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So RJ, Collins SL, Chan-Li Y, Lina I, Gelbard A, Motz KM, Hillel AT. A Comprehensive Flow Cytometry Panel for Analysis of Idiopathic Subglottic Stenosis. Otolaryngol Head Neck Surg 2024. [PMID: 38606634 DOI: 10.1002/ohn.754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/15/2024] [Accepted: 03/15/2024] [Indexed: 04/13/2024]
Abstract
OBJECTIVE To present a comprehensive flow cytometry panel for idiopathic subglottic stenosis (iSGS). STUDY DESIGN Controlled ex vivo cohort study. SETTING Tertiary care academic hospital in a metropolitan area. METHODS Flow cytometry and single-cell RNA sequencing were performed on 9 paired normal and scar tissue samples from iSGS patients. Flow cytometry was used to assess the presence of myeloid (CD11b, CD14, CD15, Siglec8), lymphoid (CD3, CD4, CD8, gamma delta [γδ], FOXP3), endothelial (CD31), fibroblast (CD90, SMA), and epithelial (CD326, CK5) markers. RESULTS On flow cytometry, iSGS scar is characterized by an increased presence of myeloid, lymphoid, endothelial, and fibroblast cell types, but a decreased presence of epithelial cells. In the myeloid lineage, iSGS scar samples demonstrated increased CD11b+ monocytes (P < .001), Siglec8+ eosinophils (P = .03), and CD14+ monocytes (P = .02). In the lymphoid lineage, iSGS scar demonstrated increased CD3+ T-cells (P < .001), CD4+ helper T-cells (P < .001), γδ+ T-cells (P < .001), and FOXP3+ regulatory T-cells (P = .002). iSGS scar exhibited specific increases in CD90+ (P = .04) and SMA+ (P < .001) fibroblasts but decreased CD326+ (E-cadherin) epithelial cells (P = .01) relative to normal samples. CONCLUSION We present a comprehensive flow cytometry panel for iSGS. This flow panel may serve as a common platform among airway scientists to elucidate the cellular mechanisms underpinning iSGS and other upper airway pathologies. Scar iSGS samples demonstrate a distinct cellular profile relative to normal iSGS specimens, exhibiting increased fibroblast, endothelial, and inflammatory cell types but decreased epithelium.
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Affiliation(s)
- Raymond J So
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Samuel L Collins
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yee Chan-Li
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ioan Lina
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alexander Gelbard
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University, Nashville, Tennessee, USA
| | - Kevin M Motz
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alexander T Hillel
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Wen X, Pu L, Wencheng Z, Tengfei M, Guangshun W. Immune cell-related prognostic risk model and tumor immune environment modulation in esophageal carcinoma based on single-cell and bulk RNA sequencing. Thorac Cancer 2024. [PMID: 38587029 DOI: 10.1111/1759-7714.15301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND Immune cells play a pivotal role in the tumor microenvironment, exerting significant influence on tumor progression and patient outcomes, but the current biomarkers are insufficient to fully capture the complex and diverse tumor immune microenvironment and the impact of immunotherapy. METHODS The advent of single-cell sequencing allows us to explore the tumor microenvironment at an unprecedented resolution, enabling the identification and characterization of distinct subsets of immune cells, thereby paving the way for the development of prognostic models using immune cells. Leveraging single-cell data, our study deeply investigated the intricacies of immune microenvironment heterogeneity in esophageal carcinoma. RESULTS We elucidated the composition, functionality, evolution, and intercellular communication patterns of immune cells, culminating in the construction of an independent prognostic model at the single-cell level. Furthermore, we conducted a comprehensive analysis of disparities in immune infiltration and immune checkpoint expression between patients categorized into high- and low-risk groups, which may impact patient prognosis. CONCLUSION In summary, our study harnessed multiomics data to delineate the immune profile of esophageal carcinoma patients, provide a method for leveraging molecular signatures of immune cells to identify potential biomarkers, while concurrently providing evidence for the potential benefits of immunotherapy.
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Affiliation(s)
- Xiao Wen
- Department of Oncology, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin, China
| | - Liu Pu
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Zhang Wencheng
- Department of Oncology, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin, China
| | - Ma Tengfei
- College of Life Sciences, Hebei University, Baoding, China
| | - Wang Guangshun
- Department of Oncology, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin, China
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3
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Liu C, Xie J, Lin B, Tian W, Wu Y, Xin S, Hong L, Li X, Liu L, Jin Y, Tang H, Deng X, Zou Y, Zheng S, Fang W, Cheng J, Dai X, Bao X, Zhao P. Pan-Cancer Single-Cell and Spatial-Resolved Profiling Reveals the Immunosuppressive Role of APOE+ Macrophages in Immune Checkpoint Inhibitor Therapy. Adv Sci (Weinh) 2024:e2401061. [PMID: 38569519 DOI: 10.1002/advs.202401061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/13/2024] [Indexed: 04/05/2024]
Abstract
The heterogeneity of macrophages influences the response to immune checkpoint inhibitor (ICI) therapy. However, few studies explore the impact of APOE+ macrophages on ICI therapy using single-cell RNA sequencing (scRNA-seq) and machine learning methods. The scRNA-seq and bulk RNA-seq data are Integrated to construct an M.Sig model for predicting ICI response based on the distinct molecular signatures of macrophage and machine learning algorithms. Comprehensive single-cell analysis as well as in vivo and in vitro experiments are applied to explore the potential mechanisms of the APOE+ macrophage in affecting ICI response. The M.Sig model shows clear advantages in predicting the efficacy and prognosis of ICI therapy in pan-cancer patients. The proportion of APOE+ macrophages is higher in ICI non-responders of triple-negative breast cancer compared with responders, and the interaction and longer distance between APOE+ macrophages and CD8+ exhausted T (Tex) cells affecting ICI response is confirmed by multiplex immunohistochemistry. In a 4T1 tumor-bearing mice model, the APOE inhibitor combined with ICI treatment shows the best efficacy. The M.Sig model using real-world immunotherapy data accurately predicts the ICI response of pan-cancer, which may be associated with the interaction between APOE+ macrophages and CD8+ Tex cells.
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Affiliation(s)
- Chuan Liu
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Jindong Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Bo Lin
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310053, China
- Innovation Centre for Information, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China
| | - Weihong Tian
- Changzhou Third People's Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, 213000, China
| | - Yifan Wu
- School of software, Zhejiang University, Ningbo, 315100, China
| | - Shan Xin
- Department of Genetics, Yale School of medicine, New Haven, CT, 06510, USA
| | - Libing Hong
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Xin Li
- Department Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Lulu Liu
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Yuzhi Jin
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yutian Zou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Shaoquan Zheng
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Weijia Fang
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Jinlin Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Xiaomeng Dai
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Xuanwen Bao
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Peng Zhao
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
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Fan Y, Huang S, Wu D, Chu M, Zhao J, Zhang J, Wang Y, Gui Y, Ye X, Wang G, Geng Y, Wang Y, Zhang Z. Immune features revealed by single-cell RNA and single-cell TCR/BCR sequencing in patients with rheumatoid arthritis receiving COVID-19 booster vaccination. J Med Virol 2024; 96:e29573. [PMID: 38566569 DOI: 10.1002/jmv.29573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/03/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, have profoundly affected human health. Booster COVID-19 vaccines have demonstrated significant efficacy in reducing infection and severe cases. However, the effects of booster COVID-19 vaccines on key immune cell subsets and their responses in rheumatoid arthritis (RA) are not well understood. By using single-cell RNA sequencing (scRNA-seq) combined with scTCR/BCR-seq analysis, a total of 8 major and 27 minor cell clusters were identified from paired peripheral blood mononuclear cells (PBMCs) which were collected 1 week before and 4 weeks after booster vaccination in stable RA patients. Booster vaccination only had limited impact on the composition and proportions of PBMCs cell clusters. CD8+ cytotoxic T cells (CD8+T_CTL) showed a trend toward an increase after vaccination, while naive B cells and conventional dendritic cells (cDCs) showed a trend toward a decrease. Transcriptomic changes were observed after booster vaccination, primarily involving T/B cell receptor signaling pathways, phagosome, antigen processing and presenting, and viral myocarditis pathways. Interferon (IFN) and pro-inflammatory response gene sets were slightly upregulated across most major cell subpopulations in COVID-19 booster-vaccinated RA individuals. Plasma neutralizing antibody titers significantly increased after booster COVID-19 vaccination (p = 0.037). Single-cell TCR/BCR analysis revealed increased B cell clone expansion and repertoire diversity postvaccination, with no consistent alterations in T cells. Several clonotypes of BCRs and TCRs were identified to be significantly over-represented after vaccination, such as IGHV3-15 and TRBV28. Our study provided a comprehensive single-cell atlas of the peripheral immune response and TCR/BCR immune repertoire profiles to inactivated SARS-CoV-2 booster vaccination in RA patients, which helps us to understand vaccine-induced immune responses better.
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Affiliation(s)
- Yong Fan
- Department of Rheumatology and Clinical Immunology, Peking University First Hospital, Beijing, China
| | - Siyuan Huang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Duo Wu
- Kindstar Global Precision Medicine Institute, Wuhan, China
| | - Ming Chu
- NHC Key Laboratory of Medical Immunology (Peking University), Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Juan Zhao
- Department of Rheumatology and Clinical Immunology, Peking University First Hospital, Beijing, China
| | - Jiaying Zhang
- Department of Rheumatology and Clinical Immunology, Peking University First Hospital, Beijing, China
| | - Yu Wang
- Department of Rheumatology and Clinical Immunology, Peking University First Hospital, Beijing, China
| | - Yanni Gui
- Department of Rheumatology and Clinical Immunology, Peking University First Hospital, Beijing, China
| | - Xiaofei Ye
- Kindstar Global Precision Medicine Institute, Wuhan, China
| | - Guiqiang Wang
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
| | - Yan Geng
- Department of Rheumatology and Clinical Immunology, Peking University First Hospital, Beijing, China
| | - Yuedan Wang
- NHC Key Laboratory of Medical Immunology (Peking University), Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Zhuoli Zhang
- Department of Rheumatology and Clinical Immunology, Peking University First Hospital, Beijing, China
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Zhang X, Xiao Q, Zhang C, Zhou Q, Xu T. Construction of a prognostic model with CAFs for predicting the prognosis and immunotherapeutic response of lung squamous cell carcinoma. J Cell Mol Med 2024; 28:e18262. [PMID: 38520221 PMCID: PMC10960179 DOI: 10.1111/jcmm.18262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/25/2024] Open
Abstract
Lung squamous cell carcinoma (LUSC) is one of the subtypes of lung cancer (LC) that contributes to approximately 25%-30% of its prevalence. Cancer-associated fibroblasts (CAFs) are key cellular components of the TME, and the large number of CAFs in tumour tissues creates a favourable environment for tumour development. However, the function of CAFs in the LUSC is complex and uncertain. First, we processed the scRNA-seq data and classified distinct types of CAFs. We also identified prognostic CAFRGs using univariate Cox analysis and conducted survival analysis. Additionally, we assessed immune cell infiltration in CAF clusters using ssGSEA. We developed a model with a significant prognostic correlation and verified the prognostic model. Furthermore, we explored the immune landscape of LUSC and further investigated the correlation between malignant features and LUSC. We identified CAFs and classified them into three categories: iCAFs, mCAFs and apCAFs. The survival analysis showed a significant correlation between apCAFs and iCAFs and LUSC patient prognosis. Kaplan-Meier analysis showed that patients in CAF cluster C showed a better survival probability compared to clusters A and B. In addition, we identified nine significant prognostic CAFRGs (CLDN1, TMX4, ALPL, PTX3, BHLHE40, TNFRSF12A, VKORC1, CST3 and ADD3) and subsequently employed multivariate Cox analysis to develop a signature and validate the model. Lastly, the correlation between CAFRG and malignant features indicates the potential role of CAFRG in promoting tumour angiogenesis, EMT and cell cycle alterations. We constructed a CAF prognostic signature for identifying potential prognostic CAFRGs and predicting the prognosis and immunotherapeutic response for LUSC. Our study may provide a more accurate prognostic assessment and immunotherapy targeting strategies for LUSC.
