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Li YY, Yuan MM, Li YY, Li S, Wang JD, Wang YF, Li Q, Li J, Chen RR, Peng JM, Du B. Cell-free DNA methylation reveals cell-specific tissue injury and correlates with disease severity and patient outcomes in COVID-19. Clin Epigenetics 2024; 16:37. [PMID: 38429730 PMCID: PMC10908074 DOI: 10.1186/s13148-024-01645-7] [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: 12/22/2023] [Accepted: 02/16/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND The recently identified methylation patterns specific to cell type allows the tracing of cell death dynamics at the cellular level in health and diseases. This study used COVID-19 as a disease model to investigate the efficacy of cell-specific cell-free DNA (cfDNA) methylation markers in reflecting or predicting disease severity or outcome. METHODS Whole genome methylation sequencing of cfDNA was performed for 20 healthy individuals, 20 cases with non-hospitalized COVID-19 and 12 cases with severe COVID-19 admitted to intensive care unit (ICU). Differentially methylated regions (DMRs) and gene ontology pathway enrichment analyses were performed to explore the locus-specific methylation difference between cohorts. The proportion of cfDNA derived from lung and immune cells to a given sample (i.e. tissue fraction) at cell-type resolution was estimated using a novel algorithm, which reflects lung injuries and immune response in COVID-19 patients and was further used to evaluate clinical severity and patient outcome. RESULTS COVID‑19 patients had globally reduced cfDNA methylation level compared with healthy controls. Compared with non-hospitalized COVID-19 patients, the cfDNA methylation pattern was significantly altered in severe patients with the identification of 11,156 DMRs, which were mainly enriched in pathways related to immune response. Markedly elevated levels of cfDNA derived from lung and more specifically alveolar epithelial cells, bronchial epithelial cells, and lung endothelial cells were observed in COVID-19 patients compared with healthy controls. Compared with non-hospitalized patients or healthy controls, severe COVID-19 had significantly higher cfDNA derived from B cells, T cells and granulocytes and lower cfDNA from natural killer cells. Moreover, cfDNA derived from alveolar epithelial cells had the optimal performance to differentiate COVID-19 with different severities, lung injury levels, SOFA scores and in-hospital deaths, with the area under the receiver operating characteristic curve of 0.958, 0.941, 0.919 and 0.955, respectively. CONCLUSION Severe COVID-19 has a distinct cfDNA methylation signature compared with non-hospitalized COVID-19 and healthy controls. Cell type-specific cfDNA methylation signature enables the tracing of COVID-19 related cell deaths in lung and immune cells at cell-type resolution, which is correlated with clinical severities and outcomes, and has extensive application prospects to evaluate tissue injuries in diseases with multi-organ dysfunction.
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Affiliation(s)
- Yuan-Yuan Li
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China
| | - Ming-Ming Yuan
- Geneplus-Beijing, Floor 9, Building 6, Medical Park Road, Zhongguancun Life Science Park, Changping District, Beijing, 102206, China
| | - Yuan-Yuan Li
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China
| | - Shan Li
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China
| | - Jing-Dong Wang
- Geneplus-Shenzhen, Building B, First Branch, Zhongcheng Life Science Park, Zhongxing Road, Kengzi Street, Pingshan District, Shenzhen, 518000, China
| | - Yu-Fei Wang
- Geneplus-Shenzhen, Building B, First Branch, Zhongcheng Life Science Park, Zhongxing Road, Kengzi Street, Pingshan District, Shenzhen, 518000, China
| | - Qian Li
- Geneplus-Beijing, Floor 9, Building 6, Medical Park Road, Zhongguancun Life Science Park, Changping District, Beijing, 102206, China
| | - Jun Li
- Geneplus-Shenzhen, Building B, First Branch, Zhongcheng Life Science Park, Zhongxing Road, Kengzi Street, Pingshan District, Shenzhen, 518000, China
| | - Rong-Rong Chen
- Geneplus-Beijing, Floor 9, Building 6, Medical Park Road, Zhongguancun Life Science Park, Changping District, Beijing, 102206, China
| | - Jin-Min Peng
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.
| | - Bin Du
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.
