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Zeng Y, Ma Q, Chen J, Kong X, Chen Z, Liu H, Liu L, Qian Y, Wang X, Lu S. Single-cell sequencing: Current applications in various tuberculosis specimen types. Cell Prolif 2024:e13698. [PMID: 38956399 DOI: 10.1111/cpr.13698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/21/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
Tuberculosis (TB) is a chronic disease caused by Mycobacterium tuberculosis (M.tb) and responsible for millions of deaths worldwide each year. It has a complex pathogenesis that primarily affects the lungs but can also impact systemic organs. In recent years, single-cell sequencing technology has been utilized to characterize the composition and proportion of immune cell subpopulations associated with the pathogenesis of TB disease since it has a high resolution that surpasses conventional techniques. This paper reviews the current use of single-cell sequencing technologies in TB research and their application in analysing specimens from various sources of TB, primarily peripheral blood and lung specimens. The focus is on how these technologies can reveal dynamic changes in immune cell subpopulations, genes and proteins during disease progression after M.tb infection. Based on the current findings, single-cell sequencing has significant potential clinical value in the field of TB research. Next, we will focus on the real-world applications of the potential targets identified through single-cell sequencing for diagnostics, therapeutics and the development of effective vaccines.
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Affiliation(s)
- Yuqin Zeng
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Quan Ma
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Jinyun Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xingxing Kong
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Zhanpeng Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Huazhen Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Lanlan Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Yan Qian
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xiaomin Wang
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Shuihua Lu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
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Elkhamary A, Gerner I, Bileck A, Oreff GL, Gerner C, Jenner F. Comparative proteomic profiling of the ovine and human PBMC inflammatory response. Sci Rep 2024; 14:14939. [PMID: 38942936 PMCID: PMC11213919 DOI: 10.1038/s41598-024-66059-0] [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: 03/23/2024] [Accepted: 06/26/2024] [Indexed: 06/30/2024] Open
Abstract
Understanding the cellular and molecular mechanisms of inflammation requires robust animal models. Sheep are commonly used in immune-related studies, yet the validity of sheep as animal models for immune and inflammatory diseases remains to be established. This cross-species comparative study analyzed the in vitro inflammatory response of ovine (oPBMCs) and human PBMCs (hPBMCs) using mass spectrometry, profiling the proteome of the secretome and whole cell lysate. Of the entire cell lysate proteome (oPBMCs: 4217, hPBMCs: 4574 proteins) 47.8% and in the secretome proteome (oPBMCs: 1913, hPBMCs: 1375 proteins) 32.8% were orthologous between species, among them 32 orthologous CD antigens, indicating the presence of six immune cell subsets. Following inflammatory stimulation, 71 proteins in oPBMCs and 176 in hPBMCs showed differential abundance, with only 7 overlapping. Network and Gene Ontology analyses identified 16 shared inflammatory-related terms and 17 canonical pathways with similar activation/inhibition patterns in both species, demonstrating significant conservation in specific immune and inflammatory responses. However, ovine PMBCs also contained a unique WC1+γδ T-cell subset, not detected in hPBMCs. Furthermore, differences in the activation/inhibition trends of seven canonical pathways and the sets of DAPs between sheep and humans, emphasize the need to consider interspecies differences in translational studies and inflammation research.
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Affiliation(s)
- A Elkhamary
- Department for Companion Animals and Horses, Veterm, University Equine Hospital, Vetmeduni Vienna, Vienna, Austria
- Department for Surgery, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - I Gerner
- Department for Companion Animals and Horses, Veterm, University Equine Hospital, Vetmeduni Vienna, Vienna, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - A Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - G L Oreff
- Department for Companion Animals and Horses, Veterm, University Equine Hospital, Vetmeduni Vienna, Vienna, Austria
| | - C Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - F Jenner
- Department for Companion Animals and Horses, Veterm, University Equine Hospital, Vetmeduni Vienna, Vienna, Austria.
- Austrian Cluster for Tissue Regeneration, Vienna, Austria.