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Affiliation(s)
- Xiang Zhang
- Lung cancer center, West China hospitalSichuan universityChengduChina
| | - Qingqing Xiao
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China HospitalSichuan UniversityChengduChina
| | - Cong Zhang
- Department of Thoracic surgeryChengdu Seventh People's Hospital (Affiliated Cancer Hospital of Chengdu Medical College)ChengduChina
| | - Qinghua Zhou
- Lung cancer center, West China hospitalSichuan universityChengduChina
| | - Tao Xu
- Department of Thoracic SurgeryThe Affiliated Hospital, Southwest Medical UniversityLuzhouChina
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Zhang X, Wang X, Wen Y, Chen S, Zhou C, Wu F. Single-cell transcriptomics reveal metastatic CLDN4+ cancer cells underlying the recurrence of malignant pleural effusion in patients with advanced non-small-cell lung cancer. Clin Transl Med 2024; 14:e1649. [PMID: 38629624 PMCID: PMC11022306 DOI: 10.1002/ctm2.1649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Recurrent malignant pleural effusion (MPE) resulting from non-small-cell lung cancer (NSCLC) is easily refractory to conventional therapeutics and lacks predictive markers. The cellular or genetic signatures of recurrent MPE still remain largely uncertain. METHODS 16 NSCLC patients with pleural effusions were recruited, followed by corresponding treatments based on primary tumours. Non-recurrent or recurrent MPE was determined after 3-6 weeks of treatments. The status of MPE was verified by computer tomography (CT) and cytopathology, and the baseline pleural fluids were collected for single-cell RNA sequencing (scRNA-seq). Samples were then integrated and profiled. Cellular communications and trajectories were inferred by bioinformatic algorithms. Comparative analysis was conducted and the results were further validated by quantitative polymerase chain reaction (qPCR) in a larger MPE cohort from the authors' centre (n = 64). RESULTS The scRNA-seq revealed that 33 590 cells were annotated as 7 major cell types and further characterized into 14 cell clusters precisely. The cell cluster C1, classified as Epithelial Cell Adhesion Molecule (EpCAM)+ metastatic cancer cell and correlated with activation of tight junction and adherence junction, was significantly enriched in the recurrent MPE group, in which Claudin-4 (CLDN4) was identified. The subset cell cluster C3 of C1, which was enriched in recurrent MPE and demonstrated a phenotype of ameboidal-type cell migration, also showed a markedly higher expression of CLDN4. Meanwhile, the expression of CLDN4 was positively correlated with E74 Like ETS Transcription Factor 3 (ELF3), EpCAM and Tumour Associated Calcium Signal Transducer 2 (TACSTD2), independent of driver-gene status. CLDN4 was also found to be associated with the expression of Hypoxia Inducible Factor 1 Subunit Alpha (HIF1A) and Vascular Endothelial Growth Factor A (VEGFA), and the cell cluster C1 was the major mediator in cellular communication of VEGFA signalling. In the extensive MPE cohort, a notably increased expression of CLDN4 in cells from pleural effusion among patients diagnosed with recurrent MPE was observed, compared with the non-recurrent group, which was also associated with a trend towards worse overall survival (OS). CONCLUSIONS CLDN4 could be considered as a predictive marker of recurrent MPE among patients with advanced NSCLC. Further validation for its clinical value in cohorts with larger sample size and in-depth mechanism studies on its biological function are warranted. TRIAL REGISTRATION Not applicable.
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Affiliation(s)
- Xiaoshen Zhang
- School of MedicineTongji UniversityShanghaiChina
- Department of Medical OncologyShanghai Pulmonary Hospital, Tongji University School of MedicineShanghaiChina
| | - Xuanhe Wang
- School of MedicineTongji UniversityShanghaiChina
- Department of Medical OncologyShanghai Pulmonary Hospital, Tongji University School of MedicineShanghaiChina
| | - Yaokai Wen
- School of MedicineTongji UniversityShanghaiChina
- Department of Medical OncologyShanghai Pulmonary Hospital, Tongji University School of MedicineShanghaiChina
| | - Shen Chen
- Department of Medical OncologyShanghai Pulmonary Hospital, Tongji University School of MedicineShanghaiChina
| | - Caicun Zhou
- Department of Medical OncologyShanghai Pulmonary Hospital, Tongji University School of MedicineShanghaiChina
| | - Fengying Wu
- Department of Medical OncologyShanghai Pulmonary Hospital, Tongji University School of MedicineShanghaiChina
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Wang Y, Jiang Y, Ni G, Li S, Balderson B, Zou Q, Liu H, Jiang Y, Sun J, Ding X. Integrating Single-Cell and Spatial Transcriptomics Reveals Heterogeneity of Early Pig Skin Development and a Subpopulation with Hair Placode Formation. Adv Sci (Weinh) 2024:e2306703. [PMID: 38561967 DOI: 10.1002/advs.202306703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/08/2024] [Indexed: 04/04/2024]
Abstract
The dermis and epidermis, crucial structural layers of the skin, encompass appendages, hair follicles (HFs), and intricate cellular heterogeneity. However, an integrated spatiotemporal transcriptomic atlas of embryonic skin has not yet been described and would be invaluable for studying skin-related diseases in humans. Here, single-cell and spatial transcriptomic analyses are performed on skin samples of normal and hairless fetal pigs across four developmental periods. The cross-species comparison of skin cells illustrated that the pig epidermis is more representative of the human epidermis than mice epidermis. Moreover, Phenome-wide association study analysis revealed that the conserved genes between pigs and humans are strongly associated with human skin-related diseases. In the epidermis, two lineage differentiation trajectories describe hair follicle (HF) morphogenesis and epidermal development. By comparing normal and hairless fetal pigs, it is found that the hair placode (Pc), the most characteristic initial structure in HFs, arises from progenitor-like OGN+/UCHL1+ cells. These progenitors appear earlier in development than the previously described early Pc cells and exhibit abnormal proliferation and migration during differentiation in hairless pigs. The study provides a valuable resource for in-depth insights into HF development, which may serve as a key reference atlas for studying human skin disease etiology using porcine models.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yao Jiang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Guiyan Ni
- Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Shujuan Li
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Brad Balderson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, 4067, Australia
| | - Quan Zou
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Huatao Liu
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yifan Jiang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jingchun Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiangdong Ding
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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Shi X, Fu Q, Mao J, Yang J, Chen Y, Lu J, Chen A, Lu N. Integration of single-cell and RNA-seq data to explore the role of focal adhesion-related genes in osteoporosis. J Cell Mol Med 2024; 28:e18271. [PMID: 38534087 DOI: 10.1111/jcmm.18271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/18/2024] [Accepted: 02/23/2024] [Indexed: 03/28/2024] Open
Abstract
Integrin-based focal adhesion is one of the major mechanosensory in osteocytes. The aim of this study was to mine the hub genes associated with focal adhesion and investigate their roles in osteoporosis based on the data of single-cell RNA sequencing and RNA-sequencing. Two hub genes (FAM129A and RNF24) with the same expression trend and AUC values greater than 0.7 in both GSE56815 and GSE56116 cohorts were uncovered. The nomogram was created to predict the risk of OP based on two hub genes. Subsequently, the competing endogenous RNA network was established based on two hub genes, 14 microRNAs and five long noncoding RNAs. Meanwhile, transcription factors-hub gene network was established based on two hub genes and 14 TFs. Finally, 73 drugs were predicted, of which there were 13 drugs targeting FAM129A and 66 drugs targeting RNF24. In both mouse and human blood samples, FAM129A expression was decreased in granulocytes and RNF24 expression was increased in monocytes. In the mouse experiment, FAM129A and anti-RNF24 were found to partially alleviate the progression of osteoporosis. In conclusion, two hub genes related to focal adhesion were identified by combined scRNA-seq and RNA-seq analyses, which might supply a new insight for the treatment and evaluation of OP.
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Affiliation(s)
- Xiaojian Shi
- Department of Orthopedic Trauma Surgery, Haimen People's Hospital, Nantong, Jiangsu, China
| | - Qiang Fu
- Department of Orthopedic Trauma Surgery, Shanghai Changzheng Hospital, Shanghai, China
| | - Jianyu Mao
- Department of Orthopedic Trauma Surgery, Shanghai Changzheng Hospital, Shanghai, China
| | - Jiajie Yang
- Department of Orthopedic Trauma Surgery, Haimen People's Hospital, Nantong, Jiangsu, China
| | - Ye Chen
- Department of Orthopedic Trauma Surgery, Haimen People's Hospital, Nantong, Jiangsu, China
| | - Jiajia Lu
- Department of Orthopedic Trauma Surgery, Haimen People's Hospital, Nantong, Jiangsu, China
- Department of Orthopedic Trauma Surgery, Shanghai Changzheng Hospital, Shanghai, China
- Department of Orthopedic Trauma Surgery, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Aimin Chen
- Department of Orthopedic Trauma Surgery, Shanghai Changzheng Hospital, Shanghai, China
- Department of Orthopedic Trauma Surgery, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Nan Lu
- Department of Orthopedic Trauma Surgery, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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Su Y, Yu Z, Yang Y, Wong KC, Li X. Distribution-Agnostic Deep Learning Enables Accurate Single-Cell Data Recovery and Transcriptional Regulation Interpretation. Adv Sci (Weinh) 2024; 11:e2307280. [PMID: 38380499 DOI: 10.1002/advs.202307280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/16/2024] [Indexed: 02/22/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a robust method for studying gene expression at the single-cell level, but accurately quantifying genetic material is often hindered by limited mRNA capture, resulting in many missing expression values. Existing imputation methods rely on strict data assumptions, limiting their broader application, and lack reliable supervision, leading to biased signal recovery. To address these challenges, authors developed Bis, a distribution-agnostic deep learning model for accurately recovering missing sing-cell gene expression from multiple platforms. Bis is an optimal transport-based autoencoder model that can capture the intricate distribution of scRNA-seq data while addressing the characteristic sparsity by regularizing the cellular embedding space. Additionally, they propose a module using bulk RNA-seq data to guide reconstruction and ensure expression consistency. Experimental results show Bis outperforms other models across simulated and real datasets, showcasing superiority in various downstream analyses including batch effect removal, clustering, differential expression analysis, and trajectory inference. Moreover, Bis successfully restores gene expression levels in rare cell subsets in a tumor-matched peripheral blood dataset, revealing developmental characteristics of cytokine-induced natural killer cells within a head and neck squamous cell carcinoma microenvironment.
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Affiliation(s)
- Yanchi Su
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Zhuohan Yu
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Yuning Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
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10
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He S, Liu SQ, Teng XY, He JY, Liu Y, Gao JH, Wu Y, Hu W, Dong ZJ, Bei JX, Xu JH. Comparative single-cell RNA sequencing analysis of immune response to inactivated vaccine and natural SARS-CoV-2 infection. J Med Virol 2024; 96:e29577. [PMID: 38572977 DOI: 10.1002/jmv.29577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/02/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Uncovering the immune response to an inactivated SARS-CoV-2 vaccine (In-Vac) and natural infection is crucial for comprehending COVID-19 immunology. Here we conducted an integrated analysis of single-cell RNA sequencing (scRNA-seq) data from serial peripheral blood mononuclear cell (PBMC) samples derived from 12 individuals receiving In-Vac compared with those from COVID-19 patients. Our study reveals that In-Vac induces subtle immunological changes in PBMC, including cell proportions and transcriptomes, compared with profound changes for natural infection. In-Vac modestly upregulates IFN-α but downregulates NF-κB pathways, while natural infection triggers hyperactive IFN-α and NF-κB pathways. Both In-Vac and natural infection alter T/B cell receptor repertoires, but COVID-19 has more significant change in preferential VJ gene, indicating a vigorous immune response. Our study reveals distinct patterns of cellular communications, including a selective activation of IL-15RA/IL-15 receptor pathway after In-Vac boost, suggesting its potential role in enhancing In-Vac-induced immunity. Collectively, our study illuminates multifaceted immune responses to In-Vac and natural infection, providing insights for optimizing SARS-CoV-2 vaccine efficacy.
