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Zhang X, Pan L, Zhang P, Wang L, Shen Y, Xu P, Ren Y, Huang W, Liu P, Wu Q, Li F. Single-cell analysis of the miRNA activities in tuberculous meningitis (TBM) model mice injected with the BCG vaccine. Int Immunopharmacol 2023; 124:110871. [PMID: 37708706 DOI: 10.1016/j.intimp.2023.110871] [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: 06/26/2023] [Revised: 08/10/2023] [Accepted: 08/27/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Our previous study revealed the transcriptome atlas of specific cell types in tuberculous meningitis (TBM) model mice injected with the BCG vaccine via scRNA sequencing. However, the activities of miRNAs in TBM at single-cell resolution remain to be explored. METHOD Cell type-specific miRNA activities were investigated by using motif enrichment analyses (miReact) on the transcriptome data of 15 cell types. The target mRNAs of miRNAs were predicted and subjected to enrichment analysis. Furthermore, miRNAs and their target mRNAs with opposite expression trends were chosen to construct functional networks. Besides, qRT-PCR and RNA scope were performed to verify the expression level of representative miRNA. RESULTS The tSNE dimensionality reduction presented 15 cell types in TBM model mice, in which microglia and endothelial cells accounted for the majority. Target mRNAs of each cell type were predicted for verification or network construction. The immune and inflammation-related miRNA-mRNA networks of macrophages and microglia, oxidative phosphorylation-related miRNA-mRNA networks of neurons, ion and protein transport-related networks of epididymal cells, and angiogenesis-related miRNA-mRNA networks of VSMCs were constructed. The miRNA activity analysis revealed that miR-21a-3p activity was increased in microglia, macrophages, neurons and epididymal cells. The result of qRT-PCR and RNA scope indicate that miR-21a-3p was significantly higher-expressed in TBM brain tissue compared with normal brain tissue. CONCLUSION In our study, an in-depth exploration of the mRNA expression and miRNA activity of macrophages, microglia, epididymal cells, neurons and vascular smooth muscle cells during TBM progression was conducted using scRNA-Seq, which provided novel insights into the immune cell engagement in TBM patients.
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Affiliation(s)
- Xiaolin Zhang
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lei Pan
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Peng Zhang
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lei Wang
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yidan Shen
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Ping Xu
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yang Ren
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Wei Huang
- Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Department of Tuberculosis, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Ping Liu
- Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Department of Tuberculosis, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Qingguo Wu
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
| | - Feng Li
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China.
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Hu X, Zhang J, Bu J, Yang K, Xu S, Pan M, Xiang D, Chen W. MiR-4733-5p promotes gallbladder carcinoma progression via directly targeting kruppel like factor 7. Bioengineered 2022; 13:10691-10706. [PMID: 35443866 PMCID: PMC9161844 DOI: 10.1080/21655979.2022.2065951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Gallbladder carcinoma (GBC) is highly aggressive with poor prognosis. Accumulating reports show that miRNAs play critical roles in tumor progression. Previous studies have identified several miRNAs that promoted or inhibited GBC cell proliferation and/or metastasis. Here, we used the Gene Expression Omnibus (GEO) dataset to identify dysregulated miRNAs in GBC, followed by validating the upregulation of the miR-4733-5p and downregulation of kruppel-like factor 7 (KLF7) in GBC biopsies by quantitative real-time PCR (RT-qPCR), in situ hybridization (ISH) staining, and immunohistochemistry (IHC) assays. GBC cell proliferation and invasion capacities mediated by miR-4733-5p were evaluated by a series of function assays in vitro, including CCK-8, colony formation assay, wound healing assay and transwell assay. Xenograft tumor model found that miR-4733-5p promoted GBC tumor growth in vivo. This study clarified that miR-4733-5p was upregulated in GBC and promoted GBC cell proliferation via directly binding to 3' untranslated region (UTR) of KLF, which was downregulated and prohibited the proliferation and migration of GBC cells.
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Affiliation(s)
- Xiaoqiang Hu
- Department of Biliary and Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Junzhe Zhang
- Department of Biliary and Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Junfeng Bu
- Department of Biliary and Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Kaini Yang
- Department of Biliary and Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Sunwang Xu
- Department of Biliary and Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Mengqiao Pan
- Department of Biliary and Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Dongxi Xiang
- Department of Biliary and Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Wei Chen
- Department of Biliary and Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China.,Shanghai Key Laboratory of Biliary Tract Disease, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine; Shanghai 200120, China.,Shanghai Research Center of Biliary Tract Disease, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
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Chen L, Fan R, Tang F. Advanced Single-cell Omics Technologies and Informatics Tools for Genomics, Proteomics, and Bioinformatics Analysis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:343-345. [PMID: 34923125 PMCID: PMC8864189 DOI: 10.1016/j.gpb.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/06/2021] [Accepted: 12/09/2021] [Indexed: 11/20/2022]
Affiliation(s)
- Luonan Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China.
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