1
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Zhao H, Gong H, Zhu P, Sun C, Sun W, Zhou Y, Wu X, Qiu A, Wen X, Zhang J, Luo D, Liu Q, Li Y. Deciphering the cellular and molecular landscapes of Wnt/β-catenin signaling in mouse embryonic kidney development. Comput Struct Biotechnol J 2024; 23:3368-3378. [PMID: 39310276 PMCID: PMC11416353 DOI: 10.1016/j.csbj.2024.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/25/2024] Open
Abstract
Background The Wnt/β-catenin signaling pathway is critical in kidney development, yet its specific effects on gene expression in different embryonic kidney cell types are not fully understood. Methods Wnt/β-catenin signaling was activated in mouse E12.5 kidneys in vitro using CHIR99021, with RNA sequencing performed afterward, and the results were compared to DMSO controls (dataset GSE131240). Differential gene expression in ureteric buds and cap mesenchyme following pathway activation (datasets GSE20325 and GSE39583) was analyzed. Single-cell RNA-seq data from the Mouse Cell Atlas was used to link differentially expressed genes (DEGs) with kidney cell types. β-catenin ChIP-seq data (GSE39837) identified direct transcriptional targets. Results Activation of Wnt/β-catenin signaling led to 917 significant DEGs, including the upregulation of Notum and Apcdd1 and the downregulation of Crym and Six2. These DEGs were involved in kidney development and immune response. Single-cell analysis identified 787 DEGs across nineteen cell subtypes, with Macrophage_Apoe high cells showing the most pronounced enrichment of Wnt/β-catenin-activated genes. Gene expression profiles in ureteric buds and cap mesenchyme differed significantly upon β-catenin manipulation, with cap mesenchyme showing a unique set of DEGs. Analysis of β-catenin ChIP-seq data revealed 221 potential direct targets, including Dpp6 and Fgf12. Conclusion This study maps the complex gene expression driven by Wnt/β-catenin signaling in embryonic kidney cell types. The identified DEGs and β-catenin targets elucidate the molecular details of kidney development and the pathway's role in immune processes, providing a foundation for further research into Wnt/β-catenin signaling in kidney development and disease.
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Affiliation(s)
- Hui Zhao
- Guangzhou National Laboratory, Guangzhou International Bio Island, No. 9 Xing Dao Huan Bei Road, Guangzhou 510005, Guangdong Province, China
| | - Hui Gong
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| | - Peide Zhu
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China
| | - Chang Sun
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Wuping Sun
- Department of Pain Medicine, Shenzhen Municipal Key Laboratory for Pain Medicine, The affiliated Nanshan People's Hospital, The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen 518060, China
| | - Yujin Zhou
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| | - Xiaoxiao Wu
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| | - Ailin Qiu
- Institute of Pharmacy and Pharmacology, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Xiaosha Wen
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| | - Jinde Zhang
- Guangdong Medical University, Zhanjiang 524023, Guangdong China
| | - Dixian Luo
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| | - Quan Liu
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
| | - Yifan Li
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital) and The 6th Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong 518052, China
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2
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Pala F, Notarangelo LD, Bosticardo M. Rediscovering the human thymus through cutting-edge technologies. J Exp Med 2024; 221:e20230892. [PMID: 39167072 PMCID: PMC11338284 DOI: 10.1084/jem.20230892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/24/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Recent technological advances have transformed our understanding of the human thymus. Innovations such as high-resolution imaging, single-cell omics, and organoid cultures, including thymic epithelial cell (TEC) differentiation and culture, and improvements in biomaterials, have further elucidated the thymus architecture, cellular dynamics, and molecular mechanisms underlying T cell development, and have unraveled previously unrecognized levels of stromal cell heterogeneity. These advancements offer unprecedented insights into thymic biology and hold promise for the development of novel therapeutic strategies for immune-related disorders.
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Affiliation(s)
- Francesca Pala
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD, USA
| | - Luigi D Notarangelo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD, USA
| | - Marita Bosticardo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD, USA
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3
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Boehm T. Understanding vertebrate immunity through comparative immunology. Nat Rev Immunol 2024:10.1038/s41577-024-01083-9. [PMID: 39317775 DOI: 10.1038/s41577-024-01083-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2024] [Indexed: 09/26/2024]
Abstract
Evolutionary immunology has entered a new era. Classical studies, using just a handful of model animal species, combined with clinical observations, provided an outline of how innate and adaptive immunity work together to ensure tissue homeostasis and to coordinate the fight against infections. However, revolutionary advances in cellular and molecular biology, genomics and methods of genetic modification now offer unprecedented opportunities. They provide immunologists with the possibility to consider, at unprecedented scale, the impact of the astounding phenotypic diversity of vertebrates on immune system function. This Perspective is intended to highlight some of the many interesting, but largely unexplored, biological phenomena that are related to immune function among the roughly 60,000 existing vertebrate species. Importantly, hypotheses arising from such wide-ranging comparative studies can be tested in representative and genetically tractable species. The emerging general principles and the discovery of their evolutionarily selected variations may inspire the future development of novel therapeutic strategies for human immune disorders.
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Affiliation(s)
- Thomas Boehm
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, University Medical Center, Freiburg, Germany.
- Max Planck Institute for Biology Tübingen, Tübingen, Germany.
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4
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Yasumizu Y, Kinoshita M, Zhang MJ, Motooka D, Suzuki K, Nojima S, Koizumi N, Okuzaki D, Funaki S, Shintani Y, Ohkura N, Morii E, Okuno T, Mochizuki H. Spatial transcriptomics elucidates medulla niche supporting germinal center response in myasthenia gravis-associated thymoma. Cell Rep 2024; 43:114677. [PMID: 39180749 DOI: 10.1016/j.celrep.2024.114677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 07/30/2024] [Accepted: 08/08/2024] [Indexed: 08/26/2024] Open
Abstract
Myasthenia gravis (MG) is etiologically associated with thymus abnormalities, but its pathology in the thymus remains unclear. In this study, we attempt to narrow down the features associated with MG using spatial transcriptome analysis of thymoma and thymic hyperplasia samples. We find that the majority of thymomas are constituted by the cortical region. However, the small medullary region is enlarged in seropositive thymomas and contains polygenic enrichment and MG-specific germinal center structures. Neuromuscular medullary thymic epithelial cells, previously identified as MG-specific autoantigen-producing cells, are enriched in the cortico-medullary junction. The medulla is characterized by a specific chemokine pattern and immune cell composition, including migratory dendritic cells and effector regulatory T cells. Similar germinal center structures and immune microenvironments are also observed in the thymic hyperplasia medulla. This study shows that the medulla and junction areas are linked to MG pathology and provides insights into future MG research.
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Affiliation(s)
- Yoshiaki Yasumizu
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan; Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
| | - Makoto Kinoshita
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Martin Jinye Zhang
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan; Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Koichiro Suzuki
- BIKEN-RIMD NGS Laboratory, Research Institute for Microbial Diseases, Osaka University, Suita, Japan; Biomedical Science Center, The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Japan
| | - Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Naoshi Koizumi
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Daisuke Okuzaki
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan; Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Soichiro Funaki
- Department of General Thoracic Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yasushi Shintani
- Department of General Thoracic Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Naganari Ohkura
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; Department of Frontier Research in Tumor Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Tatsusada Okuno
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
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5
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Sumanaweera D, Suo C, Cujba AM, Muraro D, Dann E, Polanski K, Steemers AS, Lee W, Oliver AJ, Park JE, Meyer KB, Dumitrascu B, Teichmann SA. Gene-level alignment of single-cell trajectories. Nat Methods 2024:10.1038/s41592-024-02378-4. [PMID: 39300283 DOI: 10.1038/s41592-024-02378-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 07/12/2024] [Indexed: 09/22/2024]
Abstract
Single-cell data analysis can infer dynamic changes in cell populations, for example across time, space or in response to perturbation, thus deriving pseudotime trajectories. Current approaches comparing trajectories often use dynamic programming but are limited by assumptions such as the existence of a definitive match. Here we describe Genes2Genes, a Bayesian information-theoretic dynamic programming framework for aligning single-cell trajectories. It is able to capture sequential matches and mismatches of individual genes between a reference and query trajectory, highlighting distinct clusters of alignment patterns. Across both real world and simulated datasets, it accurately inferred alignments and demonstrated its utility in disease cell-state trajectory analysis. In a proof-of-concept application, Genes2Genes revealed that T cells differentiated in vitro match an immature in vivo state while lacking expression of genes associated with TNF signaling. This demonstrates that precise trajectory alignment can pinpoint divergence from the in vivo system, thus guiding the optimization of in vitro culture conditions.
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Affiliation(s)
- Dinithi Sumanaweera
- Wellcome Sanger Institute; Wellcome Genome Campus, Hinxton, Cambridge, UK
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Chenqu Suo
- Wellcome Sanger Institute; Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Paediatrics, Cambridge University Hospitals; Hills Road, Cambridge, UK
| | - Ana-Maria Cujba
- Wellcome Sanger Institute; Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Daniele Muraro
- Wellcome Sanger Institute; Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Emma Dann
- Wellcome Sanger Institute; Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute; Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alexander S Steemers
- Wellcome Sanger Institute; Wellcome Genome Campus, Hinxton, Cambridge, UK
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Woochan Lee
- Wellcome Sanger Institute; Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Biomedical Sciences, Seoul National University, Seoul, Korea
| | - Amanda J Oliver
- Wellcome Sanger Institute; Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jong-Eun Park
- Wellcome Sanger Institute; Wellcome Genome Campus, Hinxton, Cambridge, UK
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Kerstin B Meyer
- Wellcome Sanger Institute; Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Bianca Dumitrascu
- Department of Statistics, Columbia University, New York, NY, USA
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
| | - Sarah A Teichmann
- Wellcome Sanger Institute; Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Co-director of CIFAR Macmillan Research Program, Toronto, Ontario, Canada.
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6
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Billiet L, Jansen H, Pille M, Boehme L, Sanchez Sanchez G, De Cock L, Goetgeluk G, Pascal E, De Munter S, Deseins L, Ingels J, Michiels T, De Vos R, Zolfaghari A, Vandamme N, Roels J, Kerre T, Dmitriev RI, Taghon T, Vermijlen D, Vandekerckhove B. ThymoSpheres culture: A model to study human polyclonal unconventional T cells. Eur J Immunol 2024:e2451265. [PMID: 39246170 DOI: 10.1002/eji.202451265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/10/2024]
Abstract
In vitro cultures remain crucial for studying the fundamental mechanisms of human T-cell development. Here, we introduce a novel in vitro cultivation system based on ThymoSpheres (TS): dense spheroids consisting of DLL4-expressing stromal cells and human hematopoietic precursor cells, in the absence of thymic epithelial cells. These spheroids are subsequently cultured at the air-liquid interphase. TS generate large numbers of mature T cells, are easy to manipulate, scalable, and can be repeatably sampled to monitor T-cell differentiation. The mature T cells generated from primary human hematopoietic precursor cells were extensively characterized using single-cell RNA and combined T-cell receptor (TCR) sequencing. These predominantly CD8α T cells exhibit transcriptional and TCR CDR3 characteristics similar to the recently described human polyclonal αβ unconventional T cell (UTC) lineage. This includes the expression of hallmark genes associated with agonist selection, such as IKZF2 (Helios), and the expression of various natural killer receptors. The TCR repertoire of these UTCs is polyclonal and enriched for CDR3-associated autoreactive features and early rearrangements of the TCR-α chain. In conclusion, TS cultures offer an intriguing platform to study the development of this human polyclonal UTC lineage and its inducing selection mechanisms.