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Affiliation(s)
- Shuai He
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shu-Qiang Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiang-Yun Teng
- Medical Laboratory Center, Maoming Hospital of Guangzhou University of Chinese Medicine, Maoming, China
| | - Jin-Yong He
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Yang Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia-Hui Gao
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Yue Wu
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Wei Hu
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Zhong-Jun Dong
- School of Medicine and Institute for Immunology, Tsinghua University, Beijing, China
| | - Jin-Xin Bei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jian-Hua Xu
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- Medical Laboratory Center, Maoming Hospital of Guangzhou University of Chinese Medicine, Maoming, China
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11
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Brettner L, Eder R, Schmidlin K, Geiler-Samerotte K. An ultra high-throughput, massively multiplexable, single-cell RNA-seq platform in yeasts. Yeast 2024; 41:242-255. [PMID: 38282330 DOI: 10.1002/yea.3927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 01/04/2024] [Accepted: 01/16/2024] [Indexed: 01/30/2024] Open
Abstract
Yeasts are naturally diverse, genetically tractable, and easy to grow such that researchers can investigate any number of genotypes, environments, or interactions thereof. However, studies of yeast transcriptomes have been limited by the processing capabilities of traditional RNA sequencing techniques. Here we optimize a powerful, high-throughput single-cell RNA sequencing (scRNAseq) platform, SPLiT-seq (Split Pool Ligation-based Transcriptome sequencing), for yeasts and apply it to 43,388 cells of multiple species and ploidies. This platform utilizes a combinatorial barcoding strategy to enable massively parallel RNA sequencing of hundreds of yeast genotypes or growth conditions at once. This method can be applied to most species or strains of yeast for a fraction of the cost of traditional scRNAseq approaches. Thus, our technology permits researchers to leverage "the awesome power of yeast" by allowing us to survey the transcriptome of hundreds of strains and environments in a short period of time and with no specialized equipment. The key to this method is that sequential barcodes are probabilistically appended to cDNA copies of RNA while the molecules remain trapped inside of each cell. Thus, the transcriptome of each cell is labeled with a unique combination of barcodes. Since SPLiT-seq uses the cell membrane as a container for this reaction, many cells can be processed together without the need to physically isolate them from one another in separate wells or droplets. Further, the first barcode in the sequence can be chosen intentionally to identify samples from different environments or genetic backgrounds, enabling multiplexing of hundreds of unique perturbations in a single experiment. In addition to greater multiplexing capabilities, our method also facilitates a deeper investigation of biological heterogeneity, given its single-cell nature. For example, in the data presented here, we detect transcriptionally distinct cell states related to cell cycle, ploidy, metabolic strategies, and so forth, all within clonal yeast populations grown in the same environment. Hence, our technology has two obvious and impactful applications for yeast research: the first is the general study of transcriptional phenotypes across many strains and environments, and the second is investigating cell-to-cell heterogeneity across the entire transcriptome.
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Affiliation(s)
- Leandra Brettner
- Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Rachel Eder
- Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Kara Schmidlin
- Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Kerry Geiler-Samerotte
- Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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12
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Wang X, Zhai Y, Zheng H. Deciphering the cellular heterogeneity of the insect brain with single-cell RNA sequencing. Insect Sci 2024; 31:314-327. [PMID: 37702319 DOI: 10.1111/1744-7917.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 09/14/2023]
Abstract
Insects show highly complicated adaptive and sophisticated behaviors, including spatial orientation skills, learning ability, and social interaction. These behaviors are controlled by the insect brain, the central part of the nervous system. The tiny insect brain consists of millions of highly differentiated and interconnected cells forming a complex network. Decades of research has gone into an understanding of which parts of the insect brain possess particular behaviors, but exactly how they modulate these functional consequences needs to be clarified. Detailed description of the brain and behavior is required to decipher the complexity of cell types, as well as their connectivity and function. Single-cell RNA-sequencing (scRNA-seq) has emerged recently as a breakthrough technology to understand the transcriptome at cellular resolution. With scRNA-seq, it is possible to uncover the cellular heterogeneity of brain cells and elucidate their specific functions and state. In this review, we first review the basic structure of insect brains and the links to insect behaviors mainly focusing on learning and memory. Then the scRNA applications on insect brains are introduced by representative studies. Single-cell RNA-seq has allowed researchers to classify cell subpopulations within different insect brain regions, pinpoint single-cell developmental trajectories, and identify gene regulatory networks. These developments empower the advances in neuroscience and shed light on the intricate problems in understanding insect brain functions and behaviors.
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Affiliation(s)
- Xiaofei Wang
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and In-sect Pests, Jinan, China
| | - Hao Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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13
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Wen F, Tan Z, Huang D, Xiang J. Molecular mechanism analyses of post-traumatic epilepsy and hereditary epilepsy based on 10× single-cell transcriptome sequencing technology. CNS Neurosci Ther 2024; 30:e14702. [PMID: 38572804 PMCID: PMC10993349 DOI: 10.1111/cns.14702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 03/04/2024] [Accepted: 03/10/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Single-cell RNA sequencing analysis has been usually conducted on post-traumatic epilepsy (PET) and hereditary epilepsy (HE) patients; however, the transcriptome of patients with traumatic temporal lobe epilepsy has rarely been studied. MATERIALS AND METHODS Hippocampus tissues isolated from one patient with PTE and one patient with HE were used in the present study. Single cell isolates were prepared and captured using a 10× Genomics Chromium Single-Cell 3' kit (V3) according to the manufacturer's instructions. The libraries were sequenced on an Illumina NovaSeq 6000 sequencing system. Raw data were processed, and the cells were filtered and classified using the Seurat R package. Uniform Manifold Approximation and Projection was used for visualization. Differentially expressed genes (DEGs) were identified based on a p-value ≤0.01 and log fold change (FC) ≥0.25. Gene Ontology (GO, http://geneontology.org/) and KEGG (Kyoto Encyclopedia of Genes and Genomes, www.genome.jp/kegg) analyses were performed on the DEGs for enrichment analysis. RESULTS The reads obtained from the 10× genomic platform for PTE and HE were 39.56 M and 30.08 M, respectively. The Q30 score of the RNA reads was >91.6%. After filtering, 7479 PTE cells and 9357 HE cells remained for further study. More than 96.4% of the reads were mapped to GRCh38/GRCm38. The cells were differentially distributed in two groups, with higher numbers of oligodendrocytes (6522 vs. 2532) and astrocytes (133 vs. 52), and lower numbers of microglial cells (2242 vs. 3811), and neurons (3 vs. 203) present in the HE group than in the PTE group. The DEGs in four cell clusters were identified, with 25 being in oligodendrocytes (13 upregulated and 12 downregulated), 87 in microglia cells (42 upregulated and 45 downregulated), 222 in astrocytes (115 upregulated and 107 downregulated), and 393 in neurons (305 upregulated and 88 downregulated). The genes MTND1P23 (downregulated), XIST (downregulated), and RPS4Y1 (upregulated) were commonly expressed in all four cell clusters. The DEGs in microglial cells and astrocytes were enriched in the IL-17 signaling pathway. CONCLUSION Our study explored differences in cells found in a patient with PE compared to a patient with HE, and the transcriptome in the different cells was analyzed for the first time. Studying inflammatory and immune functions might be the best approach for investigating traumatic temporal lobe epilepsy in neurons.
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Affiliation(s)
- Fang Wen
- Department of NeurologyThe Second Xiang‐Ya Hospital of Central South UniversityChangshaHunanChina
| | - Zhigang Tan
- Department of NeurosurgeryThe Second Xiang‐Ya Hospital of Central South UniversityChangshaHunanChina
| | - Dezhi Huang
- Department of NeurosurgeryThe Second Xiang‐Ya Hospital of Central South UniversityChangshaHunanChina
| | - Jun Xiang
- Department of NeurosurgeryThe Second Xiang‐Ya Hospital of Central South UniversityChangshaHunanChina
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14
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Zhang Y, Li L, Chu F, Wu H, Xiao X, Ye J, Li K. Itraconazole inhibits tumor growth via CEBPB-mediated glycolysis in colorectal cancer. Cancer Sci 2024; 115:1154-1169. [PMID: 38278779 PMCID: PMC11007002 DOI: 10.1111/cas.16082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/28/2024] Open
Abstract
Advanced colorectal cancer (CRC) is characterized by a high recurrence and metastasis rate, which is the primary cause of patient mortality. Unfortunately, effective anti-cancer drugs for CRC are still lacking in clinical practice. We screened FDA-approved drugs by utilizing targeted organoid sequencing data and found that the antifungal drug itraconazole had a potential therapeutic effect on CRC tumors. However, the effect and mechanism of itraconazole on CRC tumors have not been investigated. A cell line-derived xenograft model in tumor-bearing mice was established and single-cell RNA sequencing was performed on tumor samples from four mice with or without itraconazole treatment. The proportion of cell populations and gene expression profiles was significantly different between the two groups. We found that itraconazole could inhibit tumor growth and glycolysis. We revealed that CEBPB was a new target for itraconazole, and that silencing CEBPB could repress CRC glycolysis and tumor growth by inhibiting ENO1 expression. Clinical analysis showed that CEBPB expression was obviously elevated in CRC patients, and was associated with poor survival. In summary, itraconazole treatment remodeled cell composition and gene expression profiles. Itraconazole inhibited cell glycolysis and tumor growth via the CEBPB-ENO1 axis. In this study, we illustrate a new energy metabolism mechanism for itraconazole on tumor growth in CRC that will provide a theoretical basis for CRC targeting/combination therapy.
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Affiliation(s)
- Yong Zhang
- Branch Center of Advanced Medical Research CenterZhengzhou Central Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
- Department of GastroenterologyZhengzhou Central Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
- Medical Key Laboratory for Diagnosis and Treatment of Colorectal Cancer in Henan ProvinceZhengzhouChina
- Zhengzhou Key Laboratory for Diagnosis, Treatment and Research of Colorectal CancerZhengzhouChina
| | - Lu Li
- Department of GastroenterologyZhengzhou Central Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
- Medical Key Laboratory for Diagnosis and Treatment of Colorectal Cancer in Henan ProvinceZhengzhouChina
- Zhengzhou Key Laboratory for Diagnosis, Treatment and Research of Colorectal CancerZhengzhouChina
| | - Feifei Chu
- Department of GastroenterologyZhengzhou Central Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
- Medical Key Laboratory for Diagnosis and Treatment of Colorectal Cancer in Henan ProvinceZhengzhouChina
- Zhengzhou Key Laboratory for Diagnosis, Treatment and Research of Colorectal CancerZhengzhouChina
| | - Huili Wu
- Department of GastroenterologyZhengzhou Central Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
- Medical Key Laboratory for Diagnosis and Treatment of Colorectal Cancer in Henan ProvinceZhengzhouChina
- Zhengzhou Key Laboratory for Diagnosis, Treatment and Research of Colorectal CancerZhengzhouChina
| | - Xingguo Xiao
- Department of GastroenterologyZhengzhou Central Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
- Medical Key Laboratory for Diagnosis and Treatment of Colorectal Cancer in Henan ProvinceZhengzhouChina
- Zhengzhou Key Laboratory for Diagnosis, Treatment and Research of Colorectal CancerZhengzhouChina
| | - Jianping Ye
- Branch Center of Advanced Medical Research CenterZhengzhou Central Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
| | - Kunkun Li
- Department of GastroenterologyZhengzhou Central Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
- Medical Key Laboratory for Diagnosis and Treatment of Colorectal Cancer in Henan ProvinceZhengzhouChina
- Zhengzhou Key Laboratory for Diagnosis, Treatment and Research of Colorectal CancerZhengzhouChina
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15
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Gu Y, Zhang X, Li H, Wang R, Jin C, Wang J, Jin Z, Lu J, Ling C, Shao F, Zhang J, Shi L. Novel subsets of peripheral immune cells associated with promoting stroke recovery in mice. CNS Neurosci Ther 2024; 30:e14518. [PMID: 37905680 PMCID: PMC11017448 DOI: 10.1111/cns.14518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/03/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023] Open
Abstract
AIMS Peripheral immune cells infiltrating into the brain trigger neuroinflammation after an ischemic stroke. Partial immune cells reprogram their function for neural repair. Which immune cells promote ischemic brain recovery needs further identification. METHODS We performed single-cell transcriptomic profiling of CD45high immune cells isolated from the ischemic hemisphere at subacute (5 days) and chronic (14 days) stages after ischemic stroke. RESULTS A subset of phagocytic macrophages was associated with neuron projection regeneration and tissue remodeling. We also identified a unique type of T cells with highly expressed macrophage markers, including C1q, Apoe, Hexb, and Fcer1g, which showed high abilities in tissue remodeling, myelination regulation, wound healing, and anti-neuroinflammation. Moreover, natural killer cells decreased cytotoxicity and increased energy and metabolic function in the chronic stage after ischemic stroke. Two subgroups of neutrophils upregulated CCL signals to recruit peripheral immune cells and released CXCL2 to keep self-recruiting at the chronic stage. CONCLUSIONS We identified subsets of peripheral immune cells that may provide potential therapeutic targets for promoting poststroke recovery.
