi region. CONCLUSION: This study indicated that the 30 loci were qualified for personal identification; moreover, they could be used as complementary genetic markers for paternity testing in forensic cases for the studied populations.

17.
Cancer Med ; 8(9): 4254-4264, 2019 08.
Article in English | MEDLINE | ID: mdl-31199589

ABSTRACT

Cancer patients have been treated with various types of therapies, including conventional strategies like chemo-, radio-, and targeted therapy, as well as immunotherapy like checkpoint inhibitors, vaccine and cell therapy etc. Among the therapeutic alternatives, T-cell therapy like CAR-T (Chimeric Antigen Receptor Engineered T cell) and TCR-T (T Cell Receptor Engineered T cell), has emerged as the most promising therapeutics due to its impressive clinical efficacy. However, there are many challenges and obstacles, such as immunosuppressive tumor microenvironment, manufacturing complexity, and poor infiltration of engrafted cells, etc still, need to be overcome for further treatment with different forms of cancer. Recently, the antitumor activities of CAR-T and TCR-T cells have shown great improvement with the utilization of CRISPR/Cas9 gene editing technology. Thus, the genome editing system could be a powerful genetic tool to use for manipulating T cells and enhancing the efficacy of cell immunotherapy. This review focuses on pros and cons of various gene delivery methods, challenges, and safety issues of CRISPR/Cas9 gene editing application in T-cell-based immunotherapy.


Subject(s)
Gene Editing/methods , Neoplasms/therapy , Receptors, Antigen, T-Cell/genetics , Receptors, Chimeric Antigen/genetics , T-Lymphocytes/transplantation , Animals , CRISPR-Cas Systems , Cell- and Tissue-Based Therapy , Humans , Immunotherapy , Immunotherapy, Adoptive , Neoplasms/immunology , Receptors, Antigen, T-Cell/metabolism , Receptors, Chimeric Antigen/metabolism , T-Lymphocytes/immunology , Tumor Microenvironment
18.
Neural Regen Res ; 14(2): 319-327, 2019 Feb.
Article in English | MEDLINE | ID: mdl-30531016

ABSTRACT

Methamphetamine is an amphetamine-type psychostimulant that can damage dopaminergic neurons and cause characteristic pathological changes similar to neurodegenerative diseases such as Parkinson's disease. However, its specific mechanism of action is still unclear. In the present study, we established a Parkinson's disease pathology model by exposing SH-SY5Y cells and C57BL/6J mice to methamphetamine. In vitro experiments were performed with 0, 0.5, 1.0, 1.5, 2.0 or 2.5 mM methamphetamine for 24 hours or 2.0 mM methamphetamine for 0-, 2-, 4-, 8-, 16-, and 24-hour culture of SH-SY5Y cells. Additional experimental groups of SH-SY5Y cells were administered a nitric oxide inhibitor, 0.1 mM N-nitro-L-arginine, 1 hour before exposure to 2.0 mM methamphetamine for 24 hours. In vivo experiments: C57BL/6J mice were intraperitoneally injected with N-nitro-L-arginine (8 mg/kg), eight times, at intervals of 12 hours. Methamphetamine 15 mg/kg was intraperitoneally injected eight times, at intervals of 12 hours, but 0.5-hour after each N-nitro-L-arginine injection in the combined group. Western blot assay was used to determine the expression of nitric oxide synthase, α-synuclein (α-Syn), 5G4, nitrated α-synuclein at the residue Tyr39 (nT39 α-Syn), cleaved caspase-3, and cleaved poly ADP-ribose polymerase (PARP) in cells and mouse brain tissue. Immunofluorescence staining was conducted to measure the positive reaction of NeuN, nT39 α-Syn and 5G4. Enzyme linked immunosorbent assay was performed to determine the dopamine levels in the mouse brain. After methamphetamine exposure, α-Syn expression increased; the aggregation of α-Syn 5G4 increased; nT39 α-Syn, nitric oxide synthase, cleaved caspase-3, and cleaved PARP expression increased in the cultures of SH-SY5Y cells and in the brains of C57BL/6J mice; and dopamine levels were reduced in the mouse brain. These changes were markedly reduced when N-nitro-L-arginine was administered with methamphetamine in both SH-SY5Y cells and C57BL/6J mice. These results suggest that nT39 α-Syn aggregation is involved in methamphetamine neurotoxicity.

19.
Protein Cell ; 9(12): 1027-1038, 2018 12.
Article in English | MEDLINE | ID: mdl-29508278

ABSTRACT

Macrophages acquire distinct phenotypes during tissue stress and inflammatory responses. Macrophages are roughly categorized into two different subsets named inflammatory M1 and anti-inflammatory M2 macrophages. We herein identified a unique pathogenic macrophage subpopulation driven by IL-23 with a distinct gene expression profile including defined types of cytokines. The freshly isolated resting mouse peritoneal macrophages were stimulated with different cytokines in vitro, the expression of cytokines and chemokines were detected by microarray, real-time PCR, ELISA and multiple colors flow cytometry. Adoptive transfer of macrophages and imiquimod-induced psoriasis mice were used. In contrast to M1- and M2-polarized macrophages, IL-23-treated macrophages produce large amounts of IL-17A, IL-22 and IFN-γ. Biochemical and molecular studies showed that IL-23 induces IL-17A expression in macrophages through the signal transducer and activator of transcription 3 (STAT3)-retinoid related orphan receptor-γ T (RORγT) pathway. T-bet mediates the IFN-γ production in IL-23-treated macrophages. Importantly, IL-23-treated macrophages significantly promote the dermatitis pathogenesis in a psoriasis-like mouse model. IL-23-treated resting macrophages express a distinctive gene expression prolife compared with M1 and M2 macrophages. The identification of IL-23-induced macrophage polarization may help us to understand the contribution of macrophage subpopulation in Th17-cytokines-related pathogenesis.


Subject(s)
Cell Polarity , Imiquimod , Interleukin-23/metabolism , Macrophages/metabolism , Psoriasis/chemically induced , Psoriasis/pathology , Animals , Macrophages/pathology , Mice , Mice, Inbred C57BL , Mice, Knockout , Psoriasis/metabolism
20.
Cell Mol Immunol ; 15(5): 518-530, 2018 May.
Article in English | MEDLINE | ID: mdl-28690333

ABSTRACT

Neutrophils are heterogeneous with distinct subsets, and can switch phenotypes to exert regulatory functions on immunity. We herein demonstrate that IL-23-treated neutrophils selectively produce IL-17A, IL-17F and IL-22, and display a distinct gene expression profile in contrast to resting and lipopolysaccharide-treated neutrophils. IL-17+ neutrophils are present in the colons of mice with dextran sulfate sodium-induced colitis. Adoptive transfer of IL-23-treated neutrophils significantly promotes pathogenesis in this model. IL-23 induces neutrophil polarization through STAT3-dependent RORγt and BATF pathways. Thus, IL-23-induced neutrophil polarization expresses a unique cytokine-producing profile, which may contribute to IL-23-mediated inflammatory diseases.


Subject(s)
Cell Polarity , Interleukin-23/metabolism , Neutrophils/cytology , Neutrophils/metabolism , Animals , Colitis/immunology , Colitis/pathology , Cytokines/metabolism , Gene Expression Profiling , Mice, Inbred BALB C , Mice, Inbred C57BL , STAT3 Transcription Factor/metabolism , Th17 Cells/metabolism
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