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Lei H. Quantitative and Longitudinal Assessment of Systemic Innate Immunity in Health and Disease Using a 2D Gene Model. Biomedicines 2024; 12:969. [PMID: 38790931 PMCID: PMC11117654 DOI: 10.3390/biomedicines12050969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Dysregulation of innate immunity is deeply involved in infectious and autoimmune diseases. For a better understanding of pathogenesis and improved management of these diseases, it is of vital importance to implement convenient monitoring of systemic innate immunity. Built upon our previous works on the host transcriptional response to infection in peripheral blood, we proposed a 2D gene model for the simultaneous assessment of two major components of systemic innate immunity, including VirSig as the signature of the host response to viral infection and BacSig as the signature of the host response to bacterial infection. The revelation of dysregulation in innate immunity by this 2D gene model was demonstrated with a wide variety of transcriptome datasets. In acute infection, distinctive patterns of VirSig and BacSig activation were observed in viral and bacterial infection. In comparison, both signatures were restricted to a defined range in the vast majority of healthy adults, regardless of age. In addition, BacSig showed significant elevation during pregnancy and an upward trend during development. In tuberculosis (TB), elevation of BacSig and VirSig was observed in a significant portion of active TB patients, and abnormal BacSig was also associated with a longer treatment course. In cystic fibrosis (CF), abnormal BacSig was observed in a subset of patients, and no overall change in BacSig abnormality was observed after the drug treatment. In systemic sclerosis-associated interstitial lung disease (SSc-ILD), significant elevation of VirSig and BacSig was observed in some patients, and treatment with a drug led to the further deviation of BacSig from the control level. In systemic lupus erythematosus (SLE), positivity for the anti-Ro autoantibody was associated with significant elevation of VirSig in SLE patients, and the additive effect of VirSig/BacSig activation was also observed in SLE patients during pregnancy. Overall, these data demonstrated that the 2D gene model can be used to assess systemic innate immunity in health and disease, with the potential clinical applications including patient stratification, prescription of antibiotics, understanding of pathogenesis, and longitudinal monitoring of treatment response.
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Affiliation(s)
- Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China; ; Tel.: +86-010-8409-7276
- Cunji Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
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Gao J, Zhang Z, Yu J, Zhang N, Fu Y, Jiang X, Xia Z, Zhang Q, Wen Z. Identification of Neutrophil Extracellular Trap-Related Gene Expression Signatures in Ischemia Reperfusion Injury During Lung Transplantation: A Transcriptome Analysis and Clinical Validation. J Inflamm Res 2024; 17:981-1001. [PMID: 38370470 PMCID: PMC10871139 DOI: 10.2147/jir.s444774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 02/01/2024] [Indexed: 02/20/2024] Open
Abstract
Purpose Ischemia reperfusion injury (IRI) unavoidably occurs during lung transplantation, further contributing to primary graft dysfunction (PGD). Neutrophils are the end effectors of IRI and activated neutrophils release neutrophil extracellular traps (NETs) to further amplify damage. Nevertheless, potential contributions of NETs in IRI remain incompletely understood. This study aimed to explore NET-related gene biomarkers in IRI during lung transplantation. Methods Differential expression analysis was applied to identify differentially expressed genes (DEGs) for IRI during lung transplantation based on matrix data (GSE145989, 127003) downloaded from GEO database. The CIBERSORT and weighted gene co-expression network analysis (WGCNA) algorithms were utilized to identify key modules associated with neutrophil infiltration. Moreover, the least absolute shrinkage and selection operator regression and random forest were applied to identify potential NET-associated hub genes. Subsequently, the screened hub genes underwent further validation of an external dataset (GSE18995) and nomogram model. Based on clinical peripheral blood samples, immunofluorescence staining and dsDNA quantification were used to assess NET formation, and ELISA was applied to validate the expression of hub genes. Results Thirty-eight genes resulted from the intersection between 586 DEGs and 75 brown module genes, primarily enriched in leukocyte migration and NETs formation. Subsequently, four candidate hub genes (FCAR, MMP9, PADI4, and S100A12) were screened out via machine learning algorithms. Validation using an external dataset and nomogram model achieved better predictive value. Substantial NETs formation was demonstrated in IRI, with more pronounced NETs observed in patients with PGD ≥ 2. PADI4, S100A12, and MMP9 were all confirmed to be up-regulated after reperfusion through ELISA, with higher levels of S100A12 in PGD ≥ 2 patients compared with non-PGD patients. Conclusion We identified three potential NET-related biomarkers for IRI that provide new insights into early detection and potential therapeutic targets of IRI and PGD after lung transplantation.
