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Bejarano L, Kauzlaric A, Lamprou E, Lourenco J, Fournier N, Ballabio M, Colotti R, Maas R, Galland S, Massara M, Soukup K, Lilja J, Brouland JP, Hottinger AF, Daniel RT, Hegi ME, Joyce JA. Interrogation of endothelial and mural cells in brain metastasis reveals key immune-regulatory mechanisms. Cancer Cell 2024; 42:378-395.e10. [PMID: 38242126 DOI: 10.1016/j.ccell.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/11/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Brain metastasis (BrM) is a common malignancy, predominantly originating from lung, melanoma, and breast cancers. The vasculature is a key component of the BrM tumor microenvironment with critical roles in regulating metastatic seeding and progression. However, the heterogeneity of the major BrM vascular components, namely endothelial and mural cells, is still poorly understood. We perform single-cell and bulk RNA-sequencing of sorted vascular cell types and detect multiple subtypes enriched specifically in BrM compared to non-tumor brain, including previously unrecognized immune regulatory subtypes. We integrate the human data with mouse models, creating a platform to interrogate vascular targets for the treatment of BrM. We find that the CD276 immune checkpoint molecule is significantly upregulated in the BrM vasculature, and anti-CD276 blocking antibodies prolonged survival in preclinical trials. This study provides important insights into the complex interactions between the vasculature, immune cells, and cancer cells, with translational relevance for designing therapeutic interventions.
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Affiliation(s)
- Leire Bejarano
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Annamaria Kauzlaric
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Translational Data Science Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eleni Lamprou
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Joao Lourenco
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Translational Data Science Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nadine Fournier
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Translational Data Science Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michelle Ballabio
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Roberto Colotti
- In Vivo Imaging Facility (IVIF), University of Lausanne, Lausanne, Switzerland
| | - Roeltje Maas
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Sabine Galland
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Matteo Massara
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Klara Soukup
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Johanna Lilja
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Jean-Philippe Brouland
- Department of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Andreas F Hottinger
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Roy T Daniel
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Monika E Hegi
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Neuroscience Research Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Johanna A Joyce
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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2
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Maan H, Zhang L, Yu C, Geuenich MJ, Campbell KR, Wang B. Characterizing the impacts of dataset imbalance on single-cell data integration. Nat Biotechnol 2024:10.1038/s41587-023-02097-9. [PMID: 38429430 DOI: 10.1038/s41587-023-02097-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/13/2023] [Indexed: 03/03/2024]
Abstract
Computational methods for integrating single-cell transcriptomic data from multiple samples and conditions do not generally account for imbalances in the cell types measured in different datasets. In this study, we examined how differences in the cell types present, the number of cells per cell type and the cell type proportions across samples affect downstream analyses after integration. The Iniquitate pipeline assesses the robustness of integration results after perturbing the degree of imbalance between datasets. Benchmarking of five state-of-the-art single-cell RNA sequencing integration techniques in 2,600 integration experiments indicates that sample imbalance has substantial impacts on downstream analyses and the biological interpretation of integration results. Imbalance perturbation led to statistically significant variation in unsupervised clustering, cell type classification, differential expression and marker gene annotation, query-to-reference mapping and trajectory inference. We quantified the impacts of imbalance through newly introduced properties-aggregate cell type support and minimum cell type center distance. To better characterize and mitigate impacts of imbalance, we introduce balanced clustering metrics and imbalanced integration guidelines for integration method users.
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Affiliation(s)
- Hassaan Maan
- Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.
- Vector Institute, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
| | - Lin Zhang
- Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Chengxin Yu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Michael J Geuenich
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Kieran R Campbell
- Vector Institute, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada.
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
| | - Bo Wang
- Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.
- Vector Institute, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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3
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Andreatta M, Hérault L, Gueguen P, Gfeller D, Berenstein AJ, Carmona SJ. Semi-supervised integration of single-cell transcriptomics data. Nat Commun 2024; 15:872. [PMID: 38287014 PMCID: PMC10825117 DOI: 10.1038/s41467-024-45240-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Batch effects in single-cell RNA-seq data pose a significant challenge for comparative analyses across samples, individuals, and conditions. Although batch effect correction methods are routinely applied, data integration often leads to overcorrection and can result in the loss of biological variability. In this work we present STACAS, a batch correction method for scRNA-seq that leverages prior knowledge on cell types to preserve biological variability upon integration. Through an open-source benchmark, we show that semi-supervised STACAS outperforms state-of-the-art unsupervised methods, as well as supervised methods such as scANVI and scGen. STACAS scales well to large datasets and is robust to incomplete and imprecise input cell type labels, which are commonly encountered in real-life integration tasks. We argue that the incorporation of prior cell type information should be a common practice in single-cell data integration, and we provide a flexible framework for semi-supervised batch effect correction.