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Affiliation(s)
- Lore Billiet
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Hanne Jansen
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Melissa Pille
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Lena Boehme
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Guillem Sanchez Sanchez
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Laurenz De Cock
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Glenn Goetgeluk
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Eva Pascal
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Stijn De Munter
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lucas Deseins
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Joline Ingels
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- GMP Unit CellGenTherapies, Ghent University Hospital, Ghent, Belgium
| | - Thomas Michiels
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Robrecht De Vos
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Amin Zolfaghari
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Niels Vandamme
- VIB Single Cell Core, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jana Roels
- VIB Single Cell Core, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Tessa Kerre
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Ruslan I Dmitriev
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Bart Vandekerckhove
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- GMP Unit CellGenTherapies, Ghent University Hospital, Ghent, Belgium
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7
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Li Y, Li H, Peng C, Meng G, Lu Y, Liu H, Cui L, Zhou H, Xu Z, Sun L, Liu L, Xiong Q, Sun B, Jiao S. Unraveling the spatial organization and development of human thymocytes through integration of spatial transcriptomics and single-cell multi-omics profiling. Nat Commun 2024; 15:7784. [PMID: 39237503 PMCID: PMC11377774 DOI: 10.1038/s41467-024-51767-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 08/19/2024] [Indexed: 09/07/2024] Open
Abstract
The structural components of the thymus are essential for guiding T cell development, but a thorough spatial view is still absent. Here we develop the TSO-his tool, designed to integrate multimodal data from single-cell and spatial transcriptomics to decipher the intricate structure of human thymus. Specifically, we characterize dynamic changes in cell types and critical markers, identifying ELOVL4 as a mediator of CD4+ T cell positive selection in the cortex. Utilizing the mapping function of TSO-his, we reconstruct thymic spatial architecture at single-cell resolution and recapitulates classical cell types and their essential co-localization for T cell development; additionally, previously unknown co-localization relationships such as that of CD8αα with memory B cells and monocytes are identified. Incorporating VDJ sequencing data, we also delineate distinct intermediate thymocyte states during αβ T cell development. Overall, these insights enhance our understanding of thymic biology and may inform therapeutic interventions targeting T cell-mediated immune responses.
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Affiliation(s)
- Yanchuan Li
- Department of Cell Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Huamei Li
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Cheng Peng
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Ge Meng
- Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University, Hangzhou, China
- TCRX (KeShiHua) Therapeutics Co, Ltd. Beijing & Yunnan Pilot Free Trade Zone (Dehong Area), Beijing, China
- Department of Oncology, Department of Rheumatology and Immunology, Ruili JingCheng Hospital, Ruili, China
| | - Yijun Lu
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Honglin Liu
- Department of Pharmacy, Organoid and Regenerative Medicine Center, China-Japan Friendship Hospital, Beijing, China
| | - Li Cui
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Huan Zhou
- National Institute of Drug Clinical Trial, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Zhu Xu
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lingyun Sun
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Lihong Liu
- Department of Pharmacy, Organoid and Regenerative Medicine Center, China-Japan Friendship Hospital, Beijing, China.
| | - Qing Xiong
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China.
| | - Beicheng Sun
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China.
| | - Shiping Jiao
- Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University, Hangzhou, China.
- TCRX (KeShiHua) Therapeutics Co, Ltd. Beijing & Yunnan Pilot Free Trade Zone (Dehong Area), Beijing, China.
- Department of Oncology, Department of Rheumatology and Immunology, Ruili JingCheng Hospital, Ruili, China.
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8
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Clark PA, Gogoi M, Rodriguez-Rodriguez N, Ferreira ACF, Murphy JE, Walker JA, Crisp A, Jolin HE, Shields JD, McKenzie ANJ. Recipient tissue microenvironment determines developmental path of intestinal innate lymphoid progenitors. Nat Commun 2024; 15:7809. [PMID: 39242588 PMCID: PMC11379955 DOI: 10.1038/s41467-024-52155-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/27/2024] [Indexed: 09/09/2024] Open
Abstract
Innate lymphoid cells (ILCs) are critical in maintaining tissue homeostasis, and during infection and inflammation. Here we identify, by using combinatorial reporter mice, a rare ILC progenitor (ILCP) population, resident to the small intestinal lamina propria (siLP) in adult mice. Transfer of siLP-ILCP into recipients generates group 1 ILCs (including ILC1 and NK cells), ILC2s and ILC3s within the intestinal microenvironment, but almost exclusively group 1 ILCs in the liver, lung and spleen. Single cell gene expression analysis and high dimensional spectral cytometry analysis of the siLP-ILCPs and ILC progeny indicate that the phenotype of the group 1 ILC progeny is also influenced by the tissue microenvironment. Thus, a local pool of siLP-ILCP can contribute to pan-ILC generation in the intestinal microenvironment but has more restricted potential in other tissues, with a greater propensity than bone marrow-derived ILCPs to favour ILC1 and ILC3 production. Therefore, ILCP potential is influenced by both tissue of origin and the microenvironment during development. This may provide additional flexibility during the tuning of immune reactions.
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Affiliation(s)
- Paula A Clark
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
| | - Mayuri Gogoi
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | | | - Jane E Murphy
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Alastair Crisp
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Helen E Jolin
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Jacqueline D Shields
- Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, United Kingdom
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9
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Gu Q, Draheim M, Planchais C, He Z, Mu F, Gong S, Shen C, Zhu H, Zhivaki D, Shahin K, Collard JM, Su M, Zhang X, Mouquet H, Lo-Man R. Intestinal newborn regulatory B cell antibodies modulate microbiota communities. Cell Host Microbe 2024:S1931-3128(24)00317-2. [PMID: 39243760 DOI: 10.1016/j.chom.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 07/08/2024] [Accepted: 08/12/2024] [Indexed: 09/09/2024]
Abstract
The role of immunoglobulins produced by IL-10-producing regulatory B cells remains unknown. We found that a particular newborn regulatory B cell population (nBreg) negatively regulates the production of immunoglobulin M (IgM) via IL-10 in an autocrine manner, limiting the intensity of the polyreactive antibody response following innate activation. Based on nBreg scRNA-seq signature, we identify these cells and their repertoire in fetal and neonatal intestinal tissues. By characterizing 205 monoclonal antibodies cloned from intestinal nBreg, we show that newborn germline-encoded antibodies display reactivity against bacteria representing six different phyla of the early microbiota. nBreg-derived antibodies can influence the diversity and the cooperation between members of early microbial communities, at least in part by modulating energy metabolism. These results collectively suggest that nBreg populations help facilitate early-life microbiome establishment and shed light on the paradoxical activities of regulatory B cells in early life.
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Affiliation(s)
- Qisheng Gu
- CAS Key Laboratory of Molecular Virology and Immunology, The Center for Microbes, Development and Health, Unit of Immunity and Pediatric Infectious Diseases, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; Université Paris Cite, Paris, France
| | - Marion Draheim
- CAS Key Laboratory of Molecular Virology and Immunology, The Center for Microbes, Development and Health, Unit of Immunity and Pediatric Infectious Diseases, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Cyril Planchais
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cite, INSERM U1222, Paris, France
| | - Zihan He
- CAS Key Laboratory of Molecular Virology and Immunology, The Center for Microbes, Development and Health, Unit of Immunity and Pediatric Infectious Diseases, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Fan Mu
- CAS Key Laboratory of Molecular Virology and Immunology, The Center for Microbes, Development and Health, Unit of Immunity and Pediatric Infectious Diseases, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Shijie Gong
- CAS Key Laboratory of Molecular Virology and Immunology, The Center for Microbes, Development and Health, Unit of Immunity and Pediatric Infectious Diseases, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Chun Shen
- Children's Hospital of Fudan University, Shanghai, China
| | - Haitao Zhu
- Children's Hospital of Fudan University (Xiamen Branch), Xiamen Children's Hospital, Xiamen, China
| | - Dania Zhivaki
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Khashayar Shahin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan Microbiome Center, and Human Phenome Institute, Fudan University, Shanghai, China
| | - Jean-Marc Collard
- Enteric Bacterial Pathogens Unit & French National Reference Center for Escherichia Coli, Shigella and Salmonella, Institut Pasteur, Paris, France
| | - Min Su
- Obstetrics department, Affiliated Hospital of Nantong University, Nantong, China
| | - Xiaoming Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, The Center for Microbes, Development and Health, Unit of Innate Defense and Immune Modulation, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Hugo Mouquet
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cite, INSERM U1222, Paris, France.
| | - Richard Lo-Man
- CAS Key Laboratory of Molecular Virology and Immunology, The Center for Microbes, Development and Health, Unit of Immunity and Pediatric Infectious Diseases, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; Université Paris Cite, Paris, France.
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10
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Ransegnola BP, Pattarabanjird T, McNamara CA. Tipping the Scale: Atheroprotective IgM-Producing B Cells in Atherosclerosis. Arterioscler Thromb Vasc Biol 2024; 44:1906-1915. [PMID: 39022832 PMCID: PMC11338718 DOI: 10.1161/atvbaha.124.319847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Atherosclerosis is a chronic inflammatory disease whose progression is fueled by proinflammatory moieties and limited by anti-inflammatory mediators. Whereas oxidative damage and the generation of oxidation-specific epitopes that act as damage-associated molecular patterns are highly inflammatory, IgM antibodies produced by B-1 and marginal zone B cells counteract unrestricted inflammation by neutralizing and encouraging clearance of these proinflammatory signals. In this review, we focus on describing the identities of IgM-producing B cells in both mice and humans, elaborating the mechanisms underlying IgM production, and discussing the potential strategies to augment the production of atheroprotective IgM. In addition, we will discuss promising therapeutic interventions in humans to help tip the scale toward augmentation of IgM production and to provide atheroprotection.
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Affiliation(s)
- Brett Patrick Ransegnola
- Medical Scientist Training Program, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Department of Pathology, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Beirne B. Carter Immunology Center, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Tanyaporn Pattarabanjird
- Medical Scientist Training Program, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Beirne B. Carter Immunology Center, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Coleen A. McNamara
- Beirne B. Carter Immunology Center, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Robert M. Berne Cardiovascular Research Center, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
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11
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Ravens S, Tolosa E. Expansion of human γδ T cells in periphery: Lessons learned from development, infections, and compromised thymic function. Eur J Immunol 2024:e2451073. [PMID: 39194409 DOI: 10.1002/eji.202451073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]
Abstract
γδ T cells predominantly develop in the fetal period. Post birth they respond swiftly to environmental insults, pathogens and tumors, especially when other immune effector cells are less ready to function. Most of our understanding of γδ T-cell development, peripheral adaptation, and function derives from murine studies. The recent advancement of immunological methods allows now to decipher human γδ T-cell biology in patient cohorts and tissue samples, and to manipulate them using in vitro systems. In this review, we summarize γδ T-cell development in the human thymus, their functional adaptation to the microbial environment from birth until old age, and their capacity to expand and fill up the peripheral niche under conditions of perturbations of conventional T-cell development.