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Affiliation(s)
- Yichen Gu
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Xiaotao Zhang
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Huaming Li
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Rui Wang
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Chenghao Jin
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Junjie Wang
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Ziyang Jin
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Jianan Lu
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Chenhan Ling
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Fangjie Shao
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Jianmin Zhang
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
- Brain Research InstituteZhejiang UniversityHangzhouZhejiangChina
- Collaborative Innovation Center for Brain ScienceZhejiang UniversityHangzhouZhejiangChina
| | - Ligen Shi
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
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16
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Chen J, Peng L, Chen G, Chen Y, Zeng X, Zhang J, Zhang C, Shen H, Liao B, Luo D. Single-cell transcriptomics reveal the remodeling landscape of bladder in patients with obstruction-induced detrusor underactivity. MedComm (Beijing) 2024; 5:e490. [PMID: 38414668 PMCID: PMC10896249 DOI: 10.1002/mco2.490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
Detrusor underactivity (DUA) is a common and thorny problem in urology, which severely impairs patients' bladder function and quality of life. However, its underlying pathophysiological mechanism remains unclear. Hence, we sequenced 69,973 cells from five controls and nine patients with bladder dysfunction using single-cell RNA sequencing. Twelve distinct cell types were identified and they showed high cellular and functional heterogeneity among each group. Among them, fibroblasts, macrophages, and epithelial cells had the most intercellular communications. Their aberrant gene expressions and altered intercellular interactions were mainly involved in extracellular matrix organization, inflammation/immune regulation, and cellular injury. Further re-cluster analysis revealed an accumulation of the RBFOX1+ fibroblasts and RIPOR2+ macrophages in dysfunctional bladder wall, which mediated bladder remodeling through dysfunctional extracellular matrix organization and inflammation/immune reaction. Besides, the subtype of the epithelial cells was significantly altered. They underwent an intricate process including inflammation, damage, and repair during bladder remodeling. Overall, this work constructed the first single-cell atlas for obstruction-induced DUA, which could provide a valuable resource for deciphering the cellular heterogeneity and function changes in DUA, as well as potential strategies for bladder function improvement.
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Affiliation(s)
- Jiawei Chen
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Liao Peng
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Guo Chen
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology and Pelvic surgeryWest China School of Public Health and West China Fourth HospitalSichuan UniversitySichuanChina
| | - Yuanzhuo Chen
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Xiao Zeng
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Jie Zhang
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Chi Zhang
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Hong Shen
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Banghua Liao
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Deyi Luo
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
- Pelvic Floor Diseases CenterWest China Tianfu HospitalSichuan UniversitySichuanChina
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17
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Zhou H, He X, Huang J, Zhong Y, Zhang L, Ao X, Zhao H, Hu S, Li H, Huang J, Huang H, Liang H. Single-cell sequencing reveals the immune landscape of breast cancer patients with brain metastasis. Thorac Cancer 2024; 15:702-714. [PMID: 38316626 PMCID: PMC10961220 DOI: 10.1111/1759-7714.15243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Breast cancer has the highest incidence rate of cancer worldwide, and brain metastases (BrM) are among the most malignant cases. While some patients have benefited from immune checkpoint inhibitors (ICIs), the complex anatomical structure of the brain and the heterogeneity of metastatic tumors have made it difficult to characterize the tumor immune microenvironment (TME) of metastatic tumors. METHODS To address this, we used single-cell RNA sequencing (scRNA-seq) to analyze immune cells in the cerebrospinal fluid (CSF) of BrM patients with breast cancer, thereby providing a comprehensive view of the immune microenvironment landscape of BrM. RESULTS Based on canonical marker genes, we identified nine cell types, and further identified their subtypes through differential expression gene (DEG) analysis. We compared the changes in cells and functions in the immune microenvironment of patients with different prognoses. Our analysis revealed a series of genes that promote tumor immune function (CCR5, LYZ, IGKC, MS4A1, etc.) and inhibit tumor immune function (SCGB2A2, CD24, etc.). CONCLUSIONS The scRNA-seq in CSF provides a noninvasive method to describe the TME of breast cancer patients and guide immunotherapy.
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Grants
- 202102080096, HL Liang, 201904010331, JQ Huang Guangzhou S&T Project
- 2023A03J0430, HL Liang Guangzhou S&T City and University United Project
- 2022A1515012376, JQ Huang Project Natural Science Foundation of Guangdong Province
- 2021KTSCX091, HL Liang, 2020KTSCX105, JQ Huang Guangdong Provincial Bureau of Education Project
- 20191A011097, HL Liang Guangzhou Health S&T Project
- 202005, HS Li Clinical Key Specialty Project of Guangzhou Medical University
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Affiliation(s)
- Huaping Zhou
- Affiliated Cancer Hospital & Institute of Guangzhou Medical UniversityGuangzhouChina
| | - Xiang He
- Key Laboratory of Molecular Radiation Oncology Hunan ProvinceXiangya Hospital, Central South UniversityChangshaChina
| | - Jia Huang
- School of Health ManagementGuangzhou Medical UniversityGuangzhouChina
| | - Yumin Zhong
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of TechnologyGuangzhouChina
| | - Leyao Zhang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical UniversityGuangzhouChina
| | - Xiang Ao
- Affiliated Cancer Hospital & Institute of Guangzhou Medical UniversityGuangzhouChina
| | - Hailin Zhao
- Affiliated Cancer Hospital & Institute of Guangzhou Medical UniversityGuangzhouChina
| | - Su Hu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical UniversityGuangzhouChina
| | - Hongsheng Li
- Affiliated Cancer Hospital & Institute of Guangzhou Medical UniversityGuangzhouChina
| | - Jianqing Huang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical UniversityGuangzhouChina
- School of Health ManagementGuangzhou Medical UniversityGuangzhouChina
| | - Hongxin Huang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical UniversityGuangzhouChina
| | - Hongling Liang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical UniversityGuangzhouChina
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18
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Zhao X, Zhang X, Li F, Lu C. Exploration of the prognostic prediction value of the PANoptosis-based risk score and its correlation with tumor immunity in lung adenocarcinoma. J Gene Med 2024; 26:e3682. [PMID: 38508210 DOI: 10.1002/jgm.3682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/19/2024] [Accepted: 02/24/2024] [Indexed: 03/22/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is a common cancer with high mortality worldwide. PANoptosis is a novel inflammatory programmed cell death modality with the characteristics of pyroptosis, apoptosis and necroptosis. It is necessary to explore PANoptosis-related genes in LUAD patients and offer evidence for prognosis prediction and therapeutic strategies. Single-cell RNA sequencing data and RNA expression profiles of LUAD patients from The Cancer Genome Atlas and Gene Expression Omnibus databases are used to screen PANoptosis-related differential genes for the construction of a risk model. Fifteen PANoptosis-related markers with prognostic value were identified by Least Absolute Shrinkage and Selection Operator (LASSO)-Cox regression analysis. Kaplan-Meier analysis and receiver operating characteristic curve analysis further demonstrated the significant predictive capability. Immune infiltration, Single Nucleotide Variants (SNV) mutations, and clinical drug susceptibility were analyzed. In conclusion, a risk model of 15 PANoptosis-related genes has significant value in prognostic prediction for LUAD and has potential to direct clinical therapeutic strategies during the treatment.
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Affiliation(s)
- Xiaojian Zhao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Xuefeng Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Feng Li
- Department of Thoracic and Cardiac Surgery, Neijiang Traditional Chinese Medicine Hospital, Sichuan Province, People's Republic of China
| | - Caiping Lu
- Department of Endocrinology, Shijiazhuang people's Hospital, Shijiazhuang, Hebei Province, People's Republic of China
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19
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Tranter E, Frentsch M, Hütter-Krönke ML, Vuong GL, Busch D, Loyal L, Henze L, Rosnev S, Blau IW, Thiel A, Beule D, Bullinger L, Obermayer B, Na IK. Comparable CD8 + T-cell responses to SARS-CoV-2 vaccination in single-cell transcriptomics of recently allogeneic transplanted patients and healthy individuals. J Med Virol 2024; 96:e29539. [PMID: 38516755 DOI: 10.1002/jmv.29539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
Despite extensive research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination responses in healthy individuals, there is comparatively little known beyond antibody titers and T-cell responses in the vulnerable cohort of patients after allogeneic hematopoietic stem cell transplantation (ASCT). In this study, we assessed the serological response and performed longitudinal multimodal analyses including T-cell functionality and single-cell RNA sequencing combined with T cell receptor (TCR)/B cell receptor (BCR) profiling in the context of BNT162b2 vaccination in ASCT patients. In addition, these data were compared to publicly available data sets of healthy vaccinees. Protective antibody titers were achieved in 40% of patients. We identified a distorted B- and T-cell distribution, a reduced TCR diversity, and increased levels of exhaustion marker expression as possible causes for the poorer vaccine response rates in ASCT patients. Immunoglobulin heavy chain gene rearrangement after vaccination proved to be highly variable in ASCT patients. Changes in TCRα and TCRβ gene rearrangement after vaccination differed from patterns observed in healthy vaccinees. Crucially, ASCT patients elicited comparable proportions of SARS-CoV-2 vaccine-induced (VI) CD8+ T-cells, characterized by a distinct gene expression pattern that is associated with SARS-CoV-2 specificity in healthy individuals. Our study underlines the impaired immune system and thus the lower vaccine response rates in ASCT patients. However, since protective vaccine responses and VI CD8+ T-cells can be induced in part of ASCT patients, our data advocate early posttransplant vaccination due to the high risk of infection in this vulnerable group.
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Affiliation(s)
- Eva Tranter
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marco Frentsch
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center for Regenerative Therapies, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Marie Luise Hütter-Krönke
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Giang Lam Vuong
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - David Busch
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lucie Loyal
- Si-M/"Der Simulierte Mensch", A Science Framework of Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center of Immunomics-Regenerative Immunology and Aging, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Larissa Henze
- Si-M/"Der Simulierte Mensch", A Science Framework of Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center of Immunomics-Regenerative Immunology and Aging, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stanislav Rosnev
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Igor-Wolfgang Blau
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Thiel
- Si-M/"Der Simulierte Mensch", A Science Framework of Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center of Immunomics-Regenerative Immunology and Aging, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lars Bullinger
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
- ECRC Experimental and Clinical Research Center, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Il-Kang Na
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center for Regenerative Therapies, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
- Si-M/"Der Simulierte Mensch", A Science Framework of Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
- ECRC Experimental and Clinical Research Center, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
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20
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Shen J, Ma L, Hu J, Li Y. Single-Cell Atlas of Neonatal Mouse Hearts Reveals an Unexpected Cardiomyocyte. J Am Heart Assoc 2023; 12:e028287. [PMID: 38014657 PMCID: PMC10727353 DOI: 10.1161/jaha.122.028287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/05/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Single-cell RNA sequencing is widely used in cancer research and organ development because of its powerful ability to analyze cellular heterogeneity. However, its application in cardiomyocytes is dissatisfactory mainly because the cardiomyocytes are too large and fragile to withstand traditional single-cell approaches. METHODS AND RESULTS Through designing the isolation procedure of neonatal mouse cardiac cells, we provide detailed cellular atlases of the heart at single-cell resolution across 4 different stages after birth. We have obtained 10 000 cardiomyocytes; to our knowledge, this is the most extensive reference framework to date. Moreover, we have discovered unexpected erythrocyte-like cardiomyocyte-terminal cardiomyocytes, comprising more than a third of all cardiomyocytes. Only a few genes are highly expressed in these cardiomyocytes. They are highly differentiated cardiomyocytes that function as contraction pumps. In addition, we have identified 2 cardiomyocyte-like conducting cells, lending support to the theory that the sinoatrial node pacemaker cells are specialized cardiomyocytes. Notably, we provide an initial blueprint for comprehensive interactions between cardiomyocytes and other cardiac cells. CONCLUSIONS This mouse cardiac cell atlas improves our understanding of cardiomyocyte heterogeneity and provides a valuable reference in response to varying physiological conditions and diseases.
