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Liu Q, Wang Z, Jiang Y, Shao F, Ma Y, Zhu M, Luo Q, Bi Y, Cao L, Peng L, Zhou J, Zhao Z, Deng X, He TC, Wang S. Single-cell landscape analysis reveals distinct regression trajectories and novel prognostic biomarkers in primary neuroblastoma. Genes Dis 2022; 9:1624-1638. [PMID: 36157484 PMCID: PMC9485279 DOI: 10.1016/j.gendis.2021.12.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/07/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
Neuroblastoma (NB), which is the most common pediatric extracranial solid tumor, varies widely in its clinical presentation and outcome. NB has a unique ability to spontaneously differentiate and regress, suggesting a potential direction for therapeutic intervention. However, the underlying mechanisms of regression remain largely unknown, and more reliable prognostic biomarkers are needed for predicting trajectories for NB. We performed scRNA-seq analysis on 17 NB clinical samples and three peritumoral adrenal tissues. Primary NB displayed varied cell constitution, even among tumors of the same pathological subtype. Copy number variation patterns suggested that neuroendocrine cells represent the malignant cell type. Based on the differential expression of sets of related marker genes, a subgroup of neuroendocrine cells was identified and projected to differentiate into a subcluster of benign fibroblasts with highly expressed CCL2 and ZFP36, supporting a progressive pathway of spontaneous NB regression. We also identified prognostic markers (STMN2, TUBA1A, PAGE5, and ETV1) by evaluating intra-tumoral heterogeneity. Lastly, we determined that ITGB1 in M2-like macrophages was associated with favorable prognosis and may serve as a potential diagnostic marker and therapeutic target. In conclusion, our findings reveal novel mechanisms underlying regression and potential prognostic markers and therapeutic targets of NB.
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Affiliation(s)
- Qingqing Liu
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University; National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, PR China
| | - Zhenni Wang
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University; National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, PR China
| | - Yan Jiang
- Singleron Biotechnologies Co., Ltd, Nanjing, Jiangsu 211800, PR China
| | - Fengling Shao
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University; National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, PR China
| | - Yue Ma
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University; National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, PR China
| | - Mingzhao Zhu
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Qing Luo
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University; National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, PR China
| | - Yang Bi
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University; National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, PR China
| | - Lijian Cao
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University; National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, PR China
| | - Liang Peng
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University; National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, PR China
| | - Jianwu Zhou
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University; National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, PR China
| | - Zhenzhen Zhao
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University; National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, PR China
| | - Xiaobin Deng
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University; National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, PR China
| | - Tong-Chuan He
- Molecular and Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Shan Wang
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University; National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, PR China
- Corresponding author. Department of Pediatric Surgical Oncology, The Children's Hospital of Chongqing Medical University, Chongqing 400014, PR China.
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Monti M, Fiorentino J, Milanetti E, Gosti G, Tartaglia GG. Prediction of Time Series Gene Expression and Structural Analysis of Gene Regulatory Networks Using Recurrent Neural Networks. ENTROPY (BASEL, SWITZERLAND) 2022; 24:141. [PMID: 35205437 PMCID: PMC8871363 DOI: 10.3390/e24020141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 11/17/2022]
Abstract
Methods for time series prediction and classification of gene regulatory networks (GRNs) from gene expression data have been treated separately so far. The recent emergence of attention-based recurrent neural network (RNN) models boosted the interpretability of RNN parameters, making them appealing for the understanding of gene interactions. In this work, we generated synthetic time series gene expression data from a range of archetypal GRNs and we relied on a dual attention RNN to predict the gene temporal dynamics. We show that the prediction is extremely accurate for GRNs with different architectures. Next, we focused on the attention mechanism of the RNN and, using tools from graph theory, we found that its graph properties allow one to hierarchically distinguish different architectures of the GRN. We show that the GRN responded differently to the addition of noise in the prediction by the RNN and we related the noise response to the analysis of the attention mechanism. In conclusion, this work provides a way to understand and exploit the attention mechanism of RNNs and it paves the way to RNN-based methods for time series prediction and inference of GRNs from gene expression data.
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Affiliation(s)
- Michele Monti
- RNA System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Jonathan Fiorentino
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; (J.F.); (E.M.); (G.G.)
| | - Edoardo Milanetti
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; (J.F.); (E.M.); (G.G.)
- Department of Physics, Sapienza University of Rome, 00185 Rome, Italy
| | - Giorgio Gosti
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; (J.F.); (E.M.); (G.G.)
- Department of Physics, Sapienza University of Rome, 00185 Rome, Italy
| | - Gian Gaetano Tartaglia
- RNA System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; (J.F.); (E.M.); (G.G.)
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
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53
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Li Z, Lin F, Zhong CH, Wang S, Xue X, Shao Y. Single-Cell Sequencing to Unveil the Mystery of Embryonic Development. Adv Biol (Weinh) 2021; 6:e2101151. [PMID: 34939365 DOI: 10.1002/adbi.202101151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/05/2021] [Indexed: 12/21/2022]
Abstract
Embryonic development is a fundamental physiological process that can provide tremendous insights into stem cell biology and regenerative medicine. In this process, cell fate decision is highly heterogeneous and dynamic, and investigations at the single-cell level can greatly facilitate the understanding of the molecular roadmap of embryonic development. Rapid advances in the technology of single-cell sequencing offer a perfectly useful tool to fulfill this purpose. Despite its great promise, single-cell sequencing is highly interdisciplinary, and successful applications in specific biological contexts require a general understanding of its diversity as well as the advantage versus limitations for each of its variants. Here, the technological principles of single-cell sequencing are consolidated and its applications in the study of embryonic development are summarized. First, the technology basics are presented and the available tools for each step including cell isolation, library construction, sequencing, and data analysis are discussed. Then, the works that employed single-cell sequencing are reviewed to investigate the specific processes of embryonic development, including preimplantation, peri-implantation, gastrulation, and organogenesis. Further, insights are provided on existing challenges and future research directions.
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Affiliation(s)
- Zida Li
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518060, China.,Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Feng Lin
- Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing, 100871, China
| | - Chu-Han Zhong
- International Center for Applied Mechanics, State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Shue Wang
- Department of Chemistry, Chemical, and Biomedical Engineering, Tagliatela College of Engineering, University of New Haven, West Haven, CT, 06561, USA
| | - Xufeng Xue
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yue Shao
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, China
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54
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Zhang JL, Li YH, Wang LL, Liu HQ, Lu SY, Liu Y, Li K, Liu B, Li SY, Shao FM, Wang K, Sheng N, Li R, Cui JJ, Sun PC, Ma CX, Zhu B, Wang Z, Wan YH, Yu SS, Che Y, Wang CY, Wang C, Zhang Q, Zhao LM, Peng XZ, Cheng Z, Chang JB, Jiang JD. Azvudine is a thymus-homing anti-SARS-CoV-2 drug effective in treating COVID-19 patients. Signal Transduct Target Ther 2021; 6:414. [PMID: 34873151 PMCID: PMC8646019 DOI: 10.1038/s41392-021-00835-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/31/2021] [Accepted: 11/14/2021] [Indexed: 01/08/2023] Open
Abstract
Azvudine (FNC) is a nucleoside analog that inhibits HIV-1 RNA-dependent RNA polymerase (RdRp). Recently, we discovered FNC an agent against SARS-CoV-2, and have taken it into Phase III trial for COVID-19 patients. FNC monophosphate analog inhibited SARS-CoV-2 and HCoV-OC43 coronavirus with an EC50 between 1.2 and 4.3 μM, depending on viruses or cells, and selective index (SI) in 15-83 range. Oral administration of FNC in rats revealed a substantial thymus-homing feature, with FNC triphosphate (the active form) concentrated in the thymus and peripheral blood mononuclear cells (PBMC). Treating SARS-CoV-2 infected rhesus macaques with FNC (0.07 mg/kg, qd, orally) reduced viral load, recuperated the thymus, improved lymphocyte profiles, alleviated inflammation and organ damage, and lessened ground-glass opacities in chest X-ray. Single-cell sequencing suggested the promotion of thymus function by FNC. A randomized, single-arm clinical trial of FNC on compassionate use (n = 31) showed that oral FNC (5 mg, qd) cured all COVID-19 patients, with 100% viral ribonucleic acid negative conversion in 3.29 ± 2.22 days (range: 1-9 days) and 100% hospital discharge rate in 9.00 ± 4.93 days (range: 2-25 days). The side-effect of FNC is minor and transient dizziness and nausea in 16.12% (5/31) patients. Thus, FNC might cure COVID-19 through its anti-SARS-CoV-2 activity concentrated in the thymus, followed by promoted immunity.