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Affiliation(s)
- Jiameng Gao
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, People’s Republic of China
| | - Zhiyuan Zhang
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, People’s Republic of China
| | - Jing Yu
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, People’s Republic of China
| | - Nan Zhang
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, People’s Republic of China
| | - Yu Fu
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, People’s Republic of China
| | - Xuemei Jiang
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, People’s Republic of China
| | - Zheyu Xia
- School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Qingqing Zhang
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, People’s Republic of China
| | - Zongmei Wen
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, People’s Republic of China
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Lei H. Hypoxia and Activation of Neutrophil Degranulation-Related Genes in the Peripheral Blood of COVID-19 Patients. Viruses 2024; 16:201. [PMID: 38399976 PMCID: PMC10891603 DOI: 10.3390/v16020201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/20/2024] [Accepted: 01/21/2024] [Indexed: 02/25/2024] Open
Abstract
Severe COVID-19 is characterized by systematic hyper-inflammation and subsequent damage to various organs. Therefore, it is critical to trace this cascade of hyper-inflammation. Blood transcriptome has been routinely utilized in the interrogation of host immune response in COVID-19 and other infectious conditions. In this study, consensus gene dysregulation in the blood was obtained from 13 independent transcriptome studies on COVID-19. Among the up-regulated genes, the most prominent functional categories were neutrophil degranulation and cell cycle, which is clearly different from the classical activation of interferon signaling pathway in seasonal flu. As for the potential upstream causal factors of the atypical gene dysregulation, systemic hypoxia was further examined because it is much more widely reported in COVID-19 than that in seasonal flu. It was found that both physiological and pathological hypoxia can induce activation of neutrophil degranulation-related genes in the blood. Furthermore, COVID-19 patients with different requirement for oxygen intervention showed distinctive levels of gene expression related to neutrophil degranulation in the whole blood, which was validated in isolated neutrophils. Thus, activation of neutrophil degranulation-related genes in the blood of COVID-19 could be partially attributed to hypoxia. Interestingly, similar pattern was also observed in H1N1 infection (the cause of Spanish flu) and several other severe respiratory viral infections. As for the molecular mechanism, both HIF-dependent and HIF-independent pathways have been examined. Since the activation of neutrophil degranulation-related genes is highly correlated with disease severity in COVID-19, early detection of hypoxia and active intervention may prevent further activation of neutrophil degranulation-related genes and other harmful downstream hyper-inflammation. This common mechanism is applicable to current and future pandemic as well as the severe form of common respiratory infection.
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Affiliation(s)
- Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China; ; Tel.: +86-010-84097276
- Cunji Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
- Center of Alzheimer’s Disease, Beijing Institute for Brain Disorders, Beijing 100069, China
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Lu J, Chen Y, Zhou K, Ling Y, Qin Q, Lu W, Qin L, Mou C, Zhang J, Zheng X, Qin K. Immune characteristics of kidney transplant recipients with acute respiratory distress syndrome induced by COVID-19 at single-cell resolution. Respir Res 2024; 25:34. [PMID: 38238762 PMCID: PMC10795319 DOI: 10.1186/s12931-024-02682-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND COVID-19-induced acute respiratory distress syndrome (ARDS) can result in tissue damage and multiple organ dysfunction, especially in kidney transplant recipients (KTRs) receiving immunosuppressive drugs. Presently, single-cell research on COVID-19-induced ARDS is considerably advanced, yet knowledge about ARDS in KTRs is still constrained. METHODS Single-cell RNA sequencing (scRNA-seq) analysis was performed to construct a comprehensive single-cell immune landscape of the peripheral blood mononuclear cells (PBMCs) of eight patients with COVID-19-induced ARDS, five KTRs with COVID-19-induced ARDS, and five healthy individuals. Subsequently, we conducted a comprehensive bioinformatics analysis, including cell clustering, enrichment analysis, trajectory analysis, gene regulatory network analysis, and cell-cell interaction analysis, to investigate the heterogeneity of the immune microenvironment in KTRs with ARDS. RESULT Our study revealed that KTRs exhibit significant heterogeneity with COVID-19-induced ARDS compared with those of other individuals, with significant reductions in T cells, as well as an abnormal proliferation of B cells and monocytes. In the context of dual influences from immunosuppression and viral infection, KTRs exhibited more specific plasma cells, along with significant enrichment of dysfunctional GZMB and XAF1 double-positive effector T cells and IFI27-positive monocytes. Additionally, robust communication existed among T cells and monocytes in cytokine signaling. These effects impede the process of immune reconstitution in KTR patients. CONCLUSION Our findings suggest that KTRs with COVID-19-induced ARDS show elevated antibody levels, impaired T cell differentiation, and dysregulation of innate immunity. In summary, this study provides a theoretical foundation for a comprehensive understanding of COVID-19-induced ARDS in KTRs.
