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Wu K, Li M, Chen ZY, Lowrie DB, Fan XY. Probe Signal Values in mRNA Arrays Imply an Excessive Involvement of Neutrophil FCGR1 in Tuberculosis. Front Med (Lausanne) 2020; 7:19. [PMID: 32118006 PMCID: PMC7033432 DOI: 10.3389/fmed.2020.00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/13/2020] [Indexed: 01/21/2023] Open
Abstract
The perturbed genes from transcriptomes are often presented in terms of relative expressions against control samples. However, the probe signal values (PSVs) of genes, implying protein abundances, are often ignored. Here, we explored the PSVs in tuberculosis (TB)-relevant signature genes. The signatures from Mycobacterium tuberculosis-infected THP-1 cells were defined as induced (TMtb-i, with a derived TMtb-iNet) and repressed (TMtb-r). The signature from human blood was defined as a pulmonary TB (PTB)-specific signature (PTBsig). The analysis showed that before infection, TMtb-i and TMtb-iNet had lower PSVs and TMtb-r genes had average PSVs. In the blood of healthy donors, PTBsig (divided into up-regulated PTBsigUp and down-regulated PTBsigDn) displayed average PSVs. This was partly due to masking by the cellular heterogeneity of blood; diverse PSVs were seen in constituent cell populations (CD4/8+ T, monocytes and neutrophils). Specifically, the PSVs of PTBsigUp in the neutrophils of healthy donors were higher (implying higher protein abundances), and much higher in the neutrophils of PTB (implying excessive protein abundances). Based on the PSV patterns of PTBsigUp in four cell populations, we identified three representative highly homologous genes (FCGR1A, FCGR1B, and the pseudogene FCGR1CP, which were often poorly distinguished), of which the summed PSVs were the highest in the neutrophils of PTB patients and healthy donors. The three genes were all up-regulated and responsive to chemotherapy in the blood of PTB, as validated in an RNA-seq-based analysis. This PSV-based study confirms the excessive involvement of neutrophil FCGR1 in PTB.
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Affiliation(s)
- Kang Wu
- Key Laboratory of Medical Molecular Virology of MOE/MOH, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China.,TB Center, Shanghai Emerging and Re-emerging Institute, Shanghai, China
| | - Meng Li
- Department of Life Science, Bengbu Medical College, Bengbu, China
| | - Zhen-Yan Chen
- Key Laboratory of Medical Molecular Virology of MOE/MOH, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Douglas B Lowrie
- Key Laboratory of Medical Molecular Virology of MOE/MOH, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,TB Center, Shanghai Emerging and Re-emerging Institute, Shanghai, China
| | - Xiao-Yong Fan
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China.,TB Center, Shanghai Emerging and Re-emerging Institute, Shanghai, China
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Li P, Wang R, Dong W, Hu L, Zong B, Zhang Y, Wang X, Guo A, Zhang A, Xiang Y, Chen H, Tan C. Comparative Proteomics Analysis of Human Macrophages Infected with Virulent Mycobacterium bovis. Front Cell Infect Microbiol 2017; 7:65. [PMID: 28337427 PMCID: PMC5343028 DOI: 10.3389/fcimb.2017.00065] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/21/2017] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium bovis (M. bovis), the most common pathogens of tuberculosis (TB), is virulent to human and cattle, and transmission between cattle and humans warrants reconsideration concerning food safety and public health. Recently, efforts have begun to analyze cellular proteomic responses induced by Mycobacterium tuberculosis (M. tb). However, the underlying mechanisms by which virulent M. bovis affects human hosts are not fully understood. For the present study, we utilized a global and comparative labeling strategy of isobaric tag for relative and absolute quantitation (iTRAQ) to assess proteomic changes in the human monocyte cell line (THP-1) using a vaccine strain and two virulent strains H37Rv and M. bovis. We measured 2,032 proteins, of which 61 were significantly differentially regulated. Ingenuity Pathway Analysis was employed to investigate the canonical pathways and functional networks involved in the infection. Several pathways, most notably the phagosome maturation pathway and TNF signaling pathway, were differentially affected by virulent strain treatment, including the key proteins CCL20 and ICAM1. Our qRT-PCR results were in accordance with those obtained from iTRAQ. The key enzyme MTHFD2, which is mainly involved in metabolism pathways, as well as LAMTOR2 might be effective upon M. bovis infection. String analysis also suggested that the vacuolar protein VPS26A interacted with TBC1D9B uniquely induced by M. bovis. In this study, we have first demonstrated the application of iTRAQ to compare human protein alterations induced by virulent M. bovis infections, thus providing a conceptual understanding of mycobacteria pathogenesis within the host as well as insight into preventing and controlling TB in human and animal hosts' transmission.
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Affiliation(s)
- Pei Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Rui Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Wenqi Dong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Linlin Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Bingbing Zong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Yanyan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Xiangru Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Anding Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Yaozu Xiang
- Advanced Institute of Translational Medicine, School of Life Sciences and Technology, Tongji University Shanghai, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
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