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Affiliation(s)
- Junwei Shen
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu HospitalShanghaiChina
- Clinical Research Center for Mental DisordersShanghai Pudong New Area Mental Health Center, School of Medicine, Tongji UniversityShanghaiChina
| | - Linlin Ma
- School of Medical TechnologyShanghai University of Medicine and Health Sciences, ShanghaiShanghaiChina
| | - Jing Hu
- Shanghai First Maternity and Infant HospitalTongji University School of MedicineShanghaiChina
| | - Yanfei Li
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu HospitalShanghaiChina
- School of Medical TechnologyShanghai University of Medicine and Health Sciences, ShanghaiShanghaiChina
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21
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Zhuang Q, Liu C, Hu Y, Liu Y, Lyu Y, Liao Y, Chen L, Yang H, Mao Y. Identification of RP11-770J1.4 as immune-related lncRNA regulating the CTXN1-cGAS-STING axis in histologically lower-grade glioma. MedComm (Beijing) 2023; 4:e458. [PMID: 38116063 PMCID: PMC10728758 DOI: 10.1002/mco2.458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
Human gliomas are lethal brain cancers. Emerging evidence revealed the regulatory role of long noncoding RNAs (lncRNAs) in tumors. Here, we performed a comprehensive analysis of the expression profiles of RNAs in histologically lower-grade glioma (LGG). Enrichment analysis revealed that glioma is influenced by immune-related signatures. Survival analysis further established the close correlation between network features and glioma prognosis. Subsequent experiments showed lncRNA RP11-770J1.4 regulates CTXN1 expression through hsa-miR-124-3p. Correlation analysis identified lncRNA RP11-770J1.4 was immune related, specifically involved in the cytosolic DNA sensing pathway. Downregulated lncRNA RP11-770J1.4 resulted in increased spontaneous gene expression of the cGAS-STING pathway. Single-cell RNA sequencing analysis, along with investigations in a glioblastoma stem cell model and patient sample analysis, demonstrated the predominant localization of CTXN1 within tumor cores rather than peripheral regions. Immunohistochemistry staining established a negative correlation between CTXN1 expression and infiltration of CD8+ T cells. In vivo, Ctxn1 knockdown in GL261 cells led to decreased tumor burden and improved survival while increasing infiltration of CD8+ T cells. These findings unveil novel insights into the lncRNA RP11-770J1.4-CTXN1 as a potential immune regulatory axis, highlighting its therapeutic implications for histologically LGGs.
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Affiliation(s)
- Qiyuan Zhuang
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityShanghaiChina
| | - Chaxian Liu
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityShanghaiChina
| | - Yihan Hu
- School of Life Sciences, Fudan UniversityShanghaiChina
| | - Ying Liu
- Department of PathologySchool of Basic Medical Sciences, Fudan UniversityShanghaiChina
| | - Yingying Lyu
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityShanghaiChina
| | - Yuheng Liao
- Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology LabInstitute of Biomedical Sciences, Shanghai Medical College, Fudan UniversityShanghaiChina
| | - Liang Chen
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityShanghaiChina
- National Center for Neurological DisordersHuashan Hospital, Fudan UniversityShanghaiChina
| | - Hui Yang
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityShanghaiChina
- National Center for Neurological DisordersHuashan Hospital, Fudan UniversityShanghaiChina
- Institute for Translational Brain ResearchShanghai Medical College, Fudan UniversityShanghaiChina
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan UniversityShanghaiChina
| | - Ying Mao
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityShanghaiChina
- School of Life Sciences, Fudan UniversityShanghaiChina
- National Center for Neurological DisordersHuashan Hospital, Fudan UniversityShanghaiChina
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan UniversityShanghaiChina
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22
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Yao Y, Chen Z, Wu Q, Lu Y, Zhou X, Zhu X. Single-cell RNA sequencing of retina revealed novel transcriptional landscape in high myopia and underlying cell-type-specific mechanisms. MedComm (Beijing) 2023; 4:e372. [PMID: 37746666 PMCID: PMC10511833 DOI: 10.1002/mco2.372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/16/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023] Open
Abstract
High myopia is a leading cause of blindness worldwide with increasing prevalence. Retina percepts visual information and triggers myopia development, but the underlying etiology is not fully understood because of cellular heterogeneity. In this study, single-cell RNA sequencing analysis was performed on retinas of mouse highly myopic and control eyes to dissect the involvement of each cell type during high myopia progression. For highly myopic photoreceptors, Hk2 inhibition underlying metabolic remodeling from aerobic glycolysis toward oxidative phosphorylation and excessive oxidative stress was identified. Importantly, a novel Apoe + rod subpopulation was specifically identified in highly myopic retina. In retinal neurons of highly myopic eyes, neurodegeneration was generally discovered, and the imbalanced ON/OFF signaling driven by cone-bipolar cells and the downregulated dopamine receptors in amacrine cells were among the most predominant findings, indicating the aberrant light processing in highly myopic eyes. Besides, microglia exhibited elevated expression of cytokines and TGF-β receptors, suggesting enhanced responses to inflammation and the growth-promoting states involved in high myopia progression. Furthermore, cell-cell communication network revealed attenuated neuronal interactions and increased glial/vascular interactions in highly myopic retinas. In conclusion, this study outlines the transcriptional landscape of highly myopic retina, providing novel insights into high myopia development and prevention.
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Affiliation(s)
- Yunqian Yao
- Eye Institute and Department of OphthalmologyEye & ENT HospitalFudan UniversityShanghaiChina
- Key Laboratory of MyopiaChinese Academy of Medical SciencesNational Health Center Key Laboratory of Myopia (Fudan University)ShanghaiChina
- Shanghai Research Center of Ophthalmology and OptometryShanghaiChina
| | - Zhenhua Chen
- State Key Laboratory of Molecular Development BiologyChinese Academy of SciencesInstitute of Genetics and Developmental BiologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qingfeng Wu
- State Key Laboratory of Molecular Development BiologyChinese Academy of SciencesInstitute of Genetics and Developmental BiologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Center for Excellence in Brain Science and Intelligence TechnologyChinese Academy of SciencesBeijingChina
- Chinese Institute for Brain ResearchBeijingChina
- Beijing Children's HospitalCapital Medical UniversityBeijingChina
| | - Yi Lu
- Eye Institute and Department of OphthalmologyEye & ENT HospitalFudan UniversityShanghaiChina
- Key Laboratory of MyopiaChinese Academy of Medical SciencesNational Health Center Key Laboratory of Myopia (Fudan University)ShanghaiChina
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghaiChina
- State Key Laboratory of Medical NeurobiologyFudan UniversityShanghaiChina
| | - Xingtao Zhou
- Eye Institute and Department of OphthalmologyEye & ENT HospitalFudan UniversityShanghaiChina
- Key Laboratory of MyopiaChinese Academy of Medical SciencesNational Health Center Key Laboratory of Myopia (Fudan University)ShanghaiChina
- Shanghai Research Center of Ophthalmology and OptometryShanghaiChina
| | - Xiangjia Zhu
- Eye Institute and Department of OphthalmologyEye & ENT HospitalFudan UniversityShanghaiChina
- Key Laboratory of MyopiaChinese Academy of Medical SciencesNational Health Center Key Laboratory of Myopia (Fudan University)ShanghaiChina
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghaiChina
- State Key Laboratory of Medical NeurobiologyFudan UniversityShanghaiChina
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23
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Kang H, Sun H, Yang Y, Tuong ZK, Shu M, Wei Y, Zhang Y, Yu D, Tao Y. Autoimmune uveitis in Behçet's disease and Vogt-Koyanagi-Harada disease differ in tissue immune infiltration and T cell clonality. Clin Transl Immunology 2023; 12:e1461. [PMID: 37720629 PMCID: PMC10503407 DOI: 10.1002/cti2.1461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/16/2023] [Accepted: 08/04/2023] [Indexed: 09/19/2023] Open
Abstract
Objectives Non-infectious uveitis is often secondary to systemic autoimmune diseases, with Behçet's disease (BD) and Vogt-Koyanagi-Harada disease (VKHD) as the two most common causes. Uveitis in BD and VKHD can show similar clinical manifestations, but the underlying immunopathogenesis remains unclear. Methods To understand immune landscapes in inflammatory eye tissues, we performed single-cell RNA paired with T cell receptor (TCR) sequencing of immune cell infiltrates in aqueous humour from six patients with BD (N = 3) and VKHD (N = 3) uveitis patients. Results Although T cells strongly infiltrated in both types of autoimmune uveitis, myeloid cells only significantly presented in BD uveitis but not in VKHD uveitis. Conversely, VKHD uveitis but not BD uveitis showed an overwhelming dominance by CD4+ T cells (> 80%) within the T cell population due to expansion of CD4+ T cell clusters with effector memory (Tem) phenotypes. Correspondingly, VKHD uveitis demonstrated a selective expansion of CD4+ T cell clones which were enriched in pro-inflammatory Granzyme H+ CD4+ Tem cluster and showed TCR and Th1 pathway activation. In contrast, BD uveitis showed a preferential expansion of CD8+ T cell clones in pro-inflammatory Granzyme H+ CD8+ Tem cluster, and pathway activation for cytoskeleton remodelling, cellular adhesion and cytotoxicity. Conclusion Single-cell analyses of ocular tissues reveal distinct landscapes of immune cell infiltration and T-cell clonal expansions between VKHD and BD uveitis. Preferential involvements of pro-inflammatory CD4+ Th1 cells in VKHD and cytotoxic CD8+ T cells in BD suggest a difference in disease immunopathogenesis and can guide precision disease management.
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Affiliation(s)
- Hao Kang
- Department of Ophthalmology, Beijing Chaoyang HospitalCapital Medical UniversityBeijingChina
| | - Hongjian Sun
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- Shandong Artificial Intelligence InstituteQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Yang Yang
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- Shandong Artificial Intelligence InstituteQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Zewen K Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Children's Health Research Centre, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Minglei Shu
- Shandong Artificial Intelligence InstituteQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Yunbo Wei
- School of Pharmaceutical Sciences, Laboratory of Immunology for Environment and Health, Shandong Analysis and Test CenterQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Yu Zhang
- School of Pharmaceutical Sciences, Laboratory of Immunology for Environment and Health, Shandong Analysis and Test CenterQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Di Yu
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- Ian Frazer Centre for Children's Immunotherapy Research, Children's Health Research Centre, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Yong Tao
- Department of Ophthalmology, Beijing Chaoyang HospitalCapital Medical UniversityBeijingChina
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Su D, Jiao Z, Li S, Yue L, Li C, Deng M, Hu L, Dai L, Gao B, Wang J, Zhang H, Xiao H, Chen F, Yang H, Zhou D. Spatiotemporal single-cell transcriptomic profiling reveals inflammatory cell states in a mouse model of diffuse alveolar damage. Exploration (Beijing) 2023; 3:20220171. [PMID: 37933384 PMCID: PMC10624389 DOI: 10.1002/exp.20220171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/10/2023] [Indexed: 11/08/2023]
Abstract
Diffuse alveolar damage (DAD) triggers neutrophilic inflammation in damaged tissues of the lung, but little is known about the distinct roles of tissue structural cells in modulating the recruitment of neutrophils to damaged areas. Here, by combining single-cell and spatial transcriptomics, and using quantitative assays, we systematically analyze inflammatory cell states in a mouse model of DAD-induced neutrophilic inflammation after aerosolized intratracheal inoculation with ricin toxin. We show that homeostatic resident fibroblasts switch to a hyper-inflammatory state, and the subsequent occurrence of a CXCL1-CXCR2 chemokine axis between activated fibroblasts (AFib) as the signal sender and neutrophils as the signal receiver triggers further neutrophil recruitment. We also identify an anatomically localized inflamed niche (characterized by a close-knit spatial intercellular contact between recruited neutrophils and AFib) in peribronchial regions that facilitate the pulmonary inflammation outbreak. Our findings identify an intricate interplay between hyper-inflammatory fibroblasts and neutrophils and provide an overarching profile of dynamically changing inflammatory microenvironments during DAD progression.