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Long X, Wei J, Fang Q, Yuan X, Du J. Single-cell RNA sequencing reveals the transcriptional heterogeneity of Tbx18-positive cardiac cells during heart development. Funct Integr Genomics 2024; 24:18. [PMID: 38265516 DOI: 10.1007/s10142-024-01290-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
The T-box family transcription factor 18 (Tbx18) has been found to play a critical role in regulating the development of the mammalian heart during the primary stages of embryonic development while the cellular heterogeneity and landscape of Tbx18-positive (Tbx18+) cardiac cells remain incompletely characterized. Here, we analyzed prior published single-cell RNA sequencing (scRNA-seq) mouse heart data to explore the heterogeneity of Tbx18+ cardiac cell subpopulations and provide a comprehensive transcriptional landscape of Tbx18+ cardiac cells during their development. Bioinformatic analysis methods were utilized to identify the heterogeneity between cell groups. Based on the gene expression characteristics, Tbx18+ cardiac cells can be classified into a minimum of two distinct cell populations, namely fibroblast-like cells and cardiomyocytes. In terms of temporal heterogeneity, these cells exhibit three developmental stages, namely the MEM stage, ML_P0 stage, and P stage Tbx18+ cardiac cells. Furthermore, Tbx18+ cardiac cells encompass several cell types, including cardiac progenitor-like cells, cardiomyocytes, and epicardial/stromal cells, as determined by specific transcriptional regulatory networks. The scRNA-seq results revealed the involvement of extracellular matrix (ECM) signals and epicardial epithelial-to-mesenchymal transition (EMT) in the development of Tbx18+ cardiac cells. The utilization of a lineage-tracing model served to validate the crucial function of Tbx18 in the differentiation of cardiac cells. Consequently, these findings offer a comprehensive depiction of the cellular heterogeneity within Tbx18+ cardiac cells.
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Affiliation(s)
- Xianglin Long
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Jiangjun Wei
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Qinghua Fang
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Xin Yuan
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
| | - Jianlin Du
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
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Yajie H, Shenglan W, Wei Z, Rufang L, Tingting Y, Yunhui Z, Jie S. Global quantitative proteomic analysis profiles of host protein expression in response to Enterovirus A71 infection in bronchial epithelial cells based on tandem mass tag (TMT) peptide labeling coupled with LC-MS/MS uncovers the key role of proteasome in virus replication. Virus Res 2023; 330:199118. [PMID: 37072100 DOI: 10.1016/j.virusres.2023.199118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/30/2023] [Accepted: 04/15/2023] [Indexed: 04/20/2023]
Abstract
Enterovirus A71 (EV-A71) is a neurotropic human pathogen which mainly caused hand, foot and mouth disease (HFMD) mostly in children under 5 years-old. Generally, EV-A71-associated HFMD is a relatively self-limiting febrile disease, but there will still be a small percentage of patients with rapid disease progression and severe neurological complications. To date, the underlying mechanism of EV-A71 inducing pathological injury of central nervous system (CNS) remains largely unclear. It has been investigated and discussed the changes of mRNA, miRNA and circRNA expression profile during infection by EV-A71 in our previous studies. However, these studies were only analyzed at the RNA level, not at the protein level. It's the protein levels that ultimately do the work in the body. Here, to address this, we performed a tandem mass tag (TMT) peptide labeling coupled with LC-MS/MS approach to quantitatively identify cellular proteome changes at 24 h post-infection (hpi) in EV-A71-infected 16HBE cells. In total, 6615 proteins were identified by using TMT coupled with LC-MS/MS in this study. In the EV-A71- and mock-infected groups, 210 differentially expressed proteins were found, including 86 upregulated and 124 downregulated proteins, at 24 hpi. To ensure the validity and reliability of the proteomics data, 3 randomly selected proteins were verified by Western blot and Immunofluorescence analysis, and the results were consistent with the TMT results. Subsequently, functional enrichment analysis indicated that the up-regulated and down-regulated proteins were individually involved in various biological processes and signaling pathways, including metabolic process, AMPK signaling pathway, Neurotrophin signaling pathway, Viral myocarditis, GABAergic synapse, and so on. Moreover, among these enriched functional analysis, the "Proteasome" pathway was up-regulated, which has caught our attention. Inhibition of proteasome was found to obviously suppress the EV-A71 replication. Finally, further in-depth analysis revealed that these differentially expressed proteins contained distinct domains and localized in different subcellular components. Taken together, our data provided a comprehensive view of host cell response to EV-A71 and identified host proteins may lead to better understanding of the pathogenic mechanisms and host responses to EV-A71 infection, and also to the identification of new therapeutic targets for EV-A71 infection.