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Affiliation(s)
- Junyu Lu
- Intensive Care Unit, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, China.
- Guangxi Health Commission Key Laboratory of Emergency and Critical Medicine, Nanning, 530007, China.
| | - Yin Chen
- Intensive Care Unit, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, China
| | - Kaihuan Zhou
- Intensive Care Unit, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, China
| | - Yicong Ling
- Intensive Care Unit, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, China
| | - Qianqian Qin
- Intensive Care Unit, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, China
| | - Weisheng Lu
- Intensive Care Unit, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, China
| | - Lian Qin
- Intensive Care Unit, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, China
| | - Chenglin Mou
- Intensive Care Unit, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, China
| | - Jianfeng Zhang
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, China
- Guangxi Health Commission Key Laboratory of Emergency and Critical Medicine, Nanning, 530007, China
| | - Xiaowen Zheng
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, China.
- Guangxi Health Commission Key Laboratory of Emergency and Critical Medicine, Nanning, 530007, China.
| | - Ke Qin
- Department of Anesthesiology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, Guangxi, China.
- Department of Anesthesiology, Guilin People's Hospital, Guilin, 541002, China.
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Sofia de Olazarra A, Chen FE, Wang TH, Wang SX. Rapid, Point-of-Care Host-Based Gene Expression Diagnostics Using Giant Magnetoresistive Biosensors. ACS Sens 2023; 8:2780-2790. [PMID: 37368357 DOI: 10.1021/acssensors.3c00696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Host-based gene expression analysis is a promising tool for a broad range of clinical applications, including rapid infectious disease diagnostics and real-time disease monitoring. However, the complex instrumentation requirements and slow turnaround-times associated with traditional gene expression analysis methods have hampered their widespread adoption at the point-of-care (POC). To overcome these challenges, we have developed an automated and portable platform that utilizes polymerase chain reaction (PCR) and giant magnetoresistive (GMR) biosensors to perform rapid multiplexed, targeted gene expression analysis at the POC. As proof-of-concept, we utilized our platform to amplify and measure the expression of four genes (HERC5, HERC6, IFI27, and IFIH1) that were previously shown to be upregulated in hosts infected with influenza viruses. The compact instrument conducted highly automated PCR amplification and GMR detection to measure the expression of the four genes in multiplex, then utilized Bluetooth communication to relay results to users on a smartphone application. To validate the platform, we tested 20 cDNA samples from symptomatic patients that had been previously diagnosed as either influenza-positive or influenza-negative using a RT-PCR virology panel. A non-parametric Mann-Whitney test revealed that day 0 (day of symptom onset) gene expression was significantly different between the two groups (p < 0.0001, n = 20). Hence, we preliminarily demonstrated that our platform could accurately discriminate between symptomatic influenza and non-influenza populations based on host gene expression in ∼30 min. This study not only establishes the potential clinical utility of our proposed assay and device for influenza diagnostics but it also paves the way for broadscale and decentralized implementation of host-based gene expression diagnostics at the POC.
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Affiliation(s)
- Ana Sofia de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94035, United States
| | - Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Shan X Wang
- Department of Electrical Engineering, Stanford University, Stanford, California 94035, United States
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
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