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Affiliation(s)
- Sarina Ravens
- Institute of Immunology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Eva Tolosa
- Institute of Immunology, UKE Hamburg, Hamburg, Germany
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12
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Wei C, Ma Y, Wang M, Wang S, Yu W, Dong S, Deng W, Bie L, Zhang C, Shen W, Xia Q, Luo S, Li N. Tumor-associated macrophage clusters linked to immunotherapy in a pan-cancer census. NPJ Precis Oncol 2024; 8:176. [PMID: 39117688 PMCID: PMC11310399 DOI: 10.1038/s41698-024-00660-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Transcriptional heterogeneity of tumor-associated macrophages (TAMs) has been investigated in individual cancers, but the extent to which these states transcend tumor types and represent a general feature of cancer remains unclear. We performed pan-cancer single-cell RNA sequencing analysis across nine cancer types and identified distinct monocyte/TAM composition patterns. Using spatial analysis from clinical study tissues, we assessed TAM functions in shaping the tumor microenvironment (TME) and influencing immunotherapy. Two specific TAM clusters (pro-inflammatory and pro-tumor) and four TME subtypes showed distinct immunological features, genomic profiles, immunotherapy responses, and cancer prognosis. Pro-inflammatory TAMs resided in immune-enriched niches with exhausted CD8+ T cells, while pro-tumor TAMs were restricted to niches associated with a T-cell-excluded phenotype and hypoxia. We developed a machine learning model to predict immune checkpoint blockade response by integrating TAMs and clinical data. Our study comprehensively characterizes the common features of TAMs and highlights their interaction with the TME.
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Affiliation(s)
- Chen Wei
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Yijie Ma
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Mengyu Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Siyi Wang
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Wenyue Yu
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Shuailei Dong
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wenying Deng
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Liangyu Bie
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Chi Zhang
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wei Shen
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Qingxin Xia
- Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| | - Suxia Luo
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| | - Ning Li
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
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13
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Mattos MS, Vandendriessche S, Waisman A, Marques PE. The immunology of B-1 cells: from development to aging. Immun Ageing 2024; 21:54. [PMID: 39095816 PMCID: PMC11295433 DOI: 10.1186/s12979-024-00455-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024]
Abstract
B-1 cells have intricate biology, with distinct function, phenotype and developmental origin from conventional B cells. They generate a B cell receptor with conserved germline characteristics and biased V(D)J recombination, allowing this innate-like lymphocyte to spontaneously produce self-reactive natural antibodies (NAbs) and become activated by immune stimuli in a T cell-independent manner. NAbs were suggested as "rheostats" for the chronic diseases in advanced age. In fact, age-dependent loss of function of NAbs has been associated with clinically-relevant diseases in the elderly, such as atherosclerosis and neurodegenerative disorders. Here, we analyzed comprehensively the ontogeny, phenotypic characteristics, functional properties and emerging roles of B-1 cells and NAbs in health and disease. Additionally, after navigating through the complexities of B-1 cell biology from development to aging, therapeutic opportunities in the field are discussed.
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Affiliation(s)
- Matheus Silvério Mattos
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Louvain, Belgium
| | - Sofie Vandendriessche
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Louvain, Belgium
| | - Ari Waisman
- Institute for Molecular Medicine, University Medical Centre of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Pedro Elias Marques
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Louvain, Belgium.
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14
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Talks BJ, Mather MW, Chahal M, Coates M, Clatworthy MR, Haniffa M. Mapping Human Immunity and the Education of Waldeyer's Ring. Annu Rev Genomics Hum Genet 2024; 25:161-182. [PMID: 38594932 DOI: 10.1146/annurev-genom-120522-012938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The development and deployment of single-cell genomic technologies have driven a resolution revolution in our understanding of the immune system, providing unprecedented insight into the diversity of immune cells present throughout the body and their function in health and disease. Waldeyer's ring is the collective name for the lymphoid tissue aggregations of the upper aerodigestive tract, comprising the palatine, pharyngeal (adenoids), lingual, and tubal tonsils. These tonsils are the first immune sentinels encountered by ingested and inhaled antigens and are responsible for mounting the first wave of adaptive immune response. An effective mucosal immune response is critical to neutralizing infection in the upper airway and preventing systemic spread, and dysfunctional immune responses can result in ear, nose, and throat pathologies. This review uses Waldeyer's ring to demonstrate how single-cell technologies are being applied to advance our understanding of the immune system and highlight directions for future research.
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Affiliation(s)
- Benjamin J Talks
- Department of Otolaryngology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; , ,
| | - Michael W Mather
- Department of Otolaryngology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; , ,
| | - Manisha Chahal
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; , ,
| | - Matthew Coates
- Department of Medicine, University of Cambridge, Cambridge, UK; ,
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Hinxton, UK;
- Department of Medicine, University of Cambridge, Cambridge, UK; ,
| | - Muzlifah Haniffa
- Department of Dermatology and National Institute for Health and Care Research (NIHR) Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Sanger Institute, Hinxton, UK;
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; , ,
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15
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Palis J. Erythropoiesis in the mammalian embryo. Exp Hematol 2024; 136:104283. [PMID: 39048071 DOI: 10.1016/j.exphem.2024.104283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
Red blood cells (RBCs) comprise a critical component of the cardiovascular network, which constitutes the first functional organ system of the developing mammalian embryo. Examination of circulating blood cells in mammalian embryos revealed two distinct types of erythroid cells: large, nucleated "primitive" erythroblasts followed by smaller, enucleated "definitive" erythrocytes. This review describes the current understanding of primitive and definitive erythropoiesis gleaned from studies of mouse and human embryos and induced pluripotent stem cells (iPSCs). Primitive erythropoiesis in the mouse embryo comprises a transient wave of committed primitive erythroid progenitors (primitive erythroid colony-forming cells, EryP-CFC) in the early yolk sac that generates a robust cohort of precursors that mature in the bloodstream and enucleate. In contrast, definitive erythropoiesis has two distinct developmental origins. The first comprises a transient wave of definitive erythroid progenitors (burst-forming units erythroid, BFU-E) that emerge in the yolk sac and seed the fetal liver where they terminally mature to provide the first definitive RBCs. The second comprises hematopoietic stem cell (HSC)-derived BFU-E that terminally mature at sites colonized by HSCs particularly the fetal liver and subsequently the bone marrow. Primitive and definitive erythropoiesis are derived from endothelial identity precursors with distinct developmental origins. Although they share prototypical transcriptional regulation, primitive and definitive erythropoiesis are also characterized by distinct lineage-specific factors. The exquisitely timed, sequential production of primitive and definitive erythroid cells is necessary for the survival and growth of the mammalian embryo.
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Affiliation(s)
- James Palis
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY.
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16
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Jaeger N, Antonova AU, Kreisel D, Roan F, Lantelme E, Ziegler SF, Cella M, Colonna M. Diversity of group 1 innate lymphoid cells in human tissues. Nat Immunol 2024; 25:1460-1473. [PMID: 38956380 DOI: 10.1038/s41590-024-01885-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/31/2024] [Indexed: 07/04/2024]
Abstract
Group 1 innate lymphoid cells (ILC1s) are cytotoxic and interferon gamma-producing lymphocytes lacking antigen-specific receptors, which include ILC1s and natural killer (NK) cells. In mice, ILC1s differ from NK cells, as they develop independently of the NK-specifying transcription factor EOMES, while requiring the repressor ZFP683 (ZNF683 in humans) for tissue residency. Here we identify highly variable ILC1 subtypes across tissues through investigation of human ILC1 diversity by single-cell RNA sequencing and flow cytometry. The intestinal epithelium contained abundant mature EOMES- ILC1s expressing PRDM1 rather than ZNF683, alongside a few immature TCF7+PRDM1- ILC1s. Other tissues harbored NK cells expressing ZNF683 and EOMES transcripts; however, EOMES protein content was variable. These ZNF683+ NK cells are tissue-imprinted NK cells phenotypically resembling ILC1s. The tissue ILC1-NK spectrum also encompassed conventional NK cells and NK cells distinguished by PTGDS expression. These findings establish a foundation for evaluating phenotypic and functional changes within the NK-ILC1 spectrum in diseases.
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Affiliation(s)
- Natalia Jaeger
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alina Ulezko Antonova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel Kreisel
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Florence Roan
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA, USA
| | - Erica Lantelme
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Steven F Ziegler
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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17
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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18
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von Loeffelholz C, Winkler R, Weigel C, Piskor EM, Vivas W, Rauchfuß F, Settmacher U, Rubio I, Weis S, Gräler MH, Bauer M, Kosan C. Increased peritoneal B1-like cells during acute phase of human septic peritonitis. iScience 2024; 27:110133. [PMID: 38984201 PMCID: PMC11231613 DOI: 10.1016/j.isci.2024.110133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/13/2024] [Accepted: 05/24/2024] [Indexed: 07/11/2024] Open
Abstract
Sepsis is a life-threatening condition caused by dysregulated host responses to infection. Myeloid cell accumulation and lymphocyte decline are widely recognized phenomena in septic patients. However, the fate of specific immune cells remains unclear. Here, we report the results of a human explorative study of patients with septic peritonitis and patients undergoing abdominal surgery without sepsis. We analyzed pairwise peritoneal fluid and peripheral blood taken 24 h after surgery to characterize immediate immune cell changes. Our results show that myeloid cell expansion and lymphocyte loss occur in all patients undergoing open abdominal surgery, indicating that these changes are not specific to sepsis. However, B1-like lymphocytes were specifically increased in the peritoneal fluid of septic patients, correlating positively with sequential organ failure assessment (SOFA) and acute physiology and chronic health evaluation II (APACHE-II) clinical severity scores. In support of this notion, we identified an accumulation of peritoneal B1b lymphocytes in septic mice.