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Affiliation(s)
- Jin-Lan Zhang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China
| | - Yu-Huan Li
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China
| | - Lu-Lu Wang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China ,grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China
| | - Hong-Qi Liu
- grid.506261.60000 0001 0706 7839Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, 650031 Yunnan China
| | - Shuai-Yao Lu
- grid.506261.60000 0001 0706 7839Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, 650031 Yunnan China
| | - Yong Liu
- Genuine Biotech. Inc., Pingdingshan, 467000 Henan China
| | - Ke Li
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China
| | - Bin Liu
- grid.413247.70000 0004 1808 0969Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Wuhan, 430071 Hubei China
| | - Su-Yun Li
- grid.477982.70000 0004 7641 2271The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000 Henan China
| | - Feng-Min Shao
- grid.414011.10000 0004 1808 090XDepartment of Internal Medicine, Henan Provincial Peoples Hospital, Zhengzhou, 450003 Henan China
| | - Kun Wang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China
| | - Ning Sheng
- grid.506261.60000 0001 0706 7839State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China
| | - Rui Li
- grid.506261.60000 0001 0706 7839State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China
| | - Jin-Jin Cui
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China
| | - Pei-Chun Sun
- grid.414011.10000 0004 1808 090XDepartment of Internal Medicine, Henan Provincial Peoples Hospital, Zhengzhou, 450003 Henan China
| | - Chun-Xia Ma
- grid.506261.60000 0001 0706 7839Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, 650031 Yunnan China
| | - Bo Zhu
- grid.462338.80000 0004 0605 6769Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007 Henan China
| | - Zhe Wang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China
| | - Yuan-Hao Wan
- Genuine Biotech. Inc., Pingdingshan, 467000 Henan China
| | - Shi-Shan Yu
- grid.506261.60000 0001 0706 7839State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China
| | - Yongsheng Che
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China
| | | | - Chen Wang
- grid.506261.60000 0001 0706 7839National Clinical Research Center for Respiratory Diseases, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100005 China
| | - Qiangqian Zhang
- grid.207374.50000 0001 2189 3846School of Chemistry, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Li-Min Zhao
- grid.506261.60000 0001 0706 7839State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050 China
| | - Xiao-Zhong Peng
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, 650031, Yunnan, China.
| | - Zhenshun Cheng
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Wuhan, 430071, Hubei, China.
| | - Jun-Biao Chang
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, Henan, China. .,School of Chemistry, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Jian-Dong Jiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China. .,Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
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Tao Z, Jiang Y, Xia S. Regulation of thymic T regulatory cell differentiation by TECs in health and disease. Scand J Immunol 2021; 94:e13094. [PMID: 34780092 DOI: 10.1111/sji.13094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/22/2022]
Abstract
The thymus produces self-limiting and self-tolerant T cells through the interaction between thymocytes and thymus epithelial cells (TECs), thereby generating central immune tolerance. The TECs are composed of cortical and medullary thymic epithelial cells, which regulate the positive and negative selection of T cells, respectively. During the process of negative selection, thymocytes with self-reactive ability are deleted or differentiated into regulatory T cells (Tregs). Tregs are a subset of suppressor T cells that are important for maintaining immune homeostasis. The differentiation and development of Tregs depend on the development of TECs and other underlying molecular mechanisms. Tregs regulated by thymic epithelial cells are closely related to human health and are significant in autoimmune diseases, thymoma and pregnancy. In this review, we summarize the current molecular and transcriptional regulatory mechanisms by which TECs affect the development and function of thymic Tregs. We also review the pathophysiological models of thymic epithelial cells regulating thymic Tregs in human diseases and specific physiological conditions.
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Affiliation(s)
- Zehua Tao
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yalan Jiang
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Sheng Xia
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
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56
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Single-cell RNA-seq highlights a specific carcinoembryonic cluster in ovarian cancer. Cell Death Dis 2021; 12:1082. [PMID: 34775482 PMCID: PMC8590695 DOI: 10.1038/s41419-021-04358-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/12/2021] [Accepted: 10/20/2021] [Indexed: 12/23/2022]
Abstract
Expounding the heterogeneity for ovarian cancer (OC) with the cognition in developmental biology might be helpful to search for robust prognostic markers and effective treatments. In the present study, we employed single-cell RNA-seq with ovarian cancers, normal ovary, and embryo tissue to explore their heterogeneity. Then the differentiation process of clusters was explored; the pivotal cluster and markers were identified. Furthermore, the consensus clustering algorithm was used to explore the different clinical phenotypes in OC. At last, a prognostic model was construct and used to assess the prognosis for OCs. As a result, eight diverse clusters were identified, and the similarity existed in some clusters between embryo and tumours based on their gene expression. Meaningfully, a subtype of malignant epithelial cluster, PEG10+ EME, was associated with poor survival and was an intermediate stage of embryo to tumour. PEG10 was a CSC marker and might influence CSC self-renewal and promote cisplatin resistance via NOTCH pathway. Utilising specific gene profiles of PEG10+ EME based on public data sets, four phenotypes with different survival and clinical response to anti-PD-1/PD-L1 immunotherapy were identified. These insights allowed for the investigation of single-cell transcriptome of OCs and embryo, which advanced our current understanding of OC pathogenesis and resulted in promising therapeutic strategies.
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57
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Haunerdinger V, Moccia MD, Opitz L, Vavassori S, Dave H, Hauri-Hohl MM. Novel Combination of Surface Markers for the Reliable and Comprehensive Identification of Human Thymic Epithelial Cells by Flow Cytometry: Quantitation and Transcriptional Characterization of Thymic Stroma in a Pediatric Cohort. Front Immunol 2021; 12:740047. [PMID: 34659232 PMCID: PMC8514761 DOI: 10.3389/fimmu.2021.740047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Thymic epithelial cells (TECs) are essential in supporting the development of mature T cells from hematopoietic progenitor cells and facilitate their lineage-commitment, proliferation, T-cell receptor repertoire selection and maturation. While animal model systems have greatly aided in elucidating the contribution of stromal cells to these intricate processes, human tissue has been more difficult to study, partly due to a lack of suitable surface markers comprehensively defining human TECs. Here, we conducted a flow cytometry based surface marker screen to reliably identify and quantify human TECs and delineate medullary from cortical subsets. These findings were validated by transcriptomic and histologic means. The combination of EpCAM, podoplanin (pdpn), CD49f and CD200 comprehensively identified human TECs and not only allowed their reliable distinction in medullary and cortical subsets but also their detailed quantitation. Transcriptomic profiling of each subset in comparison to fibroblasts and endothelial cells confirmed the identity of the different stromal cell subsets sorted according to the proposed strategy. Our dataset not only demonstrated transcriptional similarities between TEC and cells of mesenchymal origin but furthermore revealed a subset-specific distribution of a specific set of extracellular matrix-related genes in TECs. This indicates that TECs significantly contribute to the distinct compartmentalization - and thus function - of the human thymus. We applied the strategy to quantify TEC subsets in 31 immunologically healthy children, which revealed sex-specific differences of TEC composition early in life. As the distribution of mature CD4- or CD8-single-positive thymocytes was correspondingly altered, the composition of the thymic epithelial compartment may directly impact on the CD4-CD8-lineage choice of thymocytes. We prove that the plain, reliable strategy proposed here to comprehensively identify human TEC subpopulations by flow cytometry based on surface marker expression is suitable to determine their frequency and phenotype in health and disease and allows sorting of live cells for downstream analysis. Its use reaches from a reliable diagnostic tool for thymic biopsies to improved phenotypic characterization of thymic grafts intended for therapeutic use.