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Affiliation(s)
- Massimo Andreatta
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Léonard Hérault
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Paul Gueguen
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Ariel J Berenstein
- Laboratorio de Biología Molecular, División Patología, Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP), CONICET-GCBA, Buenos Aires, C1425EFD, Argentina
| | - Santiago J Carmona
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland.
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
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4
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Garner LC, Amini A, FitzPatrick MEB, Lett MJ, Hess GF, Filipowicz Sinnreich M, Provine NM, Klenerman P. Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity. Nat Immunol 2023; 24:1565-1578. [PMID: 37580605 PMCID: PMC10457204 DOI: 10.1038/s41590-023-01575-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/26/2023] [Indexed: 08/16/2023]
Abstract
Mucosal-associated invariant T (MAIT) cells are innate-like T cells that recognize microbial metabolites through a semi-invariant T cell receptor (TCR). Major questions remain regarding the extent of human MAIT cell functional and clonal diversity. To address these, we analyzed the single-cell transcriptome and TCR repertoire of blood and liver MAIT cells and developed functional RNA-sequencing, a method to integrate function and TCR clonotype at single-cell resolution. MAIT cell clonal diversity was comparable to conventional memory T cells, with private TCR repertoires shared across matched tissues. Baseline functional diversity was low and largely related to tissue site. MAIT cells showed stimulus-specific transcriptional responses in vitro, with cells positioned along gradients of activation. Clonal identity influenced resting and activated transcriptional profiles but intriguingly was not associated with the capacity to produce IL-17. Overall, MAIT cells show phenotypic and functional diversity according to tissue localization, stimulation environment and clonotype.
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Affiliation(s)
- Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Ali Amini
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Michael E B FitzPatrick
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Martin J Lett
- Department of Biomedicine, Liver Immunology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Gabriel F Hess
- Division of Visceral Surgery, Clarunis University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland
| | - Magdalena Filipowicz Sinnreich
- Department of Biomedicine, Liver Immunology, University Hospital Basel and University of Basel, Basel, Switzerland
- Gastroenterology and Hepatology, University Department of Medicine, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Nicholas M Provine
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.
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5
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Tan Y, Huang J, Li D, Zou C, Liu D, Qin B. Single-cell RNA sequencing in dissecting microenvironment of age-related macular degeneration: Challenges and perspectives. Ageing Res Rev 2023; 90:102030. [PMID: 37549871 DOI: 10.1016/j.arr.2023.102030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/29/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Age-related macular degeneration (AMD) is the leading cause of blindness in individuals over the age of 50 years, yet its etiology and pathogenesis largely remain uncovered. Single-cell RNA sequencing (scRNA-seq) technologies are recently developed and have a number of advantages over conventional bulk RNA sequencing techniques in uncovering the heterogeneity of complex microenvironments containing numerous cell types and cell communications during various biological processes. In this review, we summarize the latest discovered cellular components and regulatory mechanisms during AMD development revealed by scRNA-seq. In addition, we discuss the main challenges and future directions in exploring the pathophysiology of AMD equipped with single-cell technologies. Our review underscores the importance of multimodal single-cell platforms (such as single-cell spatiotemporal multi-omics and single-cell exosome omics) as new approaches for basic and clinical AMD research in identifying biomarker, characterizing cellular responses to drug treatment and environmental stimulation.
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Affiliation(s)
- Yao Tan
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China
| | - Jianguo Huang
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China
| | - Deshuang Li
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China
| | - Chang Zou
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China; Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, China; School of Life and Health Sciences, The Chinese University of Kong Hong, Shenzhen 518000, Guangdong, China.
| | - Dongcheng Liu
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China; Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, China.
| | - Bo Qin
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China; Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, China; Aier School of Ophthalmology, Central South University, Changsha, China.