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Affiliation(s)
- Christian von Loeffelholz
- Department of Anesthesiology and Intensive Care, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07749 Jena, Germany
| | - René Winkler
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Cynthia Weigel
- Department of Anesthesiology and Intensive Care, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07749 Jena, Germany
- Center for Molecular Biomedicine (CMB), Friedrich Schiller University, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Eva-Maria Piskor
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Wolfgang Vivas
- Department of Anesthesiology and Intensive Care, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07749 Jena, Germany
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany
- Institute of Infectious Disease and Infection Control, Friedrich Schiller University, Am Klinikum 1, 07749 Jena, Germany
| | - Falk Rauchfuß
- Department of General, Visceral and Vascular Surgery, Jena University Hospital, Am Klinikum 1, 07749 Jena, Germany
| | - Utz Settmacher
- Department of General, Visceral and Vascular Surgery, Jena University Hospital, Am Klinikum 1, 07749 Jena, Germany
| | - Ignacio Rubio
- Department of Anesthesiology and Intensive Care, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07749 Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07749 Jena, Germany
| | - Sebastian Weis
- Department of Anesthesiology and Intensive Care, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07749 Jena, Germany
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany
- Institute of Infectious Disease and Infection Control, Friedrich Schiller University, Am Klinikum 1, 07749 Jena, Germany
| | - Markus H. Gräler
- Department of Anesthesiology and Intensive Care, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07749 Jena, Germany
- Center for Molecular Biomedicine (CMB), Friedrich Schiller University, Hans-Knöll-Str. 2, 07745 Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07749 Jena, Germany
| | - Michael Bauer
- Department of Anesthesiology and Intensive Care, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07749 Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07749 Jena, Germany
| | - Christian Kosan
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University, Hans-Knöll-Str. 2, 07745 Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07749 Jena, Germany
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19
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Oguchi A, Suzuki A, Komatsu S, Yoshitomi H, Bhagat S, Son R, Bonnal RJP, Kojima S, Koido M, Takeuchi K, Myouzen K, Inoue G, Hirai T, Sano H, Takegami Y, Kanemaru A, Yamaguchi I, Ishikawa Y, Tanaka N, Hirabayashi S, Konishi R, Sekito S, Inoue T, Kere J, Takeda S, Takaori-Kondo A, Endo I, Kawaoka S, Kawaji H, Ishigaki K, Ueno H, Hayashizaki Y, Pagani M, Carninci P, Yanagita M, Parrish N, Terao C, Yamamoto K, Murakawa Y. An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases. Science 2024; 385:eadd8394. [PMID: 38963856 DOI: 10.1126/science.add8394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 05/01/2024] [Indexed: 07/06/2024]
Abstract
Transcribed enhancer maps can reveal nuclear interactions underpinning each cell type and connect specific cell types to diseases. Using a 5' single-cell RNA sequencing approach, we defined transcription start sites of enhancer RNAs and other classes of coding and noncoding RNAs in human CD4+ T cells, revealing cellular heterogeneity and differentiation trajectories. Integration of these datasets with single-cell chromatin profiles showed that active enhancers with bidirectional RNA transcription are highly cell type-specific and that disease heritability is strongly enriched in these enhancers. The resulting cell type-resolved multimodal atlas of bidirectionally transcribed enhancers, which we linked with promoters using fine-scale chromatin contact maps, enabled us to systematically interpret genetic variants associated with a range of immune-mediated diseases.
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Affiliation(s)
- Akiko Oguchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shuichiro Komatsu
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Hiroyuki Yoshitomi
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shruti Bhagat
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Raku Son
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Shohei Kojima
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masaru Koido
- Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuhiro Takeuchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keiko Myouzen
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Gyo Inoue
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomoya Hirai
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Hiromi Sano
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | | | | | - Yuki Ishikawa
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Nao Tanaka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shigeki Hirabayashi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Riyo Konishi
- Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sho Sekito
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie University, Tsu, Japan
| | - Takahiro Inoue
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie University, Tsu, Japan
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhalsan Research Center, Helsinki, Finland
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Shinpei Kawaoka
- Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Integrative Bioanalytics, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Science, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hideki Ueno
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihide Hayashizaki
- K.K. DNAFORM, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Massimiliano Pagani
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi, Milan, Italy
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Motoko Yanagita
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nicholas Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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20
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O’Brien JW, Case A, Kemper C, Zhao TX, Mallat Z. Therapeutic Avenues to Modulate B-Cell Function in Patients With Cardiovascular Disease. Arterioscler Thromb Vasc Biol 2024; 44:1512-1522. [PMID: 38813699 PMCID: PMC11208059 DOI: 10.1161/atvbaha.124.319844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
The adaptive immune system plays an important role in the development and progression of atherosclerotic cardiovascular disease. B cells can have both proatherogenic and atheroprotective roles, making treatments aimed at modulating B cells important therapeutic targets. The innate-like B-cell response is generally considered atheroprotective, while the adaptive response is associated with mixed consequences for atherosclerosis. Additionally, interactions of B cells with components of the adaptive and innate immune system, including T cells and complement, also represent key points for therapeutic regulation. In this review, we discuss therapeutic approaches based on B-cell depletion, modulation of B-cell survival, manipulation of both the antibody-dependent and antibody-independent B-cell response, and emerging immunization techniques.
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Affiliation(s)
- James W. O’Brien
- Division of Cardiorespiratory Medicine, Department of Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, United Kingdom (J.W.O., A.C., T.X.Z., Z.M.)
| | - Ayden Case
- Division of Cardiorespiratory Medicine, Department of Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, United Kingdom (J.W.O., A.C., T.X.Z., Z.M.)
| | - Claudia Kemper
- Complement and Inflammation Research Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (C.K.)
| | - Tian X. Zhao
- Division of Cardiorespiratory Medicine, Department of Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, United Kingdom (J.W.O., A.C., T.X.Z., Z.M.)
- Department of Cardiology, Royal Papworth Hospital, Cambridge, United Kingdom (T.X.Z.)
| | - Ziad Mallat
- Division of Cardiorespiratory Medicine, Department of Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, United Kingdom (J.W.O., A.C., T.X.Z., Z.M.)
- Unversité de Paris, Inserm U970, Paris Cardiovascular Research Centre, France (Z.M.)
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21
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Jones PW, Mallat Z, Nus M. T-Cell/B-Cell Interactions in Atherosclerosis. Arterioscler Thromb Vasc Biol 2024; 44:1502-1511. [PMID: 38813700 PMCID: PMC11208060 DOI: 10.1161/atvbaha.124.319845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Atherosclerosis is a complex inflammatory disease in which the adaptive immune response plays an important role. While the overall impact of T and B cells in atherosclerosis is relatively well established, we are only beginning to understand how bidirectional T-cell/B-cell interactions can exert prominent atheroprotective and proatherogenic functions. In this review, we will focus on these T-cell/B-cell interactions and how we could use them to therapeutically target the adaptive immune response in atherosclerosis.
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Affiliation(s)
- Peter William Jones
- Cardiovascular Division, Department of Medicine, Heart and Lung Research Institute, University of Cambridge, United Kingdom (P.W.J., Z.M., M.N.)
| | - Ziad Mallat
- Cardiovascular Division, Department of Medicine, Heart and Lung Research Institute, University of Cambridge, United Kingdom (P.W.J., Z.M., M.N.)
- INSERM U970, Paris Cardiovascular Research Centre, France (Z.M.)
| | - Meritxell Nus
- Cardiovascular Division, Department of Medicine, Heart and Lung Research Institute, University of Cambridge, United Kingdom (P.W.J., Z.M., M.N.)
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22
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Lindeboom RGH, Worlock KB, Dratva LM, Yoshida M, Scobie D, Wagstaffe HR, Richardson L, Wilbrey-Clark A, Barnes JL, Kretschmer L, Polanski K, Allen-Hyttinen J, Mehta P, Sumanaweera D, Boccacino JM, Sungnak W, Elmentaite R, Huang N, Mamanova L, Kapuge R, Bolt L, Prigmore E, Killingley B, Kalinova M, Mayer M, Boyers A, Mann A, Swadling L, Woodall MNJ, Ellis S, Smith CM, Teixeira VH, Janes SM, Chambers RC, Haniffa M, Catchpole A, Heyderman R, Noursadeghi M, Chain B, Mayer A, Meyer KB, Chiu C, Nikolić MZ, Teichmann SA. Human SARS-CoV-2 challenge uncovers local and systemic response dynamics. Nature 2024; 631:189-198. [PMID: 38898278 PMCID: PMC11222146 DOI: 10.1038/s41586-024-07575-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
The COVID-19 pandemic is an ongoing global health threat, yet our understanding of the dynamics of early cellular responses to this disease remains limited1. Here in our SARS-CoV-2 human challenge study, we used single-cell multi-omics profiling of nasopharyngeal swabs and blood to temporally resolve abortive, transient and sustained infections in seronegative individuals challenged with pre-Alpha SARS-CoV-2. Our analyses revealed rapid changes in cell-type proportions and dozens of highly dynamic cellular response states in epithelial and immune cells associated with specific time points and infection status. We observed that the interferon response in blood preceded the nasopharyngeal response. Moreover, nasopharyngeal immune infiltration occurred early in samples from individuals with only transient infection and later in samples from individuals with sustained infection. High expression of HLA-DQA2 before inoculation was associated with preventing sustained infection. Ciliated cells showed multiple immune responses and were most permissive for viral replication, whereas nasopharyngeal T cells and macrophages were infected non-productively. We resolved 54 T cell states, including acutely activated T cells that clonally expanded while carrying convergent SARS-CoV-2 motifs. Our new computational pipeline Cell2TCR identifies activated antigen-responding T cells based on a gene expression signature and clusters these into clonotype groups and motifs. Overall, our detailed time series data can serve as a Rosetta stone for epithelial and immune cell responses and reveals early dynamic responses associated with protection against infection.
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Affiliation(s)
- Rik G H Lindeboom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Lisa M Dratva
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - David Scobie
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Helen R Wagstaffe
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | | | | | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | | | - Waradon Sungnak
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Microbiology, Faculty of Science, and Integrative Computational BioScience Center, Mahidol University, Bangkok, Thailand
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Ensocell Therapeutics, BioData Innovation Centre, Wellcome Genome Campus, Hinxton, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Rakesh Kapuge
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ben Killingley
- Department of Infectious Diseases, University College London Hospital, London, UK
| | | | | | | | | | - Leo Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
| | | | - Samuel Ellis
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Claire M Smith
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Vitor H Teixeira
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Rachel C Chambers
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Robert Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Mahdad Noursadeghi
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Benny Chain
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Andreas Mayer
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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23
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Sánchez MF, Faria S, Frühschulz S, Werkmann L, Winter C, Karimian T, Lanzerstorfer P, Plochberger B, Weghuber J, Tampé R. Engineering Mesoscale T Cell Receptor Clustering by Plug-and-Play Nanotools. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2310407. [PMID: 38924642 DOI: 10.1002/adma.202310407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 06/10/2024] [Indexed: 06/28/2024]
Abstract
T cell receptor (TCR) clustering and formation of an immune synapse are crucial for TCR signaling. However, limited information is available about these dynamic assemblies and their connection to transmembrane signaling. In this work, TCR clustering is controlled via plug-and-play nanotools based on an engineered irreversible conjugation pair and a peptide-loaded major histocompatibility complex (pMHC) molecule to compare receptor assembly in a ligand (pMHC)-induced or ligand-independent manner. A streptavidin-binding peptide displayed in both tools enabled their anchoring in streptavidin-pre-structured matrices. Strikingly, pMHC-induced clustering in the confined regions exhibit higher density and dynamics than the ligand-free approach, indicating that the size and architecture of the pMHC ligand influences TCR assembly. This approach enables the control of membrane receptor clustering with high specificity and provides the possibility to explore different modalities of receptor activation.
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Affiliation(s)
- M Florencia Sánchez
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Sevi Faria
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Stefan Frühschulz
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Lars Werkmann
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Christian Winter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Tina Karimian
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Wels, 4600, Austria
| | - Peter Lanzerstorfer
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Wels, 4600, Austria
| | - Birgit Plochberger
- University of Applied Sciences Upper Austria, Campus Linz, Linz, 4020, Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Donaueschingenstr. 13, Vienna, 1200, Austria
| | - Julian Weghuber
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Wels, 4600, Austria
- FFoQSI - Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, FFoQSI GmbH, Technopark 1D, Tulln an der Donau, 3430, Austria
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
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24
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McLean AK, Reynolds G, Pratt AG. Leveraging Multi-Tissue, Single-Cell Atlases as Tools to Elucidate Shared Mechanisms of Immune-Mediated Inflammatory Diseases. Biomedicines 2024; 12:1297. [PMID: 38927506 PMCID: PMC11201400 DOI: 10.3390/biomedicines12061297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The observation that certain therapeutic strategies for targeting inflammation benefit patients with distinct immune-mediated inflammatory diseases (IMIDs) is exemplified by the success of TNF blockade in conditions including rheumatoid arthritis, ulcerative colitis, and skin psoriasis, albeit only for subsets of individuals with each condition. This suggests intersecting "nodes" in inflammatory networks at a molecular and cellular level may drive and/or maintain IMIDs, being "shared" between traditionally distinct diagnoses without mapping neatly to a single clinical phenotype. In line with this proposition, integrative tumour tissue analyses in oncology have highlighted novel cell states acting across diverse cancers, with important implications for precision medicine. Drawing upon advances in the oncology field, this narrative review will first summarise learnings from the Human Cell Atlas in health as a platform for interrogating IMID tissues. It will then review cross-disease studies to date that inform this endeavour before considering future directions in the field.