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Wang Y, Song X, Jin M, Lu J. Characterization of the Immune Microenvironment and Identification of Biomarkers in Chronic Rhinosinusitis with Nasal Polyps Using Single-Cell RNA Sequencing and Transcriptome Analysis. J Inflamm Res 2024; 17:253-277. [PMID: 38229690 PMCID: PMC10790669 DOI: 10.2147/jir.s440409] [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: 09/19/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Purpose Chronic rhinosinusitis is a prevalent condition in the field of otorhinolaryngology; however, its pathogenesis remains to be elucidated. The immunological defense of the nasal mucosa is significantly influenced by dendritic cells (DCs). We identified specific biological indicators linked to DCs and explored their significance in cases of chronic rhinosinusitis with nasal polyps (CRSwNP). Patients and Methods We categorized cells using single-cell RNA (scRNA) sequencing, and combined transcriptome sequencing was used to identify potential candidate genes for CRSwNP. We selected three biomarkers based on two algorithms and performed enrichment and immune correlation analyses. Biomarkers were verified using training and validation sets, receiver operating characteristic curves, immunohistochemistry, and quantitative real-time reverse-transcription PCR (qRT-PCR). Variations in biomarker expression were validated using pseudotime analysis. The networks of competing transcription factor (TF)-mRNA and competing endogenous RNA (ceRNA) were established, and the protein drugs associated with these biomarkers were predicted. Results Both scRNA-seq and transcriptome data showed that DCs immune infiltration was higher in the CRSwNP group than in the control group. Three DC-related biomarkers (NR4A1, CLEC4G, and CD163) were identified. In CRSwNP, NR4A1 expression decreased, whereas CLEC4G and CD163 expression increased. All biomarkers were shown to be involved in immunological and metabolic pathways by enrichment analysis. These biomarkers were associated with γδ T cells, effector memory CD4 + T cells, regulatory T cells, and immature DCs. According to pseudotime analysis, NR4A1 and CD163 expression decreased from high to low, whereas CLEC4G expression remained low. Conclusion We screened and identified potential DC-associated biomarkers of CRSwNP progression by integrating scRNA-seq with whole transcriptome sequencing. We analyzed the biological pathways in which they were involved, explored their molecular regulatory mechanisms and related drugs, and constructed ceRNA, TF-mRNA, and biomarker-drug networks to identify new CRSwNP treatment targets, laying the groundwork for the clinical management of CRSwNP.
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Affiliation(s)
- Yakun Wang
- Department of Pathology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, People’s Republic of China
| | - Xinyu Song
- Department of Otorhinolaryngology, Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, People’s Republic of China
| | - Mulan Jin
- Department of Pathology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, People’s Republic of China
| | - Jun Lu
- Department of Pathology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, People’s Republic of China
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Narsale A, Almanza F, Tran T, Lam B, Seo D, Vu A, Long SA, Cooney L, Serti E, Davies JD. Th2 cell clonal expansion at diagnosis in human type 1 diabetes. Clin Immunol 2023; 257:109829. [PMID: 37907122 DOI: 10.1016/j.clim.2023.109829] [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: 08/27/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
Soon after diagnosis with type 1 diabetes (T1D), many patients experience a period of partial remission. A longer partial remission is associated with a better response to treatment, but the mechanism is not known. The frequency of CD4+CD25+CD127hi (127-hi) cells, a cell subset with an anti-inflammatory Th2 bias, correlates positively with length of partial remission. The purpose of this study was to further characterize the nature of the Th2 bias in 127-hi cells. Single cell RNA sequencing paired with TCR sequencing of sorted 127-hi memory cells identifies clonally expanded Th2 clusters in 127-hi cells from T1D, but not from healthy donors. The Th2 clusters express GATA3, GATA3-AS1, PTGDR2, IL17RB, IL4R and IL9R. The existence of 127-hi Th2 cell clonal expansion in T1D suggests that disease factors may induce clonal expansion of 127-hi Th2 cells that prolong partial remission and delay disease progression.
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Affiliation(s)
- Aditi Narsale
- San Diego Biomedical Research Institute, 3525 John Hopkins Court, San Diego, CA 92121, USA.
| | - Francisco Almanza
- San Diego Biomedical Research Institute, 3525 John Hopkins Court, San Diego, CA 92121, USA.
| | - Theo Tran
- San Diego Biomedical Research Institute, 3525 John Hopkins Court, San Diego, CA 92121, USA
| | - Breanna Lam
- San Diego Biomedical Research Institute, 3525 John Hopkins Court, San Diego, CA 92121, USA.
| | - David Seo
- San Diego Biomedical Research Institute, 3525 John Hopkins Court, San Diego, CA 92121, USA
| | - Alisa Vu
- San Diego Biomedical Research Institute, 3525 John Hopkins Court, San Diego, CA 92121, USA.
| | - S Alice Long
- Benaroya Research Institute, 1201 9(th) Ave, Seattle, WA 98101, USA.
| | | | | | - Joanna D Davies
- San Diego Biomedical Research Institute, 3525 John Hopkins Court, San Diego, CA 92121, USA.
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