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6
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Mo S, Qu K, Huang J, Li Q, Zhang W, Yen K. Cross-species transcriptomics reveals bifurcation point during the arterial-to-hemogenic transition. Commun Biol 2023; 6:827. [PMID: 37558796 PMCID: PMC10412572 DOI: 10.1038/s42003-023-05190-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023] Open
Abstract
Hemogenic endothelium (HE) with hematopoietic stem cell (HSC)-forming potential emerge from specialized arterial endothelial cells (AECs) undergoing the endothelial-to-hematopoietic transition (EHT) in the aorta-gonad-mesonephros (AGM) region. Characterization of this AECs subpopulation and whether this phenomenon is conserved across species remains unclear. Here we introduce HomologySeeker, a cross-species method that leverages refined mouse information to explore under-studied human EHT. Utilizing single-cell transcriptomic ensembles of EHT, HomologySeeker reveals a parallel developmental relationship between these two species, with minimal pre-HSC signals observed in human cells. The pre-HE stage contains a conserved bifurcation point between the two species, where cells progress towards HE or late AECs. By harnessing human spatial transcriptomics, we identify ligand modules that contribute to the bifurcation choice and validate CXCL12 in promoting hemogenic choice using a human in vitro differentiation system. Our findings advance human arterial-to-hemogenic transition understanding and offer valuable insights for manipulating HSC generation using in vitro models.
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Affiliation(s)
- Shaokang Mo
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Kengyuan Qu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Junfeng Huang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Qiwei Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Wenqing Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China.
| | - Kuangyu Yen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
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7
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Thiery AP, Buzzi AL, Hamrud E, Cheshire C, Luscombe NM, Briscoe J, Streit A. scRNA-sequencing in chick suggests a probabilistic model for cell fate allocation at the neural plate border. eLife 2023; 12:e82717. [PMID: 37530410 PMCID: PMC10425176 DOI: 10.7554/elife.82717] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/01/2023] [Indexed: 08/03/2023] Open
Abstract
The vertebrate 'neural plate border' is a transient territory located at the edge of the neural plate containing precursors for all ectodermal derivatives: the neural plate, neural crest, placodes and epidermis. Elegant functional experiments in a range of vertebrate models have provided an in-depth understanding of gene regulatory interactions within the ectoderm. However, these experiments conducted at tissue level raise seemingly contradictory models for fate allocation of individual cells. Here, we carry out single cell RNA sequencing of chick ectoderm from primitive streak to neurulation stage, to explore cell state diversity and heterogeneity. We characterise the dynamics of gene modules, allowing us to model the order of molecular events which take place as ectodermal fates segregate. Furthermore, we find that genes previously classified as neural plate border 'specifiers' typically exhibit dynamic expression patterns and are enriched in either neural, neural crest or placodal fates, revealing that the neural plate border should be seen as a heterogeneous ectodermal territory and not a discrete transitional transcriptional state. Analysis of neural, neural crest and placodal markers reveals that individual NPB cells co-express competing transcriptional programmes suggesting that their ultimate identify is not yet fixed. This population of 'border located undecided progenitors' (BLUPs) gradually diminishes as cell fate decisions take place. Considering our findings, we propose a probabilistic model for cell fate choice at the neural plate border. Our data suggest that the probability of a progenitor's daughters to contribute to a given ectodermal derivative is related to the balance of competing transcriptional programmes, which in turn are regulated by the spatiotemporal position of a progenitor.