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Affiliation(s)
- Anthony K. McLean
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Gary Reynolds
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Arthur G. Pratt
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Musculoskeletal Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
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25
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Curion F, Theis FJ. Machine learning integrative approaches to advance computational immunology. Genome Med 2024; 16:80. [PMID: 38862979 PMCID: PMC11165829 DOI: 10.1186/s13073-024-01350-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 05/23/2024] [Indexed: 06/13/2024] Open
Abstract
The study of immunology, traditionally reliant on proteomics to evaluate individual immune cells, has been revolutionized by single-cell RNA sequencing. Computational immunologists play a crucial role in analysing these datasets, moving beyond traditional protein marker identification to encompass a more detailed view of cellular phenotypes and their functional roles. Recent technological advancements allow the simultaneous measurements of multiple cellular components-transcriptome, proteome, chromatin, epigenetic modifications and metabolites-within single cells, including in spatial contexts within tissues. This has led to the generation of complex multiscale datasets that can include multimodal measurements from the same cells or a mix of paired and unpaired modalities. Modern machine learning (ML) techniques allow for the integration of multiple "omics" data without the need for extensive independent modelling of each modality. This review focuses on recent advancements in ML integrative approaches applied to immunological studies. We highlight the importance of these methods in creating a unified representation of multiscale data collections, particularly for single-cell and spatial profiling technologies. Finally, we discuss the challenges of these holistic approaches and how they will be instrumental in the development of a common coordinate framework for multiscale studies, thereby accelerating research and enabling discoveries in the computational immunology field.
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Affiliation(s)
- Fabiola Curion
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.
- School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
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26
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Hoedjes KM, Grath S, Posnien N, Ritchie MG, Schlötterer C, Abbott JK, Almudi I, Coronado-Zamora M, Durmaz Mitchell E, Flatt T, Fricke C, Glaser-Schmitt A, González J, Holman L, Kankare M, Lenhart B, Orengo DJ, Snook RR, Yılmaz VM, Yusuf L. From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology. Mol Ecol 2024:e17382. [PMID: 38856653 DOI: 10.1111/mec.17382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/09/2024] [Accepted: 04/29/2024] [Indexed: 06/11/2024]
Abstract
RNA sequencing (RNAseq) methodology has experienced a burst of technological developments in the last decade, which has opened up opportunities for studying the mechanisms of adaptation to environmental factors at both the organismal and cellular level. Selecting the most suitable experimental approach for specific research questions and model systems can, however, be a challenge and researchers in ecology and evolution are commonly faced with the choice of whether to study gene expression variation in whole bodies, specific tissues, and/or single cells. A wide range of sometimes polarised opinions exists over which approach is best. Here, we highlight the advantages and disadvantages of each of these approaches to provide a guide to help researchers make informed decisions and maximise the power of their study. Using illustrative examples of various ecological and evolutionary research questions, we guide the readers through the different RNAseq approaches and help them identify the most suitable design for their own projects.
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Affiliation(s)
- Katja M Hoedjes
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sonja Grath
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Nico Posnien
- Department of Developmental Biology, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Michael G Ritchie
- Centre for Biological Diversity, University of St Andrews, St Andrews, UK
| | | | | | - Isabel Almudi
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | | | - Esra Durmaz Mitchell
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Claudia Fricke
- Institute for Zoology/Animal Ecology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | | | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, Barcelona, Spain
| | - Luke Holman
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Benedict Lenhart
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Rhonda R Snook
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Vera M Yılmaz
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Leeban Yusuf
- Centre for Biological Diversity, University of St Andrews, St Andrews, UK
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Gill JS, Bansal B, Guo K, Huang F, Singh H, Hur J, Khan N, Mathur R. Mitochondrial Oxidative Stress Regulates FOXP3+ T-Cell Activity and CD4-Mediated Inflammation in Older Adults with Frailty. Int J Mol Sci 2024; 25:6235. [PMID: 38892421 PMCID: PMC11173216 DOI: 10.3390/ijms25116235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
In healthy older adults, the immune system generally preserves its response and contributes to a long, healthy lifespan. However, rapid deterioration in immune regulation can lead to chronic inflammation, termed inflammaging, which accelerates pathological aging and diminishes the quality of life in older adults with frailty. A significant limitation in current aging research is the predominant focus on comparisons between young and older populations, often overlooking the differences between healthy older adults and those experiencing pathological aging. Our study elucidates the intricate immunological dynamics of the CD4/Treg axis in frail older adults compared to comparable age-matched healthy older adults. By utilizing publicly available RNA sequencing and single-cell RNA sequencing (scRNAseq) data from peripheral blood mononuclear cells (PBMCs), we identified a specific Treg cell subset and transcriptional landscape contributing to the dysregulation of CD4+ T-cell responses. We explored the molecular mechanisms underpinning Treg dysfunction, revealing that Tregs from frail older adults exhibit reduced mitochondrial protein levels, impairing mitochondrial oxidative phosphorylation. This impairment is driven by the TNF/NF-kappa B pathway, leading to cumulative inflammation. Further, we gained a deeper understanding of the CD4/Treg axis by predicting the effects of gene perturbations on cellular signaling networks. Collectively, these findings highlight the age-related relationship between mitochondrial dysfunction in the CD4/Treg axis and its role in accelerating aging and frailty in older adults. Targeting Treg dysfunction offers a critical basis for developing tailored therapeutic strategies aimed at improving the quality of life in older adults.
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Affiliation(s)
- Jappreet Singh Gill
- Department of Geriatrics, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (J.S.G.); (B.B.); (H.S.)
- Department of Biomedical Engineering, School of Electrical Engineering and Computer Sciences, University of North Dakota, Grand Forks, ND 58292, USA
| | - Benu Bansal
- Department of Geriatrics, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (J.S.G.); (B.B.); (H.S.)
- Department of Biomedical Engineering, School of Electrical Engineering and Computer Sciences, University of North Dakota, Grand Forks, ND 58292, USA
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (K.G.); (F.H.); (J.H.)
| | - Kai Guo
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (K.G.); (F.H.); (J.H.)
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fang Huang
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (K.G.); (F.H.); (J.H.)
| | - Harpreet Singh
- Department of Geriatrics, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (J.S.G.); (B.B.); (H.S.)
| | - Junguk Hur
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (K.G.); (F.H.); (J.H.)
| | - Nadeem Khan
- Department of Oral Biology, University of Florida, Gainsville, FL 32603, USA;
| | - Ramkumar Mathur
- Department of Geriatrics, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (J.S.G.); (B.B.); (H.S.)
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28
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Tang X, Zhang Y, Zhang H, Zhang N, Dai Z, Cheng Q, Li Y. Single-Cell Sequencing: High-Resolution Analysis of Cellular Heterogeneity in Autoimmune Diseases. Clin Rev Allergy Immunol 2024; 66:376-400. [PMID: 39186216 DOI: 10.1007/s12016-024-09001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2024] [Indexed: 08/27/2024]
Abstract
Autoimmune diseases (AIDs) are complex in etiology and diverse in classification but clinically show similar symptoms such as joint pain and skin problems. As a result, the diagnosis is challenging, and usually, only broad treatments can be available. Consequently, the clinical responses in patients with different types of AIDs are unsatisfactory. Therefore, it is necessary to conduct more research to figure out the pathogenesis and therapeutic targets of AIDs. This requires research technologies with strong extraction and prediction capabilities. Single-cell sequencing technology analyses the genomic, epigenomic, or transcriptomic information at the single-cell level. It can define different cell types and states in greater detail, further revealing the molecular mechanisms that drive disease progression. These advantages enable cell biology research to achieve an unprecedented resolution and scale, bringing a whole new vision to life science research. In recent years, single-cell technology especially single-cell RNA sequencing (scRNA-seq) has been widely used in various disease research. In this paper, we present the innovations and applications of single-cell sequencing in the medical field and focus on the application contributing to the differential diagnosis and precise treatment of AIDs. Despite some limitations, single-cell sequencing has a wide range of applications in AIDs. We finally present a prospect for the development of single-cell sequencing. These ideas may provide some inspiration for subsequent research.
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Affiliation(s)
- Xuening Tang
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yudi Zhang
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Nan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Yongzhen Li
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
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29
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Chen R, Lukianova E, van der Loeff IS, Spegarova JS, Willet JDP, James KD, Ryder EJ, Griffin H, IJspeert H, Gajbhiye A, Lamoliatte F, Marin-Rubio JL, Woodbine L, Lemos H, Swan DJ, Pintar V, Sayes K, Ruiz-Morales ER, Eastham S, Dixon D, Prete M, Prigmore E, Jeggo P, Boyes J, Mellor A, Huang L, van der Burg M, Engelhardt KR, Stray-Pedersen A, Erichsen HC, Gennery AR, Trost M, Adams DJ, Anderson G, Lorenc A, Trynka G, Hambleton S. NUDCD3 deficiency disrupts V(D)J recombination to cause SCID and Omenn syndrome. Sci Immunol 2024; 9:eade5705. [PMID: 38787962 DOI: 10.1126/sciimmunol.ade5705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Inborn errors of T cell development present a pediatric emergency in which timely curative therapy is informed by molecular diagnosis. In 11 affected patients across four consanguineous kindreds, we detected homozygosity for a single deleterious missense variant in the gene NudC domain-containing 3 (NUDCD3). Two infants had severe combined immunodeficiency with the complete absence of T and B cells (T -B- SCID), whereas nine showed classical features of Omenn syndrome (OS). Restricted antigen receptor gene usage by residual T lymphocytes suggested impaired V(D)J recombination. Patient cells showed reduced expression of NUDCD3 protein and diminished ability to support RAG-mediated recombination in vitro, which was associated with pathologic sequestration of RAG1 in the nucleoli. Although impaired V(D)J recombination in a mouse model bearing the homologous variant led to milder immunologic abnormalities, NUDCD3 is absolutely required for healthy T and B cell development in humans.