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Affiliation(s)
- Veronika Haunerdinger
- Division of Stem Cell Transplantation and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Maria Domenica Moccia
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Stefano Vavassori
- Division of Immunology and Children's Research Center, University Children's Hospital, Pediatric Immunology, Zurich, Switzerland
| | - Hitendu Dave
- Division of Congenital Cardiovascular Surgery, University Children's Hospital and Children's Research Centre, Zurich, Switzerland
| | - Mathias M Hauri-Hohl
- Division of Stem Cell Transplantation and Children's Research Center, University Children's Hospital, Zurich, Switzerland
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58
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Liu C, Gong Y, Zhang H, Yang H, Zeng Y, Bian Z, Xin Q, Bai Z, Zhang M, He J, Yan J, Zhou J, Li Z, Ni Y, Wen A, Lan Y, Hu H, Liu B. Delineating spatiotemporal and hierarchical development of human fetal innate lymphoid cells. Cell Res 2021; 31:1106-1122. [PMID: 34239074 PMCID: PMC8486758 DOI: 10.1038/s41422-021-00529-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023] Open
Abstract
Whereas the critical roles of innate lymphoid cells (ILCs) in adult are increasingly appreciated, their developmental hierarchy in early human fetus remains largely elusive. In this study, we sorted human hematopoietic stem/progenitor cells, lymphoid progenitors, putative ILC progenitor/precursors and mature ILCs in the fetal hematopoietic, lymphoid and non-lymphoid tissues, from 8 to 12 post-conception weeks, for single-cell RNA-sequencing, followed by computational analysis and functional validation at bulk and single-cell levels. We delineated the early phase of ILC lineage commitment from hematopoietic stem/progenitor cells, which mainly occurred in fetal liver and intestine. We further unveiled interleukin-3 receptor as a surface marker for the lymphoid progenitors in fetal liver with T, B, ILC and myeloid potentials, while IL-3RA- lymphoid progenitors were predominantly B-lineage committed. Notably, we determined the heterogeneity and tissue distribution of each ILC subpopulation, revealing the proliferating characteristics shared by the precursors of each ILC subtype. Additionally, a novel unconventional ILC2 subpopulation (CRTH2- CCR9+ ILC2) was identified in fetal thymus. Taken together, our study illuminates the precise cellular and molecular features underlying the stepwise formation of human fetal ILC hierarchy with remarkable spatiotemporal heterogeneity.
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Affiliation(s)
- Chen Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Yandong Gong
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Han Zhang
- Department of Blood Transfusion, Daping Hospital, Army Military Medical University, Chongqing, China
| | - Hua Yang
- Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Yang Zeng
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhilei Bian
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Qian Xin
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Zhijie Bai
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Man Zhang
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Jian He
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Jing Yan
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Jie Zhou
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zongcheng Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanli Ni
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Aiqing Wen
- Department of Blood Transfusion, Daping Hospital, Army Military Medical University, Chongqing, China.
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
| | - Hongbo Hu
- Center for Immunology and Hematology, the State Key Laboratory of Biotherapy, West China Hospital, Sichuan University. Collaboration and Innovation Center for Biotherapy, Chengdu, China.
| | - Bing Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China.
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
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59
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Duah M, Li L, Shen J, Lan Q, Pan B, Xu K. Thymus Degeneration and Regeneration. Front Immunol 2021; 12:706244. [PMID: 34539637 PMCID: PMC8442952 DOI: 10.3389/fimmu.2021.706244] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/16/2021] [Indexed: 01/08/2023] Open
Abstract
The immune system’s ability to resist the invasion of foreign pathogens and the tolerance to self-antigens are primarily centered on the efficient functions of the various subsets of T lymphocytes. As the primary organ of thymopoiesis, the thymus performs a crucial role in generating a self-tolerant but diverse repertoire of T cell receptors and peripheral T cell pool, with the capacity to recognize a wide variety of antigens and for the surveillance of malignancies. However, cells in the thymus are fragile and sensitive to changes in the external environment and acute insults such as infections, chemo- and radiation-therapy, resulting in thymic injury and degeneration. Though the thymus has the capacity to self-regenerate, it is often insufficient to reconstitute an intact thymic function. Thymic dysfunction leads to an increased risk of opportunistic infections, tumor relapse, autoimmunity, and adverse clinical outcome. Thus, exploiting the mechanism of thymic regeneration would provide new therapeutic options for these settings. This review summarizes the thymus’s development, factors causing thymic injury, and the strategies for improving thymus regeneration.
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Affiliation(s)
- Maxwell Duah
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Lingling Li
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Jingyi Shen
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Qiu Lan
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Bin Pan
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Kailin Xu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
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60
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Xu Y, Zhang J, Hu Y, Li X, Sun L, Peng Y, Sun Y, Liu B, Bian Z, Rong Z. Single-cell transcriptome analysis reveals the dynamics of human immune cells during early fetal skin development. Cell Rep 2021; 36:109524. [PMID: 34380039 DOI: 10.1016/j.celrep.2021.109524] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/12/2021] [Accepted: 07/22/2021] [Indexed: 01/12/2023] Open
Abstract
The immune system of skin develops in stages in mice. However, the developmental dynamics of immune cells in human skin remains elusive. Here, we perform transcriptome profiling of CD45+ hematopoietic cells in human fetal skin at an estimated gestational age of 10-17 weeks by single-cell RNA sequencing. A total of 13 immune cell types are identified. Skin macrophages show dynamic heterogeneity over the course of skin development. A major shift in lymphoid cell developmental states occurs from the first to the second trimester that implies an in situ differentiation process. Gene expression analysis reveals a typical developmental program in immune cells in accordance with their functional maturation, possibly involving metabolic reprogramming. Finally, we identify transcription factors (TFs) that potentially regulate cellular transitions by comparing TFs and TF target gene networks. These findings provide detailed insight into how the immune system of the human skin is established during development.
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Affiliation(s)
- Yingping Xu
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China.
| | - Jun Zhang
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yongfei Hu
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Xuefei Li
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Lihua Sun
- Development of Gynaecology and Obstetrics, Nanhai Hospital, Southern Medical University, Guangzhou 528200, China
| | - Yu Peng
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yuzhe Sun
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Zhilei Bian
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, China.
| | - Zhili Rong
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China; Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China.
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61
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Li Y, Zeng W, Li T, Guo Y, Zheng G, He X, Bai L, Ding G, Jin L, Liu X. Integrative Single-Cell Transcriptomic Analysis of Human Fetal Thymocyte Development. Front Genet 2021; 12:679616. [PMID: 34276782 PMCID: PMC8284395 DOI: 10.3389/fgene.2021.679616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/03/2021] [Indexed: 11/23/2022] Open
Abstract
Intrathymic differentiation of T lymphocytes begins as early as intrauterine stage, yet the T cell lineage decisions of human fetal thymocytes at different gestational ages are not currently understood. Here, we performed integrative single-cell analyses of thymocytes across gestational ages. We identified conserved candidates underlying the selection of T cell receptor (TCR) lineages in different human fetal stages. The trajectory of early thymocyte commitment during fetal growth was also characterized. Comparisons with mouse data revealed conserved and species-specific transcriptional dynamics of thymocyte proliferation, apoptosis and selection. Genome-wide association study (GWAS) data associated with multiple autoimmune disorders were analyzed to characterize susceptibility genes that are highly expressed at specific stages during fetal thymocyte development. In summary, our integrative map describes previously underappreciated aspects of human thymocyte development, and provides a comprehensive reference for understanding T cell lymphopoiesis in a self-tolerant and functional adaptive immune system.
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Affiliation(s)
- Yuchen Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Weihong Zeng
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Tong Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yanyan Guo
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Guangyong Zheng
- Bio-Med Big Data Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoying He
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Lilian Bai
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Guolian Ding
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Li Jin
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Xinmei Liu
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
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62
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Ding J, Cardoso AA, Yoshimoto M, Kobayashi M. The Earliest T-Precursors in the Mouse Embryo Are Susceptible to Leukemic Transformation. Front Cell Dev Biol 2021; 9:634151. [PMID: 33996794 PMCID: PMC8117020 DOI: 10.3389/fcell.2021.634151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common malignancy in pediatric patients. About 10–15% of pediatric ALL belong to T-cell ALL (T-ALL), which is characterized by aggressive expansion of immature T-lymphoblasts and is categorized as high-risk leukemia. Leukemia initiating cells represent a reservoir that is responsible for the initiation and propagation of leukemia. Its perinatal origin has been suggested in some childhood acute B-lymphoblastic and myeloblastic leukemias. Therefore, we hypothesized that child T-ALL initiating cells also exist during the perinatal period. In this study, T-ALL potential of the hematopoietic precursors was found in the para-aortic splanchnopleura (P-Sp) region, but not in the extraembryonic yolk sac (YS) of the mouse embryo at embryonic day 9.5. We overexpressed the Notch intracellular domain (NICD) in the P-Sp and YS cells and transplanted them into lethally irradiated mice. NICD-overexpressing P-Sp cells rapidly developed T-ALL while YS cells failed to display leukemia propagation despite successful NICD induction. These results suggest a possible role of fetal-derived T-cell precursors as leukemia-initiating cells.