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Affiliation(s)
- Hu Yajie
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China.; Yunnan Provincial Key Laboratory of Clinical Virology
| | - Wang Shenglan
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Zhao Wei
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Li Rufang
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yang Tingting
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Zhang Yunhui
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China..
| | - Song Jie
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.
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Štukovnik Z, Bren U. Recent Developments in Electrochemical-Impedimetric Biosensors for Virus Detection. Int J Mol Sci 2022; 23:ijms232415922. [PMID: 36555560 PMCID: PMC9788240 DOI: 10.3390/ijms232415922] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Viruses, including influenza viruses, MERS-CoV (Middle East respiratory syndrome coronavirus), SARS-CoV (severe acute respiratory syndrome coronavirus), HAV (Hepatitis A virus), HBV (Hepatitis B virus), HCV (Hepatitis C virus), HIV (human immunodeficiency virus), EBOV (Ebola virus), ZIKV (Zika virus), and most recently SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), are responsible for many diseases that result in hundreds of thousands of deaths yearly. The ongoing outbreak of the COVID-19 disease has raised a global concern and intensified research on the detection of viruses and virus-related diseases. Novel methods for the sensitive, rapid, and on-site detection of pathogens, such as the recent SARS-CoV-2, are critical for diagnosing and treating infectious diseases before they spread and affect human health worldwide. In this sense, electrochemical impedimetric biosensors could be applied for virus detection on a large scale. This review focuses on the recent developments in electrochemical-impedimetric biosensors for the detection of viruses.
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Affiliation(s)
- Zala Štukovnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, 6000 Koper, Slovenia
- Institute for Environmental Protection and Sensors, Beloruska ulica 7, 2000 Maribor, Slovenia
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Identification of Transcriptome Biomarkers for Severe COVID-19 with Machine Learning Methods. Biomolecules 2022; 12:biom12121735. [PMID: 36551164 PMCID: PMC9775121 DOI: 10.3390/biom12121735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
The rapid spread of COVID-19 has become a major concern for people's lives and health all around the world. COVID-19 patients in various phases and severity require individualized treatment given that different patients may develop different symptoms. We employed machine learning methods to discover biomarkers that may accurately classify COVID-19 in various disease states and severities in this study. The blood gene expression profiles from 50 COVID-19 patients without intensive care, 50 COVID-19 patients with intensive care, 10 non-COVID-19 individuals without intensive care, and 16 non-COVID-19 individuals with intensive care were analyzed. Boruta was first used to remove irrelevant gene features in the expression profiles, and then, the minimum redundancy maximum relevance was applied to sort the remaining features. The generated feature-ranked list was fed into the incremental feature selection method to discover the essential genes and build powerful classifiers. The molecular mechanism of some biomarker genes was addressed using recent studies, and biological functions enriched by essential genes were examined. Our findings imply that genes including UBE2C, PCLAF, CDK1, CCNB1, MND1, APOBEC3G, TRAF3IP3, CD48, and GZMA play key roles in defining the different states and severity of COVID-19. Thus, a new point of reference is provided for understanding the disease's etiology and facilitating a precise therapy.
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