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Affiliation(s)
- Rui Chen
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Elena Lukianova
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Ina Schim van der Loeff
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
| | | | - Joseph D P Willet
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Kieran D James
- Institute of Immunology and Immunotherapy, University of Birmingham. B15 2TT Birmingham, UK
| | - Edward J Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Helen Griffin
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Hanna IJspeert
- Department of Immunology, Erasmus University Medical Center, Rotterdam 3000 CA, Netherlands
| | - Akshada Gajbhiye
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Frederic Lamoliatte
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Jose L Marin-Rubio
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Lisa Woodbine
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Brighton, UK
| | - Henrique Lemos
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - David J Swan
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Valeria Pintar
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Kamal Sayes
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | | | - Simon Eastham
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - David Dixon
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Penny Jeggo
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Brighton, UK
| | - Joan Boyes
- Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, UK
| | - Andrew Mellor
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Lei Huang
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Mirjam van der Burg
- Department of Immunology, Erasmus University Medical Center, Rotterdam 3000 CA, Netherlands
| | - Karin R Engelhardt
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo 0424, Norway
| | - Hans Christian Erichsen
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo 0424, Norway
| | - Andrew R Gennery
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
| | - Matthias Trost
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Graham Anderson
- Institute of Immunology and Immunotherapy, University of Birmingham. B15 2TT Birmingham, UK
| | - Anna Lorenc
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Gosia Trynka
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
- Open Targets, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Sophie Hambleton
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
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30
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Fujiwara N, Kimura G, Nakagawa H. Emerging Roles of Spatial Transcriptomics in Liver Research. Semin Liver Dis 2024; 44:115-132. [PMID: 38574750 DOI: 10.1055/a-2299-7880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Spatial transcriptomics, leveraging sequencing- and imaging-based techniques, has emerged as a groundbreaking technology for mapping gene expression within the complex architectures of tissues. This approach provides an in-depth understanding of cellular and molecular dynamics across various states of healthy and diseased livers. Through the integration of sophisticated bioinformatics strategies, it enables detailed exploration of cellular heterogeneity, transitions in cell states, and intricate cell-cell interactions with remarkable precision. In liver research, spatial transcriptomics has been particularly revelatory, identifying distinct zonated functions of hepatocytes that are crucial for understanding the metabolic and detoxification processes of the liver. Moreover, this technology has unveiled new insights into the pathogenesis of liver diseases, such as the role of lipid-associated macrophages in steatosis and endothelial cell signals in liver regeneration and repair. In the domain of liver cancer, spatial transcriptomics has proven instrumental in delineating intratumor heterogeneity, identifying supportive microenvironmental niches and revealing the complex interplay between tumor cells and the immune system as well as susceptibility to immune checkpoint inhibitors. In conclusion, spatial transcriptomics represents a significant advance in hepatology, promising to enhance our understanding and treatment of liver diseases.
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Affiliation(s)
- Naoto Fujiwara
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Genki Kimura
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Hayato Nakagawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
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31
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Irac SE, Soon MSF, Borcherding N, Tuong ZK. Single-cell immune repertoire analysis. Nat Methods 2024; 21:777-792. [PMID: 38637691 DOI: 10.1038/s41592-024-02243-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/12/2024] [Indexed: 04/20/2024]
Abstract
Single-cell T cell and B cell antigen receptor-sequencing data analysis can potentially perform in-depth assessments of adaptive immune cells that inform on understanding immune cell development to tracking clonal expansion in disease and therapy. However, it has been extremely challenging to analyze and interpret T cells and B cells and their adaptive immune receptor repertoires at the single-cell level due to not only the complexity of the data but also the underlying biology. In this Review, we delve into the computational breakthroughs that have transformed the analysis of single-cell T cell and B cell antigen receptor-sequencing data.
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Affiliation(s)
- Sergio E Irac
- Cancer Immunoregulation and Immunotherapy, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Megan Sioe Fei Soon
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Omniscope, Palo Alto, CA, USA
| | - Zewen Kelvin Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
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32
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Mangiola S, Milton M, Ranathunga N, Li-Wai-Suen C, Odainic A, Yang E, Hutchison W, Garnham A, Iskander J, Pal B, Yadav V, Rossello J, Carey VJ, Morgan M, Bedoui S, Kallies A, Papenfuss AT. A multi-organ map of the human immune system across age, sex and ethnicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.08.542671. [PMID: 38746418 PMCID: PMC11092463 DOI: 10.1101/2023.06.08.542671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Understanding tissue biology's heterogeneity is crucial for advancing precision medicine. Despite the centrality of the immune system in tissue homeostasis, a detailed and comprehensive map of immune cell distribution and interactions across human tissues and demographics remains elusive. To fill this gap, we harmonised data from 12,981 single-cell RNA sequencing samples and curated 29 million cells from 45 anatomical sites to create a comprehensive compositional and transcriptional healthy map of the healthy immune system. We used this resource and a novel multilevel modelling approach to track immune ageing and test differences across sex and ethnicity. We uncovered conserved and tissue-specific immune-ageing programs, resolved sex-dependent differential ageing and identified ethnic diversity in clinically critical immune checkpoints. This study provides a quantitative baseline of the immune system, facilitating advances in precision medicine. By sharing our immune map, we hope to catalyse further breakthroughs in cancer, infectious disease, immunology and precision medicine.
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Affiliation(s)
- S Mangiola
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - M Milton
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - N Ranathunga
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Csn Li-Wai-Suen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - A Odainic
- The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - E Yang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - W Hutchison
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - A Garnham
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - J Iskander
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - B Pal
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - V Yadav
- Systems Biology of Aging Laboratory, Columbia University; New York, USA
| | - Jfj Rossello
- Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Victoria, Australia
| | - V J Carey
- Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School, Harvard University, Boston, USA
| | - M Morgan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, NY, USA
| | - S Bedoui
- The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - A Kallies
- The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - A T Papenfuss
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
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33
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Larouche JD, Laumont CM, Trofimov A, Vincent K, Hesnard L, Brochu S, Côté C, Humeau JF, Bonneil É, Lanoix J, Durette C, Gendron P, Laverdure JP, Richie ER, Lemieux S, Thibault P, Perreault C. Transposable elements regulate thymus development and function. eLife 2024; 12:RP91037. [PMID: 38635416 PMCID: PMC11026094 DOI: 10.7554/elife.91037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Transposable elements (TEs) are repetitive sequences representing ~45% of the human and mouse genomes and are highly expressed by medullary thymic epithelial cells (mTECs). In this study, we investigated the role of TEs on T-cell development in the thymus. We performed multiomic analyses of TEs in human and mouse thymic cells to elucidate their role in T-cell development. We report that TE expression in the human thymus is high and shows extensive age- and cell lineage-related variations. TE expression correlates with multiple transcription factors in all cell types of the human thymus. Two cell types express particularly broad TE repertoires: mTECs and plasmacytoid dendritic cells (pDCs). In mTECs, transcriptomic data suggest that TEs interact with transcription factors essential for mTEC development and function (e.g., PAX1 and REL), and immunopeptidomic data showed that TEs generate MHC-I-associated peptides implicated in thymocyte education. Notably, AIRE, FEZF2, and CHD4 regulate small yet non-redundant sets of TEs in murine mTECs. Human thymic pDCs homogenously express large numbers of TEs that likely form dsRNA, which can activate innate immune receptors, potentially explaining why thymic pDCs constitutively secrete IFN ɑ/β. This study highlights the diversity of interactions between TEs and the adaptive immune system. TEs are genetic parasites, and the two thymic cell types most affected by TEs (mTEcs and pDCs) are essential to establishing central T-cell tolerance. Therefore, we propose that orchestrating TE expression in thymic cells is critical to prevent autoimmunity in vertebrates.
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Affiliation(s)
- Jean-David Larouche
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Medicine, Université de MontréalMontréalCanada
| | - Céline M Laumont
- Deeley Research Centre, BC CancerVictoriaCanada
- Department of Medical Genetics, University of British ColumbiaVancouverCanada
| | - Assya Trofimov
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Computer Science and Operations Research, Université de MontréalMontréalCanada
- Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Physics, University of WashingtonSeattleUnited States
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Sylvie Brochu
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Caroline Côté
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Juliette F Humeau
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Joel Lanoix
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | | | - Ellen R Richie
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M.D. Anderson Cancer CenterHoustonUnited States
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Biochemistry and Molecular Medicine, Université de MontréalMontrealCanada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Chemistry, Université de MontréalMontréalCanada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Medicine, Université de MontréalMontréalCanada
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Sturek JM, Hannan RT, Upadhye A, Otoupalova E, Faron ET, Atya AAE, Thomas C, Johnson V, Miller A, Garmey JC, Burdick MD, Barker TH, Kadl A, Shim YM, McNamara CA. A protective role for B-1 cells and oxidation-specific epitope IgM in lung fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589137. [PMID: 38659897 PMCID: PMC11042183 DOI: 10.1101/2024.04.11.589137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a morbid fibrotic lung disease with limited treatment options. The pathophysiology of IPF remains poorly understood, and elucidation of the cellular and molecular mechanisms of IPF pathogenesis is key to the development of new therapeutics. B-1 cells are an innate B cell population which play an important role linking innate and adaptive immunity. B-1 cells spontaneously secrete natural IgM and prevent inflammation in several disease states. One class of these IgM recognize oxidation-specific epitopes (OSE), which have been shown to be generated in lung injury and to promote fibrosis. A main B-1 cell reservoir is the pleural space, adjacent to the typical distribution of fibrosis in IPF. In this study, we demonstrate that B-1 cells are recruited to the lung during injury where they secrete IgM to OSE (IgM OSE ). We also show that the pleural B-1 cell reservoir responds to lung injury through regulation of the chemokine receptor CXCR4. Mechanistically we show that the transcription factor Id3 is a novel negative regulator of CXCR4 expression. Using mice with B-cell specific Id3 deficiency, a model of increased B-1b cells, we demonstrate decreased bleomycin-induced fibrosis compared to littermate controls. Furthermore, we show that mice deficient in secretory IgM ( sIgM -/- ) have higher mortality in response to bleomycin-induced lung injury, which is partially mitigated through airway delivery of the IgM OSE E06. Additionally, we provide insight into potential mechanisms of IgM in attenuation of fibrosis through RNA sequencing and pathway analysis, highlighting complement activation and extracellular matrix deposition as key differentially regulated pathways.
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Rodríguez-Zhurbenko N, Hernández AM. The role of B-1 cells in cancer progression and anti-tumor immunity. Front Immunol 2024; 15:1363176. [PMID: 38629061 PMCID: PMC11019000 DOI: 10.3389/fimmu.2024.1363176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
In recent years, in addition to the well-established role of T cells in controlling or promoting tumor growth, a new wave of research has demonstrated the active involvement of B cells in tumor immunity. B-cell subsets with distinct phenotypes and functions play various roles in tumor progression. Plasma cells and activated B cells have been linked to improved clinical outcomes in several types of cancer, whereas regulatory B cells have been associated with disease progression. However, we are only beginning to understand the role of a particular innate subset of B cells, referred to as B-1 cells, in cancer. Here, we summarize the characteristics of B-1 cells and review their ability to infiltrate tumors. We also describe the potential mechanisms through which B-1 cells suppress anti-tumor immune responses and promote tumor progression. Additionally, we highlight recent studies on the protective anti-tumor function of B-1 cells in both mouse models and humans. Understanding the functions of B-1 cells in tumor immunity could pave the way for designing more effective cancer immunotherapies.
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Affiliation(s)
- Nely Rodríguez-Zhurbenko
- Immunobiology Department, Immunology and Immunotherapy Division, Center of Molecular Immunology, Habana, Cuba
| | - Ana M. Hernández
- Applied Genetics Group, Department of Biochemistry, Faculty of Biology, University of Habana, Habana, Cuba
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36
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Symmank D, Richter FC, Rendeiro AF. Navigating the thymic landscape through development: from cellular atlas to tissue cartography. Genes Immun 2024; 25:102-104. [PMID: 38341523 PMCID: PMC11023925 DOI: 10.1038/s41435-024-00257-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Affiliation(s)
- Dörte Symmank
- Department of Dermatology, Medical University of Vienna, Vienna, 1090, Austria.
| | - Felix Clemens Richter
- Institute of Hygiene and Applied Immunology, Department of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, 1090, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - André F Rendeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
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37
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Bao Y, Wang G, Li H. Approaches for studying human macrophages. Trends Immunol 2024; 45:237-247. [PMID: 38580575 DOI: 10.1016/j.it.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 04/07/2024]
Abstract
Macrophages are vital tissue components involved in organogenesis, maintaining homeostasis, and responses to disease. Mouse models have significantly improved our understanding of macrophages. Further investigations into the characteristics and development of human macrophages are crucial, considering the substantial anatomical and physiological distinctions between mice and humans. Despite challenges in human macrophage research, recent studies are shedding light on the ontogeny and function of human macrophages. In this opinion, we propose combinations of cutting-edge approaches to examine the diversity, development, niche, and function of human tissue-resident macrophages. These methodologies can facilitate our exploration of human macrophages more efficiently, ideally providing new therapeutic avenues for macrophage-relevant disorders.
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Affiliation(s)
- Yuzhou Bao
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Guanlin Wang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Centre for Evolutionary Biology, Fudan University, Shanghai, China.
| | - Hanjie Li
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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38
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Gu Y, Bartolomé-Casado R, Xu C, Bertocchi A, Janney A, Heuberger C, Pearson CF, Teichmann SA, Thornton EE, Powrie F. Immune microniches shape intestinal T reg function. Nature 2024; 628:854-862. [PMID: 38570678 PMCID: PMC11041794 DOI: 10.1038/s41586-024-07251-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
The intestinal immune system is highly adapted to maintaining tolerance to the commensal microbiota and self-antigens while defending against invading pathogens1,2. Recognizing how the diverse network of local cells establish homeostasis and maintains it in the complex immune environment of the gut is critical to understanding how tolerance can be re-established following dysfunction, such as in inflammatory disorders. Although cell and molecular interactions that control T regulatory (Treg) cell development and function have been identified3,4, less is known about the cellular neighbourhoods and spatial compartmentalization that shapes microorganism-reactive Treg cell function. Here we used in vivo live imaging, photo-activation-guided single-cell RNA sequencing5-7 and spatial transcriptomics to follow the natural history of T cells that are reactive towards Helicobacter hepaticus through space and time in the settings of tolerance and inflammation. Although antigen stimulation can occur anywhere in the tissue, the lamina propria-but not embedded lymphoid aggregates-is the key microniche that supports effector Treg (eTreg) cell function. eTreg cells are stable once their niche is established; however, unleashing inflammation breaks down compartmentalization, leading to dominance of CD103+SIRPα+ dendritic cells in the lamina propria. We identify and validate the putative tolerogenic interaction between CD206+ macrophages and eTreg cells in the lamina propria and identify receptor-ligand pairs that are likely to govern the interaction. Our results reveal a spatial mechanism of tolerance in the lamina propria and demonstrate how knowledge of local interactions may contribute to the next generation of tolerance-inducing therapies.
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Affiliation(s)
- Yisu Gu
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Raquel Bartolomé-Casado
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alice Bertocchi
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Alina Janney
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Cornelia Heuberger
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
- Roche Innovation Center Zurich, Pharma Research and Early Development, F. Hoffmann-La Roche, Schlieren, Switzerland
| | - Claire F Pearson
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Emily E Thornton
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK.
- MRC Translational Immune Discovery Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK.
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Jiang A, Snell RG, Lehnert K. ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells. Bioinformatics 2024; 40:btae167. [PMID: 38539041 PMCID: PMC11007236 DOI: 10.1093/bioinformatics/btae167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
MOTIVATION In recent years, improvements in throughput of single-cell RNA-seq have resulted in a significant increase in the number of cells profiled. The generation of single-cell RNA-seq datasets comprising >1 million cells is becoming increasingly common, giving rise to demands for more efficient computational workflows. RESULTS We present an update to our single-cell RNA-seq analysis web server application, ICARUS (available at https://launch.icarus-scrnaseq.cloud.edu.au) that allows effective analysis of large-scale single-cell RNA-seq datasets. ICARUS v3 utilizes the geometric cell sketching method to subsample cells from the overall dataset for dimensionality reduction and clustering that can be then projected to the large dataset. We then extend this functionality to select a representative subset of cells for downstream data analysis applications including differential expression analysis, gene co-expression network construction, gene regulatory network construction, trajectory analysis, cell-cell communication inference, and cell cluster associations to GWAS traits. We demonstrate analysis of single-cell RNA-seq datasets using ICARUS v3 of 1.3 million cells completed within the hour. AVAILABILITY AND IMPLEMENTATION ICARUS is available at https://launch.icarus-scrnaseq.cloud.edu.au.
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Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Russell G Snell
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
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40
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Tsagiopoulou M, Rashmi S, Aguilar-Fernandez S, Nieto J, Gut IG. Multi-organ single-cell transcriptomics of immune cells uncovered organ-specific gene expression and functions. Sci Data 2024; 11:316. [PMID: 38538617 PMCID: PMC10973478 DOI: 10.1038/s41597-024-03152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
Despite the wealth of publicly available single-cell datasets, our understanding of distinct resident immune cells and their unique features in diverse human organs remains limited. To address this, we compiled a meta-analysis dataset of 114,275 CD45+ immune cells sourced from 14 organs in healthy donors. While the transcriptome of immune cells remains relatively consistent across organs, our analysis has unveiled organ-specific gene expression differences (GTPX3 in kidney, DNTT and ACVR2B in thymus). These alterations are linked to different transcriptional factor activities and pathways including metabolism. TNF-α signaling through the NFkB pathway was found in several organs and immune compartments. The presence of distinct expression profiles for NFkB family genes and their target genes, including cytokines, underscores their pivotal role in cell positioning. Taken together, immune cells serve a dual role: safeguarding the organs and dynamically adjusting to the intricacies of the host organ environment, thereby actively contributing to its functionality and overall homeostasis.
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Affiliation(s)
| | - Sonal Rashmi
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | | | - Juan Nieto
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Ivo G Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain.
- Universitat de Barcelona (UB), Barcelona, Spain.
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41
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Zhao Y, Yang M, Feng J, Wang X, Liu Y. Advances in immunotherapy for biliary tract cancers. Chin Med J (Engl) 2024; 137:524-532. [PMID: 37646139 DOI: 10.1097/cm9.0000000000002759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Indexed: 09/01/2023] Open
Abstract
ABSTRACT Biliary tract cancers (BTC), a heterogeneous disease with poor prognosis, including gallbladder cancer (GBC), intrahepatic cholangiocarcinoma (ICC), and extrahepatic cholangiocarcinoma (ECC). Although surgery is currently the primary regimen to treat BTC, most BTC patients are diagnosed at an advanced stage and miss the opportunity of surgical eradication. As a result, non-surgical therapy serves as the main intervention for advanced BTC. In recent years, immunotherapy has emerged as one of the most promising therapies in a number of solid cancers, and it includes immune checkpoint inhibitors (ICIs) monotherapy or combined therapy, tumor vaccines, oncolytic virus immunotherapy, adoptive cell therapy (ACT), and cytokine therapy. However, these therapies have been practiced in limited clinical settings in patients with BTC. In this review, we focus on the discussion of latest advances of immunotherapy in BTC and update the progress of multiple current clinical trials with different immunotherapies.
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Affiliation(s)
- Yuhao Zhao
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Cancer Institute, State Key Laboratory of Oncogenes and Related Genes, Shanghai 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai 200082, China
| | - Mao Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Cancer Institute, State Key Laboratory of Oncogenes and Related Genes, Shanghai 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai 200082, China
| | - Jiayi Feng
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Cancer Institute, State Key Laboratory of Oncogenes and Related Genes, Shanghai 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai 200082, China
| | - Xu'an Wang
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Cancer Institute, State Key Laboratory of Oncogenes and Related Genes, Shanghai 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai 200082, China
| | - Yingbin Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Cancer Institute, State Key Laboratory of Oncogenes and Related Genes, Shanghai 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai 200082, China
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42
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Wagner C, Guilliams M. Time and place: mapping human prenatal macrophages across tissues. Cell Res 2024; 34:191-192. [PMID: 37964002 PMCID: PMC10907690 DOI: 10.1038/s41422-023-00895-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Affiliation(s)
- Camille Wagner
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Ghent, Belgium.
| | - Martin Guilliams
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Ghent, Belgium.
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43
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Singhal V, Chou N, Lee J, Yue Y, Liu J, Chock WK, Lin L, Chang YC, Teo EML, Aow J, Lee HK, Chen KH, Prabhakar S. BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis. Nat Genet 2024; 56:431-441. [PMID: 38413725 PMCID: PMC10937399 DOI: 10.1038/s41588-024-01664-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Spatial omics data are clustered to define both cell types and tissue domains. We present Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an algorithm that unifies these two spatial clustering problems by embedding cells in a product space of their own and the local neighborhood transcriptome, representing cell state and microenvironment, respectively. BANKSY's spatial feature augmentation strategy improved performance on both tasks when tested on diverse RNA (imaging, sequencing) and protein (imaging) datasets. BANKSY revealed unexpected niche-dependent cell states in the mouse brain and outperformed competing methods on domain segmentation and cell typing benchmarks. BANKSY can also be used for quality control of spatial transcriptomics data and for spatially aware batch effect correction. Importantly, it is substantially faster and more scalable than existing methods, enabling the processing of millions of cell datasets. In summary, BANKSY provides an accurate, biologically motivated, scalable and versatile framework for analyzing spatially resolved omics data.
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Affiliation(s)
- Vipul Singhal
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Nigel Chou
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Joseph Lee
- Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
| | - Yifei Yue
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Republic of Singapore
| | - Jinyue Liu
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Wan Kee Chock
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Li Lin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | | | | | - Jonathan Aow
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Hwee Kuan Lee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- School of Computing, National University of Singapore, Singapore, Republic of Singapore
- Singapore Eye Research Institute, Singapore, Republic of Singapore
- International Research Laboratory on Artificial Intelligence, Singapore, Republic of Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Kok Hao Chen
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
| | - Shyam Prabhakar
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Population and Global Health, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Republic of Singapore.
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44
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Kirchberger S, Shoeb MR, Lazic D, Wenninger-Weinzierl A, Fischer K, Shaw LE, Nogueira F, Rifatbegovic F, Bozsaky E, Ladenstein R, Bodenmiller B, Lion T, Traver D, Farlik M, Schöfer C, Taschner-Mandl S, Halbritter F, Distel M. Comparative transcriptomics coupled to developmental grading via transgenic zebrafish reporter strains identifies conserved features in neutrophil maturation. Nat Commun 2024; 15:1792. [PMID: 38413586 PMCID: PMC10899643 DOI: 10.1038/s41467-024-45802-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/01/2024] [Indexed: 02/29/2024] Open
Abstract
Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defense. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized, which limits their applicability to studying human disease. Here we show, by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages, a high-resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors, including C/ebp-β, which is important for late neutrophil maturation. Cross-species comparison of zebrafish, mouse, and human samples confirms high molecular similarity of immature stages and discriminates zebrafish-specific from pan-species gene signatures. Applying the pan-species neutrophil maturation signature to RNA-sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease.