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Affiliation(s)
- Alexandre P Thiery
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College LondonLondonUnited Kingdom
| | - Ailin Leticia Buzzi
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College LondonLondonUnited Kingdom
| | - Eva Hamrud
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College LondonLondonUnited Kingdom
| | - Chris Cheshire
- Bioinformatics and Computational Biology Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Nicholas M Luscombe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - James Briscoe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Andrea Streit
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College LondonLondonUnited Kingdom
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8
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Harris RA, McAllister JM, Strauss JF. Single-Cell RNA-Seq Identifies Pathways and Genes Contributing to the Hyperandrogenemia Associated with Polycystic Ovary Syndrome. Int J Mol Sci 2023; 24:10611. [PMID: 37445796 DOI: 10.3390/ijms241310611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is a common endocrine disorder characterized by hyperandrogenemia of ovarian thecal cell origin, resulting in anovulation/oligo-ovulation and infertility. Our previous studies established that ovarian theca cells isolated and propagated from ovaries of normal ovulatory women and women with PCOS have distinctive molecular and cellular signatures that underlie the increased androgen biosynthesis in PCOS. To evaluate differences between gene expression in single-cells from passaged cultures of theca cells from ovaries of normal ovulatory women and women with PCOS, we performed single-cell RNA sequencing (scRNA-seq). Results from these studies revealed differentially expressed pathways and genes involved in the acquisition of cholesterol, the precursor of steroid hormones, and steroidogenesis. Bulk RNA-seq and microarray studies confirmed the theca cell differential gene expression profiles. The expression profiles appear to be directed largely by increased levels or activity of the transcription factors SREBF1, which regulates genes involved in cholesterol acquisition (LDLR, LIPA, NPC1, CYP11A1, FDX1, and FDXR), and GATA6, which regulates expression of genes encoding steroidogenic enzymes (CYP17A1) in concert with other differentially expressed transcription factors (SP1, NR5A2). This study provides insights into the molecular mechanisms underlying the hyperandrogenemia associated with PCOS and highlights potential targets for molecular diagnosis and therapeutic intervention.
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Affiliation(s)
- R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jan M McAllister
- Department of Pathology, Penn State Hershey College of Medicine, Hershey, PA 17033, USA
| | - Jerome F Strauss
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Villar J, Ouaknin L, Cros A, Segura E. Monocytes differentiate along two alternative pathways during sterile inflammation. EMBO Rep 2023:e56308. [PMID: 37191947 DOI: 10.15252/embr.202256308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 04/18/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023] Open
Abstract
During inflammation, monocytes differentiate within tissues into macrophages (mo-Mac) or dendritic cells (mo-DC). Whether these two populations derive from alternative differentiation pathways or represent different stages along a continuum remains unclear. Here, we address this question using temporal single-cell RNA sequencing in an in vitro model, allowing the simultaneous differentiation of human mo-Mac and mo-DC. We find divergent differentiation paths, with a fate decision occurring within the first 24 h and confirm this result in vivo using a mouse model of sterile peritonitis. Using a computational approach, we identify candidate transcription factors potentially involved in monocyte fate commitment. We demonstrate that IRF1 is necessary for mo-Mac differentiation, independently of its role in regulating transcription of interferon-stimulated genes. In addition, we describe the transcription factors ZNF366 and MAFF as regulators of mo-DC development. Our results indicate that mo-Macs and mo-DCs represent two alternative cell fates requiring distinct transcription factors for their differentiation.
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Affiliation(s)
- Javiera Villar
- Institut Curie, PSL Research University, INSERM, U932, Paris, France
| | - Léa Ouaknin
- Institut Curie, PSL Research University, INSERM, U932, Paris, France
| | - Adeline Cros
- Institut Curie, PSL Research University, INSERM, U932, Paris, France
| | - Elodie Segura
- Institut Curie, PSL Research University, INSERM, U932, Paris, France
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10
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Wang Y, Fan JL, Melms JC, Amin AD, Georgis Y, Barrera I, Ho P, Tagore S, Abril-Rodríguez G, He S, Jin Y, Biermann J, Hofree M, Caprio L, Berhe S, Khan SA, Henick BS, Ribas A, Macosko EZ, Chen F, Taylor AM, Schwartz GK, Carvajal RD, Azizi E, Izar B. Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens. Nat Genet 2023; 55:19-25. [PMID: 36624340 PMCID: PMC10155259 DOI: 10.1038/s41588-022-01268-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 11/11/2022] [Indexed: 01/10/2023]
Abstract
Single-cell genomics enables dissection of tumor heterogeneity and molecular underpinnings of drug response at an unprecedented resolution1-11. However, broad clinical application of these methods remains challenging, due to several practical and preanalytical challenges that are incompatible with typical clinical care workflows, namely the need for relatively large, fresh tissue inputs. In the present study, we show that multimodal, single-nucleus (sn)RNA/T cell receptor (TCR) sequencing, spatial transcriptomics and whole-genome sequencing (WGS) are feasible from small, frozen tissues that approximate routinely collected clinical specimens (for example, core needle biopsies). Compared with data from sample-matched fresh tissue, we find a similar quality in the biological outputs of snRNA/TCR-seq data, while reducing artifactual signals and compositional biases introduced