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Affiliation(s)
- Jixin Ding
- Department of Medicine, Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Angelo A Cardoso
- Department of Medicine, Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States.,Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States
| | - Momoko Yoshimoto
- Department of Pediatrics Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Stem Cell and Regenerative Medicine, Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Michihiro Kobayashi
- Department of Pediatrics Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Stem Cell and Regenerative Medicine, Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
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63
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Tan L, Fichtner AS, Bruni E, Odak I, Sandrock I, Bubke A, Borchers A, Schultze-Florey C, Koenecke C, Förster R, Jarek M, von Kaisenberg C, Schulz A, Chu X, Zhang B, Li Y, Panzer U, Krebs CF, Ravens S, Prinz I. A fetal wave of human type 3 effector γδ cells with restricted TCR diversity persists into adulthood. Sci Immunol 2021; 6:6/58/eabf0125. [PMID: 33893173 DOI: 10.1126/sciimmunol.abf0125] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/17/2020] [Accepted: 03/24/2021] [Indexed: 12/14/2022]
Abstract
Accumulating evidence suggests that the mouse embryonic thymus produces distinct waves of innate effector γδ T cells. However, it is unclear whether this process occurs similarly in humans and whether it comprises a dedicated subset of innate-like type 3 effector γδ T cells. Here, we present a protocol for high-throughput sequencing of TRG and TRD pairs that comprise the clonal γδTCR. In combination with single-cell RNA sequencing, multiparameter flow cytometry, and TCR sequencing, we reveal a high heterogeneity of γδ T cells sorted from neonatal and adult blood that correlated with TCR usage. Immature γδ T cell clusters displayed mixed and diverse TCRs, but effector cell types segregated according to the expression of either highly expanded individual Vδ1+ TCRs or moderately expanded semi-invariant Vγ9Vδ2+ TCRs. The Vγ9Vδ2+ T cells shared expression of genes that mark innate-like T cells, including ZBTB16 (encoding PLZF), KLRB1, and KLRC1, but consisted of distinct clusters with unrelated Vγ9Vδ2+ TCR clones characterized either by TBX21, FCGR3A, and cytotoxicity-associated gene expression (type 1) or by CCR6, RORC, IL23R, and DPP4 expression (type 3). Effector γδ T cells with type 1 and type 3 innate T cell signatures were detected in a public dataset of early embryonic thymus organogenesis. Together, this study suggests that functionally distinct waves of human innate-like effector γδ T cells with semi-invariant Vγ9Vδ2+ TCR develop in the early fetal thymus and persist into adulthood.
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Affiliation(s)
- Likai Tan
- Institute of Immunology, Hannover Medical School (MHH), Hannover, Germany.,Institute of Systems Immunology, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Elena Bruni
- Institute of Immunology, Hannover Medical School (MHH), Hannover, Germany
| | - Ivan Odak
- Institute of Immunology, Hannover Medical School (MHH), Hannover, Germany
| | - Inga Sandrock
- Institute of Immunology, Hannover Medical School (MHH), Hannover, Germany
| | - Anja Bubke
- Institute of Immunology, Hannover Medical School (MHH), Hannover, Germany
| | - Alina Borchers
- Translational Immunology, III. Department of Medicine, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Schultze-Florey
- Institute of Immunology, Hannover Medical School (MHH), Hannover, Germany.,Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Christian Koenecke
- Institute of Immunology, Hannover Medical School (MHH), Hannover, Germany.,Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School (MHH), Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Michael Jarek
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Constantin von Kaisenberg
- Department of Obstetrics, Gynecology, and Reproductive Medicine, Hannover Medical School, Hannover, Germany
| | - Ansgar Schulz
- Department of Pediatrics, University Medical Center Ulm, Ulm, Germany
| | - Xiaojing Chu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Department of Computational Biology for Individualised Medicine TWINCORE, Helmholtz Centre for Infection Research and Hannover Medical School, Hannover, Germany
| | - Bowen Zhang
- Department of Computational Biology for Individualised Medicine TWINCORE, Helmholtz Centre for Infection Research and Hannover Medical School, Hannover, Germany
| | - Yang Li
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.,Department of Computational Biology for Individualised Medicine TWINCORE, Helmholtz Centre for Infection Research and Hannover Medical School, Hannover, Germany
| | - Ulf Panzer
- Translational Immunology, III. Department of Medicine, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian F Krebs
- Translational Immunology, III. Department of Medicine, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sarina Ravens
- Institute of Immunology, Hannover Medical School (MHH), Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Immo Prinz
- Institute of Immunology, Hannover Medical School (MHH), Hannover, Germany. .,Institute of Systems Immunology, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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64
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Stephenson E, Webb S, Haniffa M. Multiomics uncovers developing immunological lineages in human. Eur J Immunol 2021; 51:764-772. [PMID: 33569778 PMCID: PMC8600952 DOI: 10.1002/eji.202048769] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/19/2020] [Indexed: 11/06/2022]
Abstract
The development of the human immune system during embryonic and fetal life has historically been difficult to research due to limited access to human tissue. Experimental animal models have been widely used to study development but cellular and molecular programmes may not be conserved across species. The advent of multiomic single-cell technologies and an increase in human developmental tissue biobank resources have facilitated single-cell multiomic studies focused on human immune development. A critical question in the near future is "How do we best reconcile scientific findings across multiple omic modalities, developmental time, and organismic space?" In this review, we discuss the application of single-cell multiomic technologies to unravel the major cellular lineages in the prenatal human immune system. We also identify key areas where the combined power of multiomics technologies can be leveraged to address specific immunological gaps in our current knowledge and explore new research horizons in human development.
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Affiliation(s)
- Emily Stephenson
- Biosciences InstituteNewcastle UniversityNewcastle Upon TyneNE2 4HHUK
| | - Simone Webb
- Biosciences InstituteNewcastle UniversityNewcastle Upon TyneNE2 4HHUK
| | - Muzlifah Haniffa
- Biosciences InstituteNewcastle UniversityNewcastle Upon TyneNE2 4HHUK
- Department of Dermatology and NIHR Newcastle Biomedical Research CentreNewcastle Hospitals NHS Foundation TrustNewcastle Upon TyneUK
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65
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Li Y, Li K, Zhu L, Li B, Zong D, Cai P, Jiang C, Du P, Lin J, Qu K. Development of double-positive thymocytes at single-cell resolution. Genome Med 2021; 13:49. [PMID: 33771202 PMCID: PMC8004397 DOI: 10.1186/s13073-021-00861-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/25/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND T cells generated from thymopoiesis are essential for the immune system, and recent single-cell studies have contributed to our understanding of the development of thymocytes at the genetic and epigenetic levels. However, the development of double-positive (DP) T cells, which comprise the majority of thymocytes, has not been well investigated. METHODS We applied single-cell sequencing to mouse thymocytes and analyzed the transcriptome data using Seurat. By applying unsupervised clustering, we defined thymocyte subtypes and validated DP cell subtypes by flow cytometry. We classified the cell cycle phases of each cell according to expression of cell cycle phase-specific genes. For immune synapse detection, we used immunofluorescent staining and ImageStream-based flow cytometry. We studied and integrated human thymocyte data to verify the conservation of our findings and also performed cross-species comparisons to examine species-specific gene regulation. RESULTS We classified blast, rearrangement, and selection subtypes of DP thymocytes and used the surface markers CD2 and Ly6d to identify these subtypes by flow cytometry. Based on this new classification, we found that the proliferation of blast DP cells is quite different from that of double-positive cells and other cell types, which tend to exit the cell cycle after a single round. At the DP cell selection stage, we observed that CD8-associated immune synapses formed between thymocytes, indicating that CD8sp selection occurred among thymocytes themselves. Moreover, cross-species comparison revealed species-specific transcription factors (TFs) that contribute to the transcriptional differences of thymocytes from humans and mice. CONCLUSIONS Our study classified DP thymocyte subtypes of different developmental stages and provided new insight into the development of DP thymocytes at single-cell resolution, furthering our knowledge of the fundamental immunological process of thymopoiesis.
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Affiliation(s)
- Young Li
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Kun Li
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Lianbang Zhu
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Bin Li
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Dandan Zong
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Pengfei Cai
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Chen Jiang
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Pengcheng Du
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Jun Lin
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Kun Qu
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China.
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Sciences, University of Science and Technology of China, Hefei, 230021, Anhui, China.
- School of Data Science, University of Science and Technology of China, Hefei, 230027, Anhui, China.
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66
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Le J, Park JE, Ha VL, Luong A, Branciamore S, Rodin AS, Gogoshin G, Li F, Loh YHE, Camacho V, Patel SB, Welner RS, Parekh C. Single-Cell RNA-Seq Mapping of Human Thymopoiesis Reveals Lineage Specification Trajectories and a Commitment Spectrum in T Cell Development. Immunity 2021; 52:1105-1118.e9. [PMID: 32553173 DOI: 10.1016/j.immuni.2020.05.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/20/2020] [Accepted: 05/22/2020] [Indexed: 12/21/2022]
Abstract
The challenges in recapitulating in vivo human T cell development in laboratory models have posed a barrier to understanding human thymopoiesis. Here, we used single-cell RNA sequencing (sRNA-seq) to interrogate the rare CD34+ progenitor and the more differentiated CD34- fractions in the human postnatal thymus. CD34+ thymic progenitors were comprised of a spectrum of specification and commitment states characterized by multilineage priming followed by gradual T cell commitment. The earliest progenitors in the differentiation trajectory were CD7- and expressed a stem-cell-like transcriptional profile, but had also initiated T cell priming. Clustering analysis identified a CD34+ subpopulation primed for the plasmacytoid dendritic lineage, suggesting an intrathymic dendritic specification pathway. CD2 expression defined T cell commitment stages where loss of B cell potential preceded that of myeloid potential. These datasets delineate gene expression profiles spanning key differentiation events in human thymopoiesis and provide a resource for the further study of human T cell development.
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Affiliation(s)
- Justin Le
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Jeong Eun Park
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Vi Luan Ha
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Annie Luong
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Sergio Branciamore
- Department of Computational and Quantitative Medicine, and Diabetes and Metabolism Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Andrei S Rodin
- Department of Computational and Quantitative Medicine, and Diabetes and Metabolism Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Grigoriy Gogoshin
- Department of Computational and Quantitative Medicine, and Diabetes and Metabolism Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Fan Li
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | | | - Virginia Camacho
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sweta B Patel
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert S Welner
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Chintan Parekh
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA; Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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67
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Kreins AY, Bonfanti P, Davies EG. Current and Future Therapeutic Approaches for Thymic Stromal Cell Defects. Front Immunol 2021; 12:655354. [PMID: 33815417 PMCID: PMC8012524 DOI: 10.3389/fimmu.2021.655354] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
Inborn errors of thymic stromal cell development and function lead to impaired T-cell development resulting in a susceptibility to opportunistic infections and autoimmunity. In their most severe form, congenital athymia, these disorders are life-threatening if left untreated. Athymia is rare and is typically associated with complete DiGeorge syndrome, which has multiple genetic and environmental etiologies. It is also found in rare cases of T-cell lymphopenia due to Nude SCID and Otofaciocervical Syndrome type 2, or in the context of genetically undefined defects. This group of disorders cannot be corrected by hematopoietic stem cell transplantation, but upon timely recognition as thymic defects, can successfully be treated by thymus transplantation using cultured postnatal thymic tissue with the generation of naïve T-cells showing a diverse repertoire. Mortality after this treatment usually occurs before immune reconstitution and is mainly associated with infections most often acquired pre-transplantation. In this review, we will discuss the current approaches to the diagnosis and management of thymic stromal cell defects, in particular those resulting in athymia. We will discuss the impact of the expanding implementation of newborn screening for T-cell lymphopenia, in combination with next generation sequencing, as well as the role of novel diagnostic tools distinguishing between hematopoietic and thymic stromal cell defects in facilitating the early consideration for thymus transplantation of an increasing number of patients and disorders. Immune reconstitution after the current treatment is usually incomplete with relatively common inflammatory and autoimmune complications, emphasizing the importance for improving strategies for thymus replacement therapy by optimizing the current use of postnatal thymus tissue and developing new approaches using engineered thymus tissue.
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Affiliation(s)
- Alexandra Y. Kreins
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Paola Bonfanti
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Epithelial Stem Cell Biology & Regenerative Medicine Laboratory, The Francis Crick Institute, London, United Kingdom
- Institute of Immunity & Transplantation, University College London, London, United Kingdom
| | - E. Graham Davies
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
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68
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Tao H, Li L, Liao NS, Schluns KS, Luckhart S, Sleasman JW, Zhong XP. Thymic Epithelial Cell-Derived IL-15 and IL-15 Receptor α Chain Foster Local Environment for Type 1 Innate Like T Cell Development. Front Immunol 2021; 12:623280. [PMID: 33732245 PMCID: PMC7957058 DOI: 10.3389/fimmu.2021.623280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/10/2021] [Indexed: 12/20/2022] Open
Abstract
Expression of tissue-restricted antigens (TRAs) in thymic epithelial cells (TECs) ensures negative selection of highly self-reactive T cells to establish central tolerance. Whether some of these TRAs could exert their canonical biological functions to shape thymic environment to regulate T cell development is unclear. Analyses of publicly available databases have revealed expression of transcripts at various levels of many cytokines and cytokine receptors such as IL-15, IL-15Rα, IL-13, and IL-23a in both human and mouse TECs. Ablation of either IL-15 or IL-15Rα in TECs selectively impairs type 1 innate like T cell, such as iNKT1 and γδT1 cell, development in the thymus, indicating that TECs not only serve as an important source of IL-15 but also trans-present IL-15 to ensure type 1 innate like T cell development. Because type 1 innate like T cells are proinflammatory, our data suggest the possibility that TEC may intrinsically control thymic inflammatory innate like T cells to influence thymic environment.
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Affiliation(s)
- Huishan Tao
- Department of Pediatrics-Allergy and Immunology, Duke University Medical Center, Durham, NC, United States
| | - Lei Li
- Department of Pediatrics-Allergy and Immunology, Duke University Medical Center, Durham, NC, United States
| | - Nan-Shih Liao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Kimberly S Schluns
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Shirley Luckhart
- Department of Entomology, Plant Pathology and Nematology, Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - John W Sleasman
- Department of Pediatrics-Allergy and Immunology, Duke University Medical Center, Durham, NC, United States
| | - Xiao-Ping Zhong
- Department of Pediatrics-Allergy and Immunology, Duke University Medical Center, Durham, NC, United States.,Department of Immunology, Duke University Medical Center, Durham, NC, United States.,Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
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69
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Rothenberg EV. Single-cell insights into the hematopoietic generation of T-lymphocyte precursors in mouse and human. Exp Hematol 2021; 95:1-12. [PMID: 33454362 PMCID: PMC8018899 DOI: 10.1016/j.exphem.2020.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 01/29/2023]
Abstract
T-Cell development is a major branch of lymphoid development and a key output of hematopoiesis, especially in early life, but the molecular requirements for T-cell potential have remained obscure. Considerable advances have now been made toward solving this problem through single-cell transcriptome studies, interfaced with in vitro differentiation assays that monitor potential efficiently at the single-cell level. This review focuses on a series of recent reports studying mouse and human early T-cell precursors, both in the developing fetus and in stringently purified postnatal samples of intrathymic and prethymic T-lineage precursors. Cross-comparison of results reveals a robustly conserved core program in mouse and human, but with some informative and provocative variations between species and between ontogenic states. Repeated findings are the multipotent progenitor regulatory signature of thymus-seeding cells and the proximity of the T-cell program to dendritic cell programs, especially to plasmacytoid dendritic cells in humans.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA.