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Grants
- St. Anna Kinderkrebsforschung (to S.T.M., R.L., F.H., and M.D.), the Austrian Research Promotion Agency (FFG) (project 7940628, Danio4Can to M.D.), a German Academic Exchange Service postdoctoral fellowship and an EMBO fellowship (to M.D.), the Austrian Science Fund (FWF) through grants TAI454 (to F.H. and M.D.), TAI732 (to F.H.), I4162 (ERA-NET/Transcan-2 LIQUIDHOPE; to S.T.M.), P35841 (MAPMET; to S.T.M.), P34152 (to T.L.), P 30642 (to C.S.) and the Alex’s Lemonade Stand Foundation for Childhood Cancer 20-17258 (to F.H. and M.D.), and the Swiss Government Excellence Scholarship (to D.L.), and the EC H2020 grant no. 826494 (PRIMAGE; to R.L.), and by the European Commission within the FP7 Framework program (Fungitect-Grant No 602125 to T.L.).
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Affiliation(s)
| | - Mohamed R Shoeb
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Daria Lazic
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | | | - Kristin Fischer
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Lisa E Shaw
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Filomena Nogueira
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia - Labordiagnostik GmbH, Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, Max Perutz Labs, Campus Vienna Biocenter, Vienna, Austria
| | | | - Eva Bozsaky
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ruth Ladenstein
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zürich, Switzerland
| | - Thomas Lion
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia - Labordiagnostik GmbH, Vienna, Austria
- Medical University of Vienna, Department of Pediatrics, Vienna, Austria
| | - David Traver
- Cell and Developmental Biology, University of California, San Diego, CA, USA
| | - Matthias Farlik
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Christian Schöfer
- Medical University of Vienna, Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Vienna, Austria
| | | | | | - Martin Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
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45
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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Balachandran S, Prada-Medina CA, Mensah MA, Kakar N, Nagel I, Pozojevic J, Audain E, Hitz MP, Kircher M, Sreenivasan VKA, Spielmann M. STIGMA: Single-cell tissue-specific gene prioritization using machine learning. Am J Hum Genet 2024; 111:338-349. [PMID: 38228144 PMCID: PMC10870135 DOI: 10.1016/j.ajhg.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 01/18/2024] Open
Abstract
Clinical exome and genome sequencing have revolutionized the understanding of human disease genetics. Yet many genes remain functionally uncharacterized, complicating the establishment of causal disease links for genetic variants. While several scoring methods have been devised to prioritize these candidate genes, these methods fall short of capturing the expression heterogeneity across cell subpopulations within tissues. Here, we introduce single-cell tissue-specific gene prioritization using machine learning (STIGMA), an approach that leverages single-cell RNA-seq (scRNA-seq) data to prioritize candidate genes associated with rare congenital diseases. STIGMA prioritizes genes by learning the temporal dynamics of gene expression across cell types during healthy organogenesis. To assess the efficacy of our framework, we applied STIGMA to mouse limb and human fetal heart scRNA-seq datasets. In a cohort of individuals with congenital limb malformation, STIGMA prioritized 469 variants in 345 genes, with UBA2 as a notable example. For congenital heart defects, we detected 34 genes harboring nonsynonymous de novo variants (nsDNVs) in two or more individuals from a set of 7,958 individuals, including the ortholog of Prdm1, which is associated with hypoplastic left ventricle and hypoplastic aortic arch. Overall, our findings demonstrate that STIGMA effectively prioritizes tissue-specific candidate genes by utilizing single-cell transcriptome data. The ability to capture the heterogeneity of gene expression across cell populations makes STIGMA a powerful tool for the discovery of disease-associated genes and facilitates the identification of causal variants underlying human genetic disorders.
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Affiliation(s)
- Saranya Balachandran
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Cesar A Prada-Medina
- Human Molecular Genetics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Martin A Mensah
- Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; BIH Charité Digital Clinician Scientist Program, BIH Biomedical Innovation Academy, Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Naseebullah Kakar
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany; Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Inga Nagel
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Jelena Pozojevic
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Enrique Audain
- Institute of Medical Genetics, Carl von Ossietzky University, 26129 Oldenburg, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck; Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, 24105 Kiel, Germany
| | - Marc-Phillip Hitz
- Institute of Medical Genetics, Carl von Ossietzky University, 26129 Oldenburg, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck; Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, 24105 Kiel, Germany
| | - Martin Kircher
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Varun K A Sreenivasan
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany.
| | - Malte Spielmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany; Human Molecular Genetics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck.
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Luo Y, Guo J, Wen J, Zhao W, Huang K, Liu Y, Wang G, Luo R, Niu T, Feng Y, Xu H, Kim P, Zhou X. StemDriver: a knowledgebase of gene functions for hematopoietic stem cell fate determination. Nucleic Acids Res 2024; 52:D1042-D1052. [PMID: 37953308 PMCID: PMC10767831 DOI: 10.1093/nar/gkad1063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/14/2023] Open
Abstract
StemDriver is a comprehensive knowledgebase dedicated to the functional annotation of genes participating in the determination of hematopoietic stem cell fate, available at http://biomedbdc.wchscu.cn/StemDriver/. By utilizing single-cell RNA sequencing data, StemDriver has successfully assembled a comprehensive lineage map of hematopoiesis, capturing the entire continuum from the initial formation of hematopoietic stem cells to the fully developed mature cells. Extensive exploration and characterization were conducted on gene expression features corresponding to each lineage commitment. At the current version, StemDriver integrates data from 42 studies, encompassing a diverse range of 14 tissue types spanning from the embryonic phase to adulthood. In order to ensure uniformity and reliability, all data undergo a standardized pipeline, which includes quality data pre-processing, cell type annotation, differential gene expression analysis, identification of gene categories correlated with differentiation, analysis of highly variable genes along pseudo-time, and exploration of gene expression regulatory networks. In total, StemDriver assessed the function of 23 839 genes for human samples and 29 533 genes for mouse samples. Simultaneously, StemDriver also provided users with reference datasets and models for cell annotation. We believe that StemDriver will offer valuable assistance to research focused on cellular development and hematopoiesis.
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Affiliation(s)
- Yangyang Luo
- Department of Hematology and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jingjing Guo
- Department of Hematology and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jianguo Wen
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Weiling Zhao
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Kexin Huang
- Department of Hematology and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yang Liu
- Department of Hematology and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Grant Wang
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ruihan Luo
- Department of Hematology and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ting Niu
- Department of Hematology and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yuzhou Feng
- Department of Hematology and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Haixia Xu
- Department of Hematology and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Pora Kim
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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48
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Wang G, Wu S, Xiong Z, Qu H, Fang X, Bao Y. CROST: a comprehensive repository of spatial transcriptomics. Nucleic Acids Res 2024; 52:D882-D890. [PMID: 37791883 PMCID: PMC10773281 DOI: 10.1093/nar/gkad782] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/07/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023] Open
Abstract
The development of spatial transcriptome sequencing technology has revolutionized our comprehension of complex tissues and propelled life and health sciences into an era of spatial omics. However, the current availability of databases for accessing and analyzing spatial transcriptomic data is limited. In response, we have established CROST (https://ngdc.cncb.ac.cn/crost), a comprehensive repository of spatial transcriptomics. CROST encompasses high-quality samples and houses 182 spatial transcriptomic datasets from diverse species, organs, and diseases, comprising 1033 sub-datasets and 48 043 tumor-related spatially variable genes (SVGs). Additionally, it encompasses a standardized spatial transcriptome data processing pipeline, integrates single-cell RNA sequencing deconvolution spatial transcriptomics data, and evaluates correlation, colocalization, intercellular communication, and biological function annotation analyses. Moreover, CROST integrates the transcriptome, epigenome, and genome to explore tumor-associated SVGs and provides a comprehensive understanding of their roles in cancer progression and prognosis. Furthermore, CROST provides two online tools, single-sample gene set enrichment analysis and SpatialAP, for users to annotate and analyze the uploaded spatial transcriptomics data. The user-friendly interface of CROST facilitates browsing, searching, analyzing, visualizing, and downloading desired information. Collectively, CROST offers fresh and comprehensive insights into tissue structure and a foundation for understanding multiple biological mechanisms in diseases, particularly in tumor tissues.
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Affiliation(s)
- Guoliang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuang Xiong
- Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou 350002, China
| | - Hongzhu Qu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangdong Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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49
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Suo C, Polanski K, Dann E, Lindeboom RGH, Vilarrasa-Blasi R, Vento-Tormo R, Haniffa M, Meyer KB, Dratva LM, Tuong ZK, Clatworthy MR, Teichmann SA. Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins. Nat Biotechnol 2024; 42:40-51. [PMID: 37055623 PMCID: PMC10791579 DOI: 10.1038/s41587-023-01734-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/07/2023] [Indexed: 04/15/2023]
Abstract
Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here we introduce Dandelion, a computational pipeline for scVDJ-seq analysis. It enables the application of standard V(D)J analysis workflows to single-cell datasets, delivering improved V(D)J contig annotation and the identification of nonproductive and partially spliced contigs. We devised a strategy to create an AIR feature space that can be used for both differential V(D)J usage analysis and pseudotime trajectory inference. The application of Dandelion improved the alignment of human thymic development trajectories of double-positive T cells to mature single-positive CD4/CD8 T cells, generating predictions of factors regulating lineage commitment. Dandelion analysis of other cell compartments provided insights into the origins of human B1 cells and ILC/NK cell development, illustrating the power of our approach. Dandelion is available at https://www.github.com/zktuong/dandelion .
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Affiliation(s)
- Chenqu Suo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Paediatrics, Cambridge University Hospitals, Cambridge, UK
| | | | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | | | | | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lisa M Dratva
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Zewen Kelvin Tuong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
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50
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Bhattachan P, Jeschke MG. SINGLE-CELL TRANSCRIPTOME ANALYSIS IN HEALTH AND DISEASE. Shock 2024; 61:19-27. [PMID: 37962963 PMCID: PMC10883422 DOI: 10.1097/shk.0000000000002274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
ABSTRACT The analysis of the single-cell transcriptome has emerged as a powerful tool to gain insights on the basic mechanisms of health and disease. It is widely used to reveal the cellular diversity and complexity of tissues at cellular resolution by RNA sequencing of the whole transcriptome from a single cell. Equally, it is applied to discover an unknown, rare population of cells in the tissue. The prime advantage of single-cell transcriptome analysis is the detection of stochastic nature of gene expression of the cell in tissue. Moreover, the availability of multiple platforms for the single-cell transcriptome has broadened its approaches to using cells of different sizes and shapes, including the capture of short or full-length transcripts, which is helpful in the analysis of challenging biological samples. And with the development of numerous packages in R and Python, new directions in the computational analysis of single-cell transcriptomes can be taken to characterize healthy versus diseased tissues to obtain novel pathological insights. Downstream analysis such as differential gene expression analysis, gene ontology term analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, cell-cell interaction analysis, and trajectory analysis has become standard practice in the workflow of single-cell transcriptome analysis to further examine the biology of different cell types. Here, we provide a broad overview of single-cell transcriptome analysis in health and disease conditions currently applied in various studies.
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