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Affiliation(s)
- Duo Su
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- Reproductive Genetics CenterBethune International Peace HospitalShijiazhuangChina
| | - Zhouguang Jiao
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- State Key Laboratory of Biochemical Engineering, Institute of Process EngineeringChinese Academy of SciencesBeijingChina
| | - Sha Li
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
| | - Liya Yue
- Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina
| | - Cuidan Li
- Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina
| | - Mengyun Deng
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Lingfei Hu
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Lupeng Dai
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
| | - Bo Gao
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
| | - Jinglin Wang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Hanchen Zhang
- Beijing National Laboratory for Molecular Science, State Key Laboratory of Polymer Physical and ChemistryInstitute of Chemistry, Chinese Academy of ScienceBeijingChina
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Science, State Key Laboratory of Polymer Physical and ChemistryInstitute of Chemistry, Chinese Academy of ScienceBeijingChina
| | - Fei Chen
- Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina
| | - Huiying Yang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
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25
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Suzuki T. Overview of single-cell RNA sequencing analysis and its application to spermatogenesis research. Reprod Med Biol 2023; 22:e12502. [PMID: 36726594 PMCID: PMC9884325 DOI: 10.1002/rmb2.12502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 12/18/2022] [Accepted: 01/10/2023] [Indexed: 01/30/2023] Open
Abstract
Background Single-cell transcriptomics allows parallel analysis of multiple cell types in tissues. Because testes comprise somatic cells and germ cells at various stages of spermatogenesis, single-cell RNA sequencing is a powerful tool for investigating the complex process of spermatogenesis. However, single-cell RNA sequencing analysis needs extensive knowledge of experimental technologies and bioinformatics, making it difficult for many, particularly experimental biologists and clinicians, to use it. Methods Aiming to make single-cell RNA sequencing analysis familiar, this review article presents an overview of experimental and computational methods for single-cell RNA sequencing analysis with a history of transcriptomics. In addition, combining the PubMed search and manual curation, this review also provides a summary of recent novel insights into human and mouse spermatogenesis obtained using single-cell RNA sequencing analyses. Main Findings Single-cell RNA sequencing identified mesenchymal cells and type II innate lymphoid cells as novel testicular cell types in the adult mouse testes, as well as detailed subtypes of germ cells. This review outlines recent discoveries into germ cell development and subtypes, somatic cell development, and cell-cell interactions. Conclusion The findings on spermatogenesis obtained using single-cell RNA sequencing may contribute to a deeper understanding of spermatogenesis and provide new directions for male fertility therapy.
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Affiliation(s)
- Takahiro Suzuki
- RIKEN Center for Integrated Medical Science (IMS)Yokohama CityKanagawaJapan
- Graduate School of Medical Life ScienceYokohama City UniversityYokohama CityKanagawaJapan
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26
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Zhuang L, Wang Y, Chen Z, Li Z, Wang Z, Jia K, Zhao J, Zhang H, Xie H, Lu L, Chen K, Chen L, Fukuda K, Sano M, Zhang R, Liu J, Yan X. Global Characteristics and Dynamics of Single Immune Cells After Myocardial Infarction. J Am Heart Assoc 2022; 11:e027228. [PMID: 36515244 PMCID: PMC9798793 DOI: 10.1161/jaha.122.027228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background Myocardial infarction (MI) is characterized by the emergence of dead or dying cardiomyocytes and excessive immune cell infiltration after coronary vessel occlusion. However, the complex transcriptional profile, pathways, cellular interactome, and transcriptional regulators of immune subpopulations after MI remain elusive. Methods and Results Here, male C57BL/6 mice were subjected to MI surgery and monitored for 1 day and 7 days, or sham surgery for 7 days, then cardiac CD45-positive immune cells were collected for single-cell RNA sequencing to determine immune heterogeneity. A total of 30 135 CD45+ immune cells were partitioned into macrophages, monocytes, neutrophils, dendritic cells, and T or B cells for further analysis. We showed that macrophages enriched for Olr1 and differentially expressed Gpnmb represented 2 crucial ischemia-associated macrophages with distinct proinflammatory and prophagocytic capabilities. In contrast to the proinflammatory subset of macrophages enriched for Olr1, Gpnmb-positive macrophages exhibited higher phagocytosis and fatty acid oxidation preference, which could be abolished by etomoxir treatment. In addition to macrophages, MI triggered prompt recruitment of neutrophils into murine hearts, which constituted the sequential cell-fate from naïve S100a4-positive, to activated Sell-high, to aging Icam1-high neutrophils. In silico tools predicted that the excessively expanded neutrophils at 1 day were attributed to chemokine C-C motif ligand/chemokine C-X-C motif ligand pathways, whereas CD80/inducible T-cell costimulator (ICOS) signaling was responsible for the immunosuppressive response at day 7 after MI. Finally, the Fos/AP-1 (activator protein 1) regulon was identified as the critical regulator of proinflammatory responses, which was significantly activated in patients with dilated cardiomyopathy and ischemic cardiomyopathy. We showed the enriched Fos/AP-1 target gene loci in genome-wide association study signals for coronary artery diseases and MI. Targeting Fos/AP-1 with the selective inhibitor T5224 blunted leukocyte infiltration and alleviated cardiac dysfunction in the preclinical murine MI model. Conclusions Taken together, this single-cell RNA sequencing data lay the groundwork for the understanding of immune cell heterogeneity and dynamics in murine ischemic hearts. Moreover, Fos/AP-1 inhibition mitigates inflammatory responses and cardiac dysfunction, which might provide potential therapeutic benefits for heart failure intervention after MI.
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Affiliation(s)
- Lingfang Zhuang
- Department of Cardiovascular Medicine, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiPR China,Institute of Cardiovascular DiseasesShanghai Jiao Tong University School of MedicineShanghaiPR China
| | - Yaqiong Wang
- Department of Nephrology, Zhongshan HospitalFudan UniversityShanghaiPR China
| | - Zhaoyang Chen
- Cardiology department, Union HospitalFujian Medical UniversityFuzhouPR China
| | - Zhigang Li
- Department of Cardiovascular Medicine, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiPR China,Institute of Cardiovascular DiseasesShanghai Jiao Tong University School of MedicineShanghaiPR China
| | - Ziyang Wang
- Department of Cardiovascular Medicine, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiPR China,Institute of Cardiovascular DiseasesShanghai Jiao Tong University School of MedicineShanghaiPR China
| | - Kangni Jia
- Department of Cardiovascular Medicine, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiPR China,Institute of Cardiovascular DiseasesShanghai Jiao Tong University School of MedicineShanghaiPR China
| | - Jiaxin Zhao
- Department of Cardiovascular Medicine, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiPR China,Institute of Cardiovascular DiseasesShanghai Jiao Tong University School of MedicineShanghaiPR China
| | - Hang Zhang
- Department of Cardiovascular Medicine, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiPR China,Institute of Cardiovascular DiseasesShanghai Jiao Tong University School of MedicineShanghaiPR China
| | - Hongyang Xie
- Department of Cardiovascular Medicine, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiPR China,Institute of Cardiovascular DiseasesShanghai Jiao Tong University School of MedicineShanghaiPR China
| | - Lin Lu
- Department of Cardiovascular Medicine, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiPR China,Institute of Cardiovascular DiseasesShanghai Jiao Tong University School of MedicineShanghaiPR China
| | - Kang Chen
- Department of Cardiovascular Medicine, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiPR China
| | - Lei Chen
- Shanghai Institute of ImmunologyShanghai Jiao Tong University School of MedicineShanghaiPR China
| | - Keiichi Fukuda
- Department of CardiologyKeio University School of MedicineTokyoJapan
| | - Motoaki Sano
- Department of CardiologyKeio University School of MedicineTokyoJapan
| | - Ruiyan Zhang
- Department of Cardiovascular Medicine, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiPR China,Institute of Cardiovascular DiseasesShanghai Jiao Tong University School of MedicineShanghaiPR China
| | - Jun Liu
- Department of Cardiovascular Surgery, Shanghai East HospitalTongji University School of MedicineShanghaiPR China
| | - Xiaoxiang Yan
- Department of Cardiovascular Medicine, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiPR China,Institute of Cardiovascular DiseasesShanghai Jiao Tong University School of MedicineShanghaiPR China
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Hu X, Wu M, Ma T, Zhang Y, Zou C, Wang R, Zhang Y, Ren Y, Li Q, Liu H, Li H, Wang T, Sun X, Yang Y, Tang M, Li X, Li J, Gao X, Li T, Zhou X. Single-cell transcriptomics reveals distinct cell response between acute and chronic pulmonary infection of Pseudomonas aeruginosa. MedComm (Beijing) 2022; 3:e193. [PMID: 36514779 PMCID: PMC9732387 DOI: 10.1002/mco2.193] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/31/2022] [Accepted: 11/09/2022] [Indexed: 12/14/2022] Open
Abstract
Knowledge of the changes in the immune microenvironment during pulmonary bacterial acute and chronic infections is limited. The dissection of immune system may provide a basis for effective therapeutic strategies against bacterial infection. Here, we describe a single immune cell atlas of mouse lungs after acute and chronic Pseudomonas aeruginosa infection using single-cell transcriptomics, multiplex immunohistochemistry, and flow cytometry. Our single-cell transcriptomic analysis revealed large-scale comprehensive changes in immune cell composition and high variation in cell-cell interactions after acute and chronic P. aeruginosa infection. Bacterial infection reprograms the genetic architecture of immune cell populations. We identified specific immune cell types, including Cxcl2+ B cells and interstitial macrophages, in response to acute and chronic infection, such as their proportions, distribution, and functional status. Importantly, the patterns of immune cell response are drastically different between acute and chronic infection models. The distinct molecular signatures highlight the importance of the highly dynamic cell-cell interaction process in different pathological conditions, which has not been completely revealed previously. These findings provide a comprehensive and unbiased immune cellular landscape for respiratory pathogenesis in mice, enabling further understanding of immunologic mechanisms in infection and inflammatory diseases.
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Affiliation(s)
- Xueli Hu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Mingbo Wu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Teng Ma
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yige Zhang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Chaoyu Zou
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Ruihuan Wang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yongxin Zhang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yuan Ren
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina,State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Qianqian Li
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Huan Liu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Heyue Li
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Taolin Wang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Xiaolong Sun
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Miao Tang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Xuefeng Li
- Department of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Jing Li
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Xiang Gao
- Department of Neurosurgery and Institute of NeurosurgeryState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalWest China Medical SchoolSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Taiwen Li
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Xikun Zhou
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
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Zhang J, Zhang H, Zhang L, Li D, Qi M, Zhang L, Yu H, Wang D, Jiang G, Wang X, Zhu X, Zhang P. Single-Cell Transcriptome Identifies Drug-Resistance Signature and Immunosuppressive Microenvironment in Metastatic Small Cell Lung Cancer. Adv Genet (Hoboken) 2022; 3:2100060. [PMID: 36618022 PMCID: PMC9744506 DOI: 10.1002/ggn2.202100060] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 01/11/2023]
Abstract
Small cell lung cancer (SCLC) is a deadly neuroendocrine malignancy with high metastasis. However, the heterogeneity of metastatic SCLC at the single-cell level remains elusive. The single-cell transcriptome of a total of 24 081 cells in metastatic lymph node samples from seven SCLC patients via endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is examined. Genomic alterations are also examined by whole exome sequencing (WES) and the immune infiltration between SCLC and non-SCLC (NSCLC) is compared using public single-cell RNA sequencing (scRNA-seq) data. It is identified that malignant cells in lymph-node metastatic SCLC have inter-patient and intra-tumor heterogeneity characterized by distinct ASCL1 and NEUROD1 expression patterns. High expression of genes such as FZD8 in WNT pathway is associated with drug resistance in malignant cells. Compared to NSCLC, SCLC harbors a unique immunosuppressive tumor microenvironment. Malignant cells exhibit a pattern of attenuated MHC-I antigen presentation-related gene expression, which is associated with relatively low proportion of exhausted T cells. Natural killer (NK) cells display impaired antitumor function with high expression of TGFBR2. This work characterizes the inter-patient and intra-tumor heterogeneity of metastatic SCLC and uncovers the exhaustion signatures in NK cells, which may pave the way for novel treatments for SCLC including immune checkpoint blockade-based immunotherapy.
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Affiliation(s)
- Jing Zhang
- Department of Thoracic SurgeryShanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghai200433China
| | - Haiping Zhang
- Department of Medical OncologyShanghai Pulmonary HospitalSchool of MedicineTongji UniversityShanghai200433China
| | - Lele Zhang
- Department of Thoracic SurgeryShanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghai200433China,Central LaboratoryShanghai Pulmonary HospitalSchool of MedicineTongji UniversityShanghai200433China
| | - Dianke Li
- Department of Thoracic SurgeryShanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghai200433China
| | - Mengfan Qi
- Department of Thoracic SurgeryShanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghai200433China
| | - Liping Zhang
- Department of PathologyShanghai Pulmonary HospitalSchool of MedicineTongji UniversityShanghai200433China
| | - Huansha Yu
- Department of Thoracic SurgeryShanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghai200433China
| | - Di Wang
- Department of Thoracic SurgeryShanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghai200433China
| | - Gening Jiang
- Department of Thoracic SurgeryShanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghai200433China
| | - Xujun Wang
- SJTU‐Yale Joint Center for BiostatisticsSchool of Life Science and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Xianmin Zhu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Peng Zhang
- Department of Thoracic SurgeryShanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghai200433China
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Ding Y, Ouyang Z, Zhang C, Zhu Y, Xu Q, Sun H, Qu J, Sun Y. Tyrosine phosphatase SHP2 exacerbates psoriasis-like skin inflammation in mice via ERK5-dependent NETosis. MedComm (Beijing) 2022; 3:e120. [PMID: 35281792 PMCID: PMC8906448 DOI: 10.1002/mco2.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/29/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
Psoriasis is a chronic inflammatory skin disease, often accompanied by increased infiltration of immune cells, especially neutrophils. However, the detailed mechanism of the neutrophil function in psoriasis progression remains unclear. Here, we found that both Src homology-2 domain-containing protein tyrosine phosphatase-2 (SHP2) and neutrophils were highly correlated to developing psoriasis by single-cell ribonucleic acid (RNA) sequencing and experiment verification. The deficiency of SHP2 in neutrophils significantly alleviated psoriasis-like phenotype in an imiquimod-induced murine model. Interestingly, high levels of neutrophil extracellular traps (NETs) were produced in the inflamed lesions of psoriatic patients. In addition, imiquimod-induced psoriasis-like symptoms were remarkably ameliorated in peptidyl arginine deiminase 4 (PAD4) knockout mice, which cannot form NETs. Mechanistically, RNA-seq analysis revealed that SHP2 promoted the formation of NETs in neutrophils via the ERK5 pathway. Functionally, this mechanism resulted in the infiltration of pro-inflammatory cytokines such as TNF-α, IL-1β, IL-6, IL-17A, and CXCL-15, which enhances the inflammatory response in skin lesions and reinforces the cross-talk between neutrophils and keratinocytes, ultimately aggravating psoriasis. Our findings uncover a role for SHP2 in NET release and subsequent cell death known as NETosis in the progression of psoriasis and suggest that SHP2 may be a promising therapeutic target for psoriasis.
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Affiliation(s)
- Yan Ding
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life SciencesNanjing UniversityNanjingChina
| | - Zijun Ouyang
- Institute of Marine Biomedicine, School of Food and DrugShenzhen PolytechnicShenzhenGuangdongChina
| | - Chenyang Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life SciencesNanjing UniversityNanjingChina
| | - Yuyu Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life SciencesNanjing UniversityNanjingChina
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life SciencesNanjing UniversityNanjingChina
| | - Haiyan Sun
- Institute of Marine Biomedicine, School of Food and DrugShenzhen PolytechnicShenzhenGuangdongChina
| | - Jiao Qu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life SciencesNanjing UniversityNanjingChina
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life SciencesNanjing UniversityNanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC)Nanjing UniversityNanjingChina
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30
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Yang Y, Yang M, Shi D, Chen K, Zhao J, He S, Bai Y, Shen P, Ni H. Single-cell RNA Seq reveals cellular landscape-specific characteristics and potential etiologies for adolescent idiopathic scoliosis. JOR Spine 2021; 4:e1184. [PMID: 35005449 PMCID: PMC8717101 DOI: 10.1002/jsp2.1184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUNDS Abnormal vertebral growth and development have been found in adolescent idiopathic scoliosis (AIS) patients, and the proliferation and differentiation of bone development-related cells play important roles in its pathogenesis. However, a comprehensive single-cell-level differentiation roadmap in AIS has not been achieved. METHODS The present study compared the single-cell level cellular landscapes of spinal cancellous bone tissues between AIS patients and healthy subjects using high throughput single-cell RNA sequencing (scRNA-seq), which covers multiple cellular lineages including osteoblast, chondrocyte, osteoclast and related immunocytes. We constructed the differentiation trajectories of bone development-related cell lineages through pseudotime analysis, and the intercellular-communication networks between bone development-related cells and immunocytes were further developed. RESULTS A total of 11 distinct cell clusters were identified according to the genome-wide transcriptome profiles. t-Distributed stochastic neighbor embedding (t-SNE) analysis showed that mesenchymal stem cells (MSC) were classified into three subtypes: MSC-LOXL2, MSC-IGFBP5, and MSC-GJA1. Gene ontology (GO) analysis showed that MSC-GJA1 might possess greater osteoblast differentiation potential than the others. MSC-IGFBP5 was the specific MSC subtype observed only in AIS. There were two distinct gene expression clusters: OB-DPT and OB-OLFML2B, and the counts of osteoblasts derived from AIS was significantly less than that of non-AIS subjects. In AIS patients, MSC-IGFBP5 failed to differentiate into osteoblasts and exhibited negative regulation of cell proliferation and enhanced cell death. CPC-PCNA was found to be the specific chondrocyte progenitor cell (CPC) subtype observed only in AIS patients. The cell counts of OC-BIRC3 in AIS were less than those in controls. Pseudotime analysis suggested two possible distinct osteoclast differentiation patterns in AIS and control subjects. Monocytes in AIS mainly differentiated into OC-CRISP3. CONCLUSIONS Our single-cell analysis first revealed differences existed in the cellular states between AIS patients and healthy subjects and found the differentiation disruption of specific MSC and CPC clusters in AIS. Cell communication analysis provided the possible pathogenesis of osteoblast and chondrocyte differentiation dysfunction in AIS.
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Affiliation(s)
- Yilin Yang
- Department of Orthopaedic SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Mingyuan Yang
- Department of OrthopaedicsChanghai Hospital, Navy Medical UniversityShanghaiChina
| | - Dongliang Shi
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center)Tongji University School of MedicineShanghaiChina
| | - Kai Chen
- Department of OrthopaedicsChanghai Hospital, Navy Medical UniversityShanghaiChina
| | - Jian Zhao
- Department of OrthopaedicsChanghai Hospital, Navy Medical UniversityShanghaiChina
| | - Shisheng He
- Department of Orthopaedics, Shanghai 10th People's HospitalTongji UniversityShanghaiChina
| | - Yushu Bai
- Department of OrthopaedicsChanghai Hospital, Navy Medical UniversityShanghaiChina
| | - Pinquan Shen
- Department of Pediatric Orthopaedics, Xinhua HospitalShanghai Jiaotong UniversityShanghaiChina
| | - Haijian Ni
- Department of Orthopaedics, Shanghai 10th People's HospitalTongji UniversityShanghaiChina
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31
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Ni G, Yang X, Li J, Wu X, Liu Y, Li H, Chen S, Fogarty CE, Frazer IH, Chen G, Liu X, Wang T. Intratumoral injection of caerin 1.1 and 1.9 peptides increases the efficacy of vaccinated TC-1 tumor-bearing mice with PD-1 blockade by modulating macrophage heterogeneity and the activation of CD8 + T cells in the tumor microenvironment. Clin Transl Immunology 2021; 10:e1335. [PMID: 34429969 PMCID: PMC8369845 DOI: 10.1002/cti2.1335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 06/25/2021] [Accepted: 08/05/2021] [Indexed: 12/11/2022] Open
Abstract
Objectives Developing a vaccine formula that alters the tumor-infiltrating lymphocytes to be more immune active against a tumor is key to the improvement of clinical responses to immunotherapy. Here, we demonstrate that, in conjunction with E7 antigen-specific immunotherapy, and IL-10 and PD-1 blockade, intratumoral administration of caerin 1.1/1.9 peptides improves TC-1 tumor microenvironment (TME) to be more immune active than injection of a control peptide. Methods We compared the survival time of vaccinated TC-1 tumor-bearing mice with PD-1 and IL-10 blockade, in combination with a further injection of caerin 1.1/1.9 or control peptides. The tumor-infiltrating haematopoietic cells were examined by flow cytometry. Single-cell transcriptomics and proteomics were used to quantify changes in cellular activity across different cell types within the TME. Results The injection of caerin 1.1/1.9 increased the efficacy of vaccinated TC-1 tumor-bearing mice with anti-PD-1 treatment and largely expanded the populations of macrophages and NK cells with higher immune activation level, while reducing immunosuppressive macrophages. More activated CD8+ T cells were induced with higher populations of memory and effector-memory CD8+ T subsets. Computational integration of the proteome with the single-cell transcriptome supported activation of Stat1-modulated apoptosis and significant reduction in immune-suppressive B-cell function following caerin 1.1 and 1.9 treatment. Conclusions Caerin 1.1/1.9-containing treatment results in improved antitumor responses. Harnessing the novel candidate genes preferentially enriched in the immune active cell populations may allow further exploration of distinct macrophages, T cells and their functions in TC-1 tumors.
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Affiliation(s)
- Guoying Ni
- Cancer Research Institute First People's Hospital of Foshan Foshan Guangdong China.,Genecology Research Centre University of the Sunshine Coast Maroochydore DC QLD Australia.,The First Affiliated Hospital/Clinical Medical School Guangdong Pharmaceutical University Guangzhou China
| | - Xiaodan Yang
- The First Affiliated Hospital/Clinical Medical School Guangdong Pharmaceutical University Guangzhou China
| | - Junjie Li
- The First Affiliated Hospital/Clinical Medical School Guangdong Pharmaceutical University Guangzhou China
| | - Xiaolian Wu
- Cancer Research Institute First People's Hospital of Foshan Foshan Guangdong China
| | - Ying Liu
- Cancer Research Institute First People's Hospital of Foshan Foshan Guangdong China
| | - Hejie Li
- Genecology Research Centre University of the Sunshine Coast Maroochydore DC QLD Australia
| | - Shu Chen
- Cancer Research Institute First People's Hospital of Foshan Foshan Guangdong China
| | - Conor E Fogarty
- Genecology Research Centre University of the Sunshine Coast Maroochydore DC QLD Australia
| | - Ian H Frazer
- Faculty of Medicine University of Queensland Diamantina Institute Translational Research Institute The University of Queensland Woolloongabba QLD Australia
| | - Guoqiang Chen
- Cancer Research Institute First People's Hospital of Foshan Foshan Guangdong China
| | - Xiaosong Liu
- Cancer Research Institute First People's Hospital of Foshan Foshan Guangdong China.,Genecology Research Centre University of the Sunshine Coast Maroochydore DC QLD Australia.,The First Affiliated Hospital/Clinical Medical School Guangdong Pharmaceutical University Guangzhou China
| | - Tianfang Wang
- Genecology Research Centre University of the Sunshine Coast Maroochydore DC QLD Australia
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32
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Alquicira‐Hernandez J, Powell JE, Phan TG. No evidence that plasmablasts transdifferentiate into developing neutrophils in severe COVID-19 disease. Clin Transl Immunology 2021; 10:e1308. [PMID: 34221402 PMCID: PMC8245277 DOI: 10.1002/cti2.1308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/07/2021] [Accepted: 06/11/2021] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES A recent single-cell RNA sequencing study by Wilk et al. suggested that plasmablasts can transdifferentiate into 'developing neutrophils' in patients with severe COVID-19 disease. We explore the evidence for this. METHODS We downloaded the original data and code used by the authors in their study to replicate their findings and explore the possibility that regressing out variables may have led the authors to overfit their data. RESULTS The lineage relationship between plasmablasts and developing neutrophils breaks down when key features are not regressed out, and the data are not overfitted during the analysis. CONCLUSION Plasmablasts do not transdifferentiate into developing neutrophils. The single-cell RNA sequencing is a powerful technique for biological discovery and hypothesis generation. However, caution should be exercised in the bioinformatic analysis and interpretation of the data and findings cross-validated by orthogonal techniques.
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Affiliation(s)
- José Alquicira‐Hernandez
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- Institute for Molecular BioscienceUniversity of QueenslandSt LuciaQLDAustralia
| | - Joseph E Powell
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- UNSW Cellular Genomics Futures InstituteUniversity of New South WalesSydneyNSWAustralia
| | - Tri Giang Phan
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- St Vincent’s Clinical SchoolFaculty of MedicineUNSW SydneyDarlinghurstNSWAustralia
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33
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Calcagno DM, Zhang C, Toomu A, Huang K, Ninh VK, Miyamoto S, Aguirre AD, Fu Z, Heller Brown J, King KR. SiglecF(HI) Marks Late-Stage Neutrophils of the Infarcted Heart: A Single-Cell Transcriptomic Analysis of Neutrophil Diversification. J Am Heart Assoc 2021; 10:e019019. [PMID: 33525909 PMCID: PMC7955351 DOI: 10.1161/jaha.120.019019] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background Neutrophils are thought to be short‐lived first responders to tissue injuries such as myocardial infarction (MI), but little is known about their diversification or dynamics. Methods and Results We permanently ligated the left anterior descending coronary arteries of mice and performed single‐cell RNA sequencing and analysis of >28 000 neutrophil transcriptomes isolated from the heart, peripheral blood, and bone marrow of mice on days 1 to 4 after MI or at steady‐state. Unsupervised clustering of cardiac neutrophils revealed 5 major subsets, 3 of which originated in the bone marrow, including a late‐emerging granulocyte expressing SiglecF, a marker classically used to define eosinophils. SiglecFHI neutrophils represented ≈25% of neutrophils on day 1 and grew to account for >50% of neutrophils by day 4 post‐MI. Validation studies using quantitative polymerase chain reaction of fluorescent‐activated cell sorter sorted Ly6G+SiglecFHI and Ly6G+SiglecFLO neutrophils confirmed the distinct nature of these populations. To confirm that the cells were neutrophils rather than eosinophils, we infarcted GATA‐deficient mice (∆dblGATA) and observed similar quantities of infiltrating Ly6G+SiglecFHI cells despite marked reductions of conventional eosinophils. In contrast to other neutrophil subsets, Ly6G+SiglecFHI neutrophils expressed high levels of Myc‐regulated genes, which are associated with longevity and are consistent with the persistence of this population on day 4 after MI. Conclusions Overall, our data provide a spatial and temporal atlas of neutrophil specialization in response to MI and reveal a dynamic proinflammatory cardiac Ly6G+SigF+(Myc+NFϰB+) neutrophil that has been overlooked because of negative selection.
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Affiliation(s)
- David M Calcagno
- Department of Bioengineering Jacobs School of Engineering University of California San Diego La Jolla CA
| | - Claire Zhang
- Department of Bioengineering Jacobs School of Engineering University of California San Diego La Jolla CA
| | - Avinash Toomu
- Department of Bioengineering Jacobs School of Engineering University of California San Diego La Jolla CA
| | - Kenneth Huang
- Division of Cardiology and Cardiovascular Institute Department of Medicine University of California San Diego La Jolla CA
| | - Van K Ninh
- Department of Pharmacology University of California San Diego La Jolla CA
| | - Shigeki Miyamoto
- Department of Pharmacology University of California San Diego La Jolla CA
| | - Aaron D Aguirre
- Cardiology Division Center for Systems Biology Wellman Center for Photomedicine Massachusetts General Hospital Boston MA.,Harvard Medical School Boston MA
| | - Zhenxing Fu
- Division of Cardiology and Cardiovascular Institute Department of Medicine University of California San Diego La Jolla CA
| | - Joan Heller Brown
- Department of Pharmacology University of California San Diego La Jolla CA
| | - Kevin R King
- Department of Bioengineering Jacobs School of Engineering University of California San Diego La Jolla CA.,Division of Cardiology and Cardiovascular Institute Department of Medicine University of California San Diego La Jolla CA
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34
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Sagar, Pokrovskii M, Herman JS, Naik S, Sock E, Zeis P, Lausch U, Wegner M, Tanriver Y, Littman DR, Grün D. Deciphering the regulatory landscape of fetal and adult γδ T-cell development at single-cell resolution. EMBO J 2020; 39:e104159. [PMID: 32627520 PMCID: PMC7327493 DOI: 10.15252/embj.2019104159] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/15/2020] [Accepted: 04/22/2020] [Indexed: 01/15/2023] Open
Abstract
γδ T cells with distinct properties develop in the embryonic and adult thymus and have been identified as critical players in a broad range of infections, antitumor surveillance, autoimmune diseases, and tissue homeostasis. Despite their potential value for immunotherapy, differentiation of γδ T cells in the thymus is incompletely understood. Here, we establish a high-resolution map of γδ T-cell differentiation from the fetal and adult thymus using single-cell RNA sequencing. We reveal novel sub-types of immature and mature γδ T cells and identify an unpolarized thymic population which is expanded in the blood and lymph nodes. Our detailed comparative analysis reveals remarkable similarities between the gene networks active during fetal and adult γδ T-cell differentiation. By performing a combined single-cell analysis of Sox13, Maf, and Rorc knockout mice, we demonstrate sequential activation of these factors during IL-17-producing γδ T-cell (γδT17) differentiation. These findings substantially expand our understanding of γδ T-cell ontogeny in fetal and adult life. Our experimental and computational strategy provides a blueprint for comparing immune cell differentiation across developmental stages.
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Affiliation(s)
- Sagar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Pokrovskii
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Josip S Herman
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Shruti Naik
- Department of Pathology and Ronald O. Perelman Department of Dermatology, NYU School of Medicine, New York, NY, USA
| | - Elisabeth Sock
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Patrice Zeis
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Ute Lausch
- Institute of Medical Microbiology and Hygiene, University Medical Center Freiburg, Freiburg, Germany
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Yakup Tanriver
- Institute of Medical Microbiology and Hygiene, University Medical Center Freiburg, Freiburg, Germany.,Department of Internal Medicine IV, University Medical Center Freiburg, Freiburg, Germany
| | - Dan R Littman
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,The Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Dominic Grün
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,CIBSS-Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
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35
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Chen Z, Lu Y, Zhang K, Xiao Y, Lu J, Fan R. Multiplexed, Sequential Secretion Analysis of the Same Single Cells Reveals Distinct Effector Response Dynamics Dependent on the Initial Basal State. Adv Sci (Weinh) 2019; 6:1801361. [PMID: 31065513 PMCID: PMC6498135 DOI: 10.1002/advs.201801361] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/03/2019] [Indexed: 05/10/2023]
Abstract
The effector response of immune cells dictated by an array of secreted proteins is a highly dynamic process, requiring sequential measurement of all relevant proteins from single cells. Herein, a microchip-based, 10-plexed, sequential secretion assay on the same single cells and at the scale of ≈5000 single cells measured simultaneously over 4 time points are shown. It is applied to investigating the time course of single human macrophage response to toll-like receptor 4 (TLR4) ligand lipopolysaccharide (LPS) and reveals four distinct activation modes for different proteins in single cells. Protein secretion dynamics classifies the cells into two major activation states dependent on the basal state of each cell. Single-cell RNA sequencing performed on the same samples at the matched time points further demonstrates the existence of two major activation states at the transcriptional level, which are enriched for translation versus inflammatory programs, respectively. These results show a cell-intrinsic heterogeneous response in a phenotypically homogeneous cell population. This work demonstrates the longitudinal tracking of protein secretion signature in thousands of single cells at multiple time points, providing dynamic information to better understand how individual immune cells react to pathogenic challenges over time and how they together constitute a population response.
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Affiliation(s)
- Zhuo Chen
- Department of Biomedical EngineeringYale UniversityNew HavenCT06520USA
| | - Yao Lu
- Department of Biomedical EngineeringYale UniversityNew HavenCT06520USA
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023China
| | - Kerou Zhang
- Department of Biomedical EngineeringYale UniversityNew HavenCT06520USA
| | - Yang Xiao
- Department of Biomedical EngineeringYale UniversityNew HavenCT06520USA
| | - Jun Lu
- Department of GeneticsYale School of MedicineNew HavenCT06520USA
- Yale Stem Cell CenterNew HavenCT06520USA
| | - Rong Fan
- Department of Biomedical EngineeringYale UniversityNew HavenCT06520USA
- Department of GeneticsYale School of MedicineNew HavenCT06520USA
- Yale Stem Cell CenterNew HavenCT06520USA
- Yale Cancer CenterNew HavenCT06520USA
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36
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Alberti-Servera L, von Muenchow L, Tsapogas P, Capoferri G, Eschbach K, Beisel C, Ceredig R, Ivanek R, Rolink A. Single-cell RNA sequencing reveals developmental heterogeneity among early lymphoid progenitors. EMBO J 2017; 36:3619-3633. [PMID: 29030486 DOI: 10.15252/embj.201797105] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/11/2017] [Accepted: 09/13/2017] [Indexed: 12/21/2022] Open
Abstract
Single-cell RNA sequencing is a powerful technology for assessing heterogeneity within defined cell populations. Here, we describe the heterogeneity of a B220+CD117intCD19-NK1.1- uncommitted hematopoietic progenitor having combined lymphoid and myeloid potential. Phenotypic and functional assays revealed four subpopulations within the progenitor with distinct lineage developmental potentials. Among them, the Ly6D+SiglecH-CD11c- fraction was lymphoid-restricted exhibiting strong B-cell potential, whereas the Ly6D-SiglecH-CD11c- fraction showed mixed lympho-myeloid potential. Single-cell RNA sequencing of these subsets revealed that the latter population comprised a mixture of cells with distinct lymphoid and myeloid transcriptional signatures and identified a subgroup as the potential precursor of Ly6D+SiglecH-CD11c- Subsequent functional assays confirmed that B220+CD117intCD19-NK1.1- single cells are, with rare exceptions, not bipotent for lymphoid and myeloid lineages. A B-cell priming gradient was observed within the Ly6D+SiglecH-CD11c- subset and we propose a herein newly identified subgroup as the direct precursor of the first B-cell committed stage. Therefore, the apparent multipotency of B220+CD117intCD19-NK1.1- progenitors results from underlying heterogeneity at the single-cell level and highlights the validity of single-cell transcriptomics for resolving cellular heterogeneity and developmental relationships among hematopoietic progenitors.
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Affiliation(s)
- Llucia Alberti-Servera
- Developmental and Molecular Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Lilly von Muenchow
- Developmental and Molecular Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Panagiotis Tsapogas
- Developmental and Molecular Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Giuseppina Capoferri
- Developmental and Molecular Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Katja Eschbach
- Genomics Facility, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christian Beisel
- Genomics Facility, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Rhodri Ceredig
- Discipline of Physiology, College of Medicine & Nursing Health Science National University of Ireland, Galway, Ireland
| | - Robert Ivanek
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Antonius Rolink
- Developmental and Molecular Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
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37
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Abstract
Alternative transcription start sites (TSSs) have been extensively studied genome‐wide for many cell types and have been shown to be important during development and to regulate transcript abundance between cell types. Likewise, single‐cell gene expression has been extensively studied for many cell types. However, how single cells use TSSs has not yet been examined. In particular, it is unknown whether alternative TSSs are independently expressed, or whether they are co‐activated or even mutually exclusive in single cells. Here, we use a previously published single‐cell RNA‐seq dataset, comprising thousands of cells, to study alternative TSS usage. We find that alternative TSS usage is a regulated process, and the correlation between two TSSs expressed in single cells of the same cell type is surprisingly high. Our findings indicate that TSSs generally are regulated by common factors rather than being independently regulated or stochastically expressed.
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Affiliation(s)
- Kasper Karlsson
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter Lönnerberg
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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