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70
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Mansurkhodzhaev A, Barbosa CRR, Mishto M, Liepe J. Proteasome-Generated cis-Spliced Peptides and Their Potential Role in CD8 + T Cell Tolerance. Front Immunol 2021; 12:614276. [PMID: 33717099 PMCID: PMC7943738 DOI: 10.3389/fimmu.2021.614276] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/28/2021] [Indexed: 01/09/2023] Open
Abstract
The human immune system relies on the capability of CD8+ T cells to patrol body cells, spot infected cells and eliminate them. This cytotoxic response is supposed to be limited to infected cells to avoid killing of healthy cells. To enable this, CD8+ T cells have T Cell Receptors (TCRs) which should discriminate between self and non-self through the recognition of antigenic peptides bound to Human Leukocyte Antigen class I (HLA-I) complexes-i.e., HLA-I immunopeptidomes-of patrolled cells. The majority of these antigenic peptides are produced by proteasomes through either peptide hydrolysis or peptide splicing. Proteasome-generated cis-spliced peptides derive from a given antigen, are immunogenic and frequently presented by HLA-I complexes. Theoretically, they also have a very large sequence variability, which might impinge upon our model of self/non-self discrimination and central and peripheral CD8+ T cell tolerance. Indeed, a large variety of cis-spliced epitopes might enlarge the pool of viral-human zwitter epitopes, i.e., peptides that may be generated with the exact same sequence from both self (human) and non-self (viral) antigens. Antigenic viral-human zwitter peptides may be recognized by CD8+ thymocytes and T cells, induce clonal deletion or other tolerance processes, thereby restraining CD8+ T cell response against viruses. To test this hypothesis, we computed in silico the theoretical frequency of zwitter non-spliced and cis-spliced epitope candidates derived from human proteome (self) and from the proteomes of a large pool of viruses (non-self). We considered their binding affinity to the representative HLA-A*02:01 complex, self-antigen expression in Medullary Thymic Epithelial cells (mTECs) and the relative frequency of non-spliced and cis-spliced peptides in HLA-I immunopeptidomes. Based on the present knowledge of proteasome-catalyzed peptide splicing and neglecting CD8+ TCR degeneracy, our study suggests that, despite their frequency, the portion of the cis-spliced peptides we investigated could only marginally impinge upon the variety of functional CD8+ cytotoxic T cells (CTLs) involved in anti-viral response.
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Affiliation(s)
- Artem Mansurkhodzhaev
- Quantitative and Systems Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Camila R. R. Barbosa
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) and Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) and Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
- Francis Crick Institute, London, United Kingdom
| | - Juliane Liepe
- Quantitative and Systems Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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71
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Bautista JL, Cramer NT, Miller CN, Chavez J, Berrios DI, Byrnes LE, Germino J, Ntranos V, Sneddon JB, Burt TD, Gardner JM, Ye CJ, Anderson MS, Parent AV. Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla. Nat Commun 2021; 12:1096. [PMID: 33597545 PMCID: PMC7889611 DOI: 10.1038/s41467-021-21346-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 01/22/2021] [Indexed: 01/02/2023] Open
Abstract
The thymus' key function in the immune system is to provide the necessary environment for the development of diverse and self-tolerant T lymphocytes. While recent evidence suggests that the thymic stroma is comprised of more functionally distinct subpopulations than previously appreciated, the extent of this cellular heterogeneity in the human thymus is not well understood. Here we use single-cell RNA sequencing to comprehensively profile the human thymic stroma across multiple stages of life. Mesenchyme, pericytes and endothelial cells are identified as potential key regulators of thymic epithelial cell differentiation and thymocyte migration. In-depth analyses of epithelial cells reveal the presence of ionocytes as a medullary population, while the expression of tissue-specific antigens is mapped to different subsets of epithelial cells. This work thus provides important insight on how the diversity of thymic cells is established, and how this heterogeneity contributes to the induction of immune tolerance in humans.
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Affiliation(s)
- Jhoanne L Bautista
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Nathan T Cramer
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Corey N Miller
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Chavez
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - David I Berrios
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lauren E Byrnes
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joe Germino
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Vasilis Ntranos
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Julie B Sneddon
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
- Department of Cell and Tissue Biology, School of Dentistry, University of California, San Francisco, San Francisco, CA, USA
| | - Trevor D Burt
- Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Division of Neonatology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Division of Neonatology and the Children's Health & Discovery Initiative, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - James M Gardner
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Chun J Ye
- Bakar Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark S Anderson
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Audrey V Parent
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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72
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Deng Y, Chen H, Zeng Y, Wang K, Zhang H, Hu H. Leaving no one behind: tracing every human thymocyte by single-cell RNA-sequencing. Semin Immunopathol 2021; 43:29-43. [PMID: 33449155 DOI: 10.1007/s00281-020-00834-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 12/22/2020] [Indexed: 02/05/2023]
Abstract
The thymus is the primary organ for T-cell development, providing an essential microenvironment consisting of the appropriate cytokine milieu and specialized stromal cells. Thymus-seeding progenitors from circulation immigrate into the thymus and undergo the stepwise T-cell specification, commitment, and selection processes. The transcriptional factors, epigenetic regulators, and signaling pathways involved in the T-cell development have been intensively studied using mouse models. Despite our growing knowledge of T-cell development, major questions remain unanswered regarding the ontogeny and early events of T-cell development at the fetal stage, especially in humans. The recently developed single-cell RNA-sequencing technique provides an ideal tool to investigate the heterogeneity of T-cell precursors and the molecular mechanisms underlying the divergent fates of certain T-cell precursors at the single-cell level. In this review, we aim to summarize the current progress of the study on human thymus organogenesis and thymocyte and thymic epithelial cell development, which is to shed new lights on developing novel strategies for in vitro T-cell regeneration and thymus rejuvenation.
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Affiliation(s)
- Yujun Deng
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Hong Chen
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yang Zeng
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China.,State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100071, China
| | - Keyue Wang
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Huiyuan Zhang
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China.
| | - Hongbo Hu
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China.
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73
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Liu C, Lan Y, Liu B, Zhang H, Hu H. T Cell Development: Old Tales Retold By Single-Cell RNA Sequencing. Trends Immunol 2021; 42:165-175. [PMID: 33446417 DOI: 10.1016/j.it.2020.12.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023]
Abstract
Mammalian T cell development initiates from the migration of hematopoietic progenitors to the thymus, which undergo cell proliferation, T-lineage specification and commitment, as well as positive and negative selection. These processes are precisely controlled at multiple levels and have been intensively studied using gene-modified animal models and in vitro coculture systems. However, several long-standing questions, including the characterization of the rare but crucial progenitors/precursors and the molecular mechanisms underlying their fate decision, have been dampened because of cell scarcity and lack of appropriate techniques. Single-cell RNA sequencing (scRNA-seq) makes it possible to investigate and resolve some of these questions, leading to new remarkable progress in identifying and characterizing early thymic progenitors and delineating the refined developmental trajectories of conventional and unconventional T cells.
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Affiliation(s)
- Chen Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Bing Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China; Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China; State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Huiyuan Zhang
- Department of Rheumatology and Immunology, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
| | - Hongbo Hu
- Department of Rheumatology and Immunology, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
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74
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Wang H, He J, Xu C, Chen X, Yang H, Shi S, Liu C, Zeng Y, Wu D, Bai Z, Wang M, Wen Y, Su P, Xia M, Huang B, Ma C, Bian L, Lan Y, Cheng T, Shi L, Liu B, Zhou J. Decoding Human Megakaryocyte Development. Cell Stem Cell 2020; 28:535-549.e8. [PMID: 33340451 DOI: 10.1016/j.stem.2020.11.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 09/25/2020] [Accepted: 11/10/2020] [Indexed: 12/25/2022]
Abstract
Despite our growing understanding of embryonic immune development, rare early megakaryocytes (MKs) remain relatively understudied. Here we used single-cell RNA sequencing of human MKs from embryonic yolk sac (YS) and fetal liver (FL) to characterize the transcriptome, cellular heterogeneity, and developmental trajectories of early megakaryopoiesis. In the YS and FL, we found heterogeneous MK subpopulations with distinct developmental routes and patterns of gene expression that could reflect early functional specialization. Intriguingly, we identified a subpopulation of CD42b+CD14+ MKs in vivo that exhibit high expression of genes associated with immune responses and can also be derived from human embryonic stem cells (hESCs) in vitro. Furthermore, we identified THBS1 as an early marker for MK-biased embryonic endothelial cells. Overall, we provide important insights and invaluable resources for dissection of the molecular and cellular programs underlying early human megakaryopoiesis.
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Affiliation(s)
- Hongtao Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Jian He
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Changlu Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Xiaoyuan Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Hua Yang
- Tianjin Central Hospital of Gynecology Obstetrics, Tianjin 300052, China
| | - Shujuan Shi
- Tianjin Central Hospital of Gynecology Obstetrics, Tianjin 300052, China
| | - Cuicui Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Yang Zeng
- Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Dan Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Zhijie Bai
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Mengge Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Yuqi Wen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Pei Su
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Meijuan Xia
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Baiming Huang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Chunyu Ma
- Department of Gynecology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Lihong Bian
- Department of Gynecology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China.
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China; Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China.
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China.
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75
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Liggett LA, Sankaran VG. Unraveling Hematopoiesis through the Lens of Genomics. Cell 2020; 182:1384-1400. [PMID: 32946781 PMCID: PMC7508400 DOI: 10.1016/j.cell.2020.08.030] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/14/2020] [Accepted: 08/17/2020] [Indexed: 01/07/2023]
Abstract
Hematopoiesis has long served as a paradigm of stem cell biology and tissue homeostasis. In the past decade, the genomics revolution has ushered in powerful new methods for investigating the hematopoietic system that have provided transformative insights into its biology. As part of the advances in genomics, increasingly accurate deep sequencing and novel methods of cell tracking have revealed hematopoiesis to be more of a continuous and less of a discrete and punctuated process than originally envisioned. In part, this continuous nature of hematopoiesis is made possible by the emergent outcomes of vast, interconnected regulatory networks that influence cell fates and lineage commitment. It is also becoming clear how these mechanisms are modulated by genetic variation present throughout the population. This review describes how these recently uncovered complexities are reshaping our concept of tissue development and homeostasis while opening up a more comprehensive future understanding of hematopoiesis.
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Affiliation(s)
- L Alexander Liggett
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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76
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Shangguan Y, Li C, Lin H, Ou M, Tang D, Dai Y, Yan Q. Application of single-cell RNA sequencing in embryonic development. Genomics 2020; 112:4547-4551. [PMID: 32781204 DOI: 10.1016/j.ygeno.2020.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 12/20/2022]
Abstract
Embryonic development is a complex process that is regulated by a series of precise cellular behaviours. The limited number of cells in the early stages of embryonic development represents a challenge for studying early gene regulation and maintaining cell sternness. Single-cell sequencing is a new technology for high-throughput sequencing analysis at the single-cell level that not only reflects the heterogeneity between cells but also reveals gene expression characteristics in different cells from limited samples. Currently, the widespread application of single-cell RNA sequencing technology is gradually changing our understanding of disease pathogenesis. This article reviews the application of single-cell RNA sequencing in embryonic development in recent years and provides innovative ideas for research on embryonic development and the treatment of diseases related to embryonic development.
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Affiliation(s)
- Yu Shangguan
- College of Life Science, Guangxi Normal University, Guilin, Guangxi 541004, China; Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Chunhong Li
- College of Life Science, Guangxi Normal University, Guilin, Guangxi 541004, China; Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Hua Lin
- Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China
| | - Minglin Ou
- Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China
| | - Donge Tang
- Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China.
| | - Yong Dai
- Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China.
| | - Qiang Yan
- College of Life Science, Guangxi Normal University, Guilin, Guangxi 541004, China; Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China.
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77
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Deciphering human macrophage development at single-cell resolution. Nature 2020; 582:571-576. [DOI: 10.1038/s41586-020-2316-7] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 03/11/2020] [Indexed: 01/20/2023]
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78
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Abstract
The blood and immune systems develop in parallel during early prenatal life. Waves of hematopoiesis separated in anatomical space and time give rise to circulating and tissue-resident immune cells. Previous observations have relied on animal models, which differ from humans in both their developmental timeline and exposure to microorganisms. Decoding the composition of the human immune system is now tractable using single-cell multi-omics approaches. Large-scale single-cell genomics, imaging technologies, and the Human Cell Atlas initiative have together enabled a systems-level mapping of the developing human immune system and its emergent properties. Although the precise roles of specific immune cells during development require further investigation, the system as a whole displays malleable and responsive properties according to developmental need and environmental challenge.
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Affiliation(s)
- Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Faculty of Medical Sciences, Newcastle upon Tyne NE2 4HH, UK
| | - Berthold Gottgens
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
- Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 2XY, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
- Department of Physics/Cavendish Laboratory, University of Cambridge, JJ Thomson Ave., Cambridge CB3 0HE, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
- Biosciences Institute, Newcastle University, Faculty of Medical Sciences, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
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79
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Abstract
Technological advances in characterizing molecular heterogeneity at the single cell level have ushered in a deeper understanding of the biological diversity of cells present in tissues including atherosclerotic plaques. New subsets of cells have been discovered among cell types previously considered homogenous. The commercial availability of systems to obtain transcriptomes and matching surface phenotypes from thousands of single cells is rapidly changing our understanding of cell types and lineage identity. Emerging methods to infer cellular functions are beginning to shed new light on the interplay of components involved in multifaceted disease responses, like atherosclerosis. Here, we provide a technical guide for design, implementation, assembly, and interpretations of current single cell transcriptomics approaches from the perspective of employing these tools for advancing cardiovascular disease research.
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Affiliation(s)
- Jesse W. Williams
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN USA
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN USA
| | - Holger Winkels
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA USA
| | - Christopher P. Durant
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA USA
| | - Konstantin Zaitsev
- Computer Technologies Department, Information Technologies, Mechanics, and Optics University, Saint Petersburg, Russia
| | - Yanal Ghosheh
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA USA
| | - Klaus Ley
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA USA
- Department of Bioengineering, University of California San Diego, CA, USA
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80
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Lavaert M, Liang KL, Vandamme N, Park JE, Roels J, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Vandekerckhove B, Leclercq G, Regev A, Van Vlierberghe P, Guilliams M, Teichmann SA, Saeys Y, Taghon T. Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes. Immunity 2020; 52:1088-1104.e6. [PMID: 32304633 DOI: 10.1016/j.immuni.2020.03.019] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/04/2020] [Accepted: 03/27/2020] [Indexed: 10/24/2022]
Abstract
During postnatal life, thymopoiesis depends on the continuous colonization of the thymus by bone-marrow-derived hematopoietic progenitors that migrate through the bloodstream. The current understanding of the nature of thymic immigrants is largely based on data from pre-clinical models. Here, we employed single-cell RNA sequencing (scRNA-seq) to examine the immature postnatal thymocyte population in humans. Integration of bone marrow and peripheral blood precursor datasets identified two putative thymus seeding progenitors that varied in expression of CD7; CD10; and the homing receptors CCR7, CCR9, and ITGB7. Whereas both precursors supported T cell development, only one contributed to intrathymic dendritic cell (DC) differentiation, predominantly of plasmacytoid dendritic cells. Trajectory inference delineated the transcriptional dynamics underlying early human T lineage development, enabling prediction of transcription factor (TF) modules that drive stage-specific steps of human T cell development. This comprehensive dataset defines the expression signature of immature human thymocytes and provides a resource for the further study of human thymopoiesis.
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Affiliation(s)
- Marieke Lavaert
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium
| | - Kai Ling Liang
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Juliette Roels
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Monica S Kowalczyk
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Sciences Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Timothy L Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Haematology Department, Royal Victoria Infirmary, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Bart Vandekerckhove
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Georges Leclercq
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Martin Guilliams
- Laboratory of Myeloid Cell Ontogeny and Functional Specialization, VIB Center for Inflammation Research, Ghent, Belgium; Faculty of Sciences, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Tom Taghon
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.
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81
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Park JE, Botting RA, Domínguez Conde C, Popescu DM, Lavaert M, Kunz DJ, Goh I, Stephenson E, Ragazzini R, Tuck E, Wilbrey-Clark A, Roberts K, Kedlian VR, Ferdinand JR, He X, Webb S, Maunder D, Vandamme N, Mahbubani KT, Polanski K, Mamanova L, Bolt L, Crossland D, de Rita F, Fuller A, Filby A, Reynolds G, Dixon D, Saeb-Parsy K, Lisgo S, Henderson D, Vento-Tormo R, Bayraktar OA, Barker RA, Meyer KB, Saeys Y, Bonfanti P, Behjati S, Clatworthy MR, Taghon T, Haniffa M, Teichmann SA. A cell atlas of human thymic development defines T cell repertoire formation. Science 2020; 367:367/6480/eaay3224. [PMID: 32079746 DOI: 10.1126/science.aay3224] [Citation(s) in RCA: 338] [Impact Index Per Article: 84.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 01/16/2020] [Indexed: 11/03/2022]
Abstract
The thymus provides a nurturing environment for the differentiation and selection of T cells, a process orchestrated by their interaction with multiple thymic cell types. We used single-cell RNA sequencing to create a cell census of the human thymus across the life span and to reconstruct T cell differentiation trajectories and T cell receptor (TCR) recombination kinetics. Using this approach, we identified and located in situ CD8αα+ T cell populations, thymic fibroblast subtypes, and activated dendritic cell states. In addition, we reveal a bias in TCR recombination and selection, which is attributed to genomic position and the kinetics of lineage commitment. Taken together, our data provide a comprehensive atlas of the human thymus across the life span with new insights into human T cell development.
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Affiliation(s)
- Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rachel A Botting
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | | | - Dorin-Mirel Popescu
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marieke Lavaert
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Daniel J Kunz
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK.,Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Issac Goh
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Emily Stephenson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Roberta Ragazzini
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, Francis Crick Institute, London NW1 1AT, UK.,Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Veronika R Kedlian
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - Xiaoling He
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK
| | - Simone Webb
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Daniel Maunder
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - David Crossland
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.,Department of Adult Congenital Heart Disease and Paediatric Cardiology/Cardiothoracic Surgery, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Fabrizio de Rita
- Department of Adult Congenital Heart Disease and Paediatric Cardiology/Cardiothoracic Surgery, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Andrew Fuller
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Andrew Filby
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Gary Reynolds
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David Dixon
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Steven Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Deborah Henderson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Omer A Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK.,WT-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Paola Bonfanti
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, Francis Crick Institute, London NW1 1AT, UK.,Great Ormond Street Institute of Child Health, University College London, London, UK.,Institute of Immunity and Transplantation, University College London, London, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Department of Paediatrics, University of Cambridge, Cambridge CB2 0SP, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK.,Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Tom Taghon
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. .,Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. .,Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
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82
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Park JE, Botting RA, Domínguez Conde C, Popescu DM, Lavaert M, Kunz DJ, Goh I, Stephenson E, Ragazzini R, Tuck E, Wilbrey-Clark A, Roberts K, Kedlian VR, Ferdinand JR, He X, Webb S, Maunder D, Vandamme N, Mahbubani KT, Polanski K, Mamanova L, Bolt L, Crossland D, de Rita F, Fuller A, Filby A, Reynolds G, Dixon D, Saeb-Parsy K, Lisgo S, Henderson D, Vento-Tormo R, Bayraktar OA, Barker RA, Meyer KB, Saeys Y, Bonfanti P, Behjati S, Clatworthy MR, Taghon T, Haniffa M, Teichmann SA. A cell atlas of human thymic development defines T cell repertoire formation. Science 2020. [DOI: 10.1126/science.aay3224 32079746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rachel A. Botting
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | | | - Dorin-Mirel Popescu
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marieke Lavaert
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Daniel J. Kunz
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Issac Goh
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Emily Stephenson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Roberta Ragazzini
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, Francis Crick Institute, London NW1 1AT, UK
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Veronika R. Kedlian
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - John R. Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - Xiaoling He
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK
| | - Simone Webb
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Daniel Maunder
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Krishnaa T. Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - David Crossland
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Adult Congenital Heart Disease and Paediatric Cardiology/Cardiothoracic Surgery, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Fabrizio de Rita
- Department of Adult Congenital Heart Disease and Paediatric Cardiology/Cardiothoracic Surgery, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Andrew Fuller
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Andrew Filby
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Gary Reynolds
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David Dixon
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Steven Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Deborah Henderson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Omer A. Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Roger A. Barker
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK
- WT-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Kerstin B. Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Paola Bonfanti
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, Francis Crick Institute, London NW1 1AT, UK
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Institute of Immunity and Transplantation, University College London, London, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0SP, UK
| | - Menna R. Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Tom Taghon
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
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83
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Pereira R, Oliveira J, Sousa M. Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics. J Clin Med 2020; 9:E132. [PMID: 31947757 PMCID: PMC7019349 DOI: 10.3390/jcm9010132] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/15/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022] Open
Abstract
Clinical genetics has an important role in the healthcare system to provide a definitive diagnosis for many rare syndromes. It also can have an influence over genetics prevention, disease prognosis and assisting the selection of the best options of care/treatment for patients. Next-generation sequencing (NGS) has transformed clinical genetics making possible to analyze hundreds of genes at an unprecedented speed and at a lower price when comparing to conventional Sanger sequencing. Despite the growing literature concerning NGS in a clinical setting, this review aims to fill the gap that exists among (bio)informaticians, molecular geneticists and clinicians, by presenting a general overview of the NGS technology and workflow. First, we will review the current NGS platforms, focusing on the two main platforms Illumina and Ion Torrent, and discussing the major strong points and weaknesses intrinsic to each platform. Next, the NGS analytical bioinformatic pipelines are dissected, giving some emphasis to the algorithms commonly used to generate process data and to analyze sequence variants. Finally, the main challenges around NGS bioinformatics are placed in perspective for future developments. Even with the huge achievements made in NGS technology and bioinformatics, further improvements in bioinformatic algorithms are still required to deal with complex and genetically heterogeneous disorders.
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Affiliation(s)
- Rute Pereira
- Laboratory of Cell Biology, Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto (UP), 4050-313 Porto, Portugal;
- Biology and Genetics of Reproduction Unit, Multidisciplinary Unit for Biomedical Research (UMIB), ICBAS-UP, 4050-313 Porto, Portugal;
| | - Jorge Oliveira
- Biology and Genetics of Reproduction Unit, Multidisciplinary Unit for Biomedical Research (UMIB), ICBAS-UP, 4050-313 Porto, Portugal;
- UnIGENe and CGPP–Centre for Predictive and Preventive Genetics-Institute for Molecular and Cell Biology (IBMC), i3S-Institute for Research and Innovation in Health-UP, 4200-135 Porto, Portugal
| | - Mário Sousa
- Laboratory of Cell Biology, Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto (UP), 4050-313 Porto, Portugal;
- Biology and Genetics of Reproduction Unit, Multidisciplinary Unit for Biomedical Research (UMIB), ICBAS-UP, 4050-313 Porto, Portugal;
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84
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Xu G, Liu Y, Li H, Liu L, Zhang S, Zhang Z. Dissecting the human immune system with single cell RNA sequencing technology. J Leukoc Biol 2019; 107:613-623. [PMID: 31803960 DOI: 10.1002/jlb.5mr1019-179r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/24/2019] [Accepted: 11/13/2019] [Indexed: 12/23/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful new technology allowing the analysis of transcriptomes from individual cell and is ideally suited to dissect immune cell heterogeneity. ScRNA-seq has already been applied to identify novel immune cell subsets, elaborate cellular differentiation trajectories, and elucidate immunopathogenic mechanisms. Here, we briefly discuss the recent progresses and challenges in the scRNA-seq technology including the workflow, recent applications in immunology, and potential hurdles that need to be overcome. This review will highlight how single cell technology promotes our understanding of human immunology.
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Affiliation(s)
- Gang Xu
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, China.,Guangdong Key Lab of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Longgang District, Shenzhen, China
| | - Yang Liu
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, China.,Guangdong Key Lab of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Longgang District, Shenzhen, China
| | - Hanjie Li
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lei Liu
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, China.,Guangdong Key Lab of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Longgang District, Shenzhen, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zheng Zhang
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, China.,Guangdong Key Lab of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Longgang District, Shenzhen, China.,Key Laboratory of Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
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85
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Abstract
In this issue of Immunity, Zeng et al. use single-cell RNA sequencing analyses of rare samples to shed light on the emergence of thymic stromal cell types, the first developing T lymphocytes, and their possible pre-thymic precursors in the early human fetus.
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Affiliation(s)
- Wen Zhou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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86
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Guiding T lymphopoiesis from pluripotent stem cells by defined transcription factors. Cell Res 2019; 30:21-33. [PMID: 31729468 PMCID: PMC6951346 DOI: 10.1038/s41422-019-0251-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/15/2019] [Indexed: 12/22/2022] Open
Abstract
Achievement of immunocompetent and therapeutic T lymphopoiesis from pluripotent stem cells (PSCs) is a central aim in T cell regenerative medicine. To date, preferentially reconstituting T lymphopoiesis in vivo from PSCs remains a practical challenge. Here we documented that synergistic and transient expression of Runx1 and Hoxa9 restricted in the time window of endothelial-to-hematopoietic transition and hematopoietic maturation stages in a PSC differentiation scheme (iR9-PSC) in vitro induced preferential generation of engraftable hematopoietic progenitors capable of homing to thymus and developing into mature T cells in primary and secondary immunodeficient recipients. Single-cell transcriptome and functional analyses illustrated the cellular trajectory of T lineage induction from PSCs, unveiling the T-lineage specification determined at as early as hemogenic endothelial cell stage and identifying the bona fide pre-thymic progenitors. The induced T cells distributed normally in central and peripheral lymphoid organs and exhibited abundant TCRαβ repertoire. The regenerative T lymphopoiesis restored immune surveillance in immunodeficient mice. Furthermore, gene-edited iR9-PSCs produced tumor-specific T cells in vivo that effectively eradicated tumor cells. This study provides insight into universal generation of functional and therapeutic T cells from the unlimited and editable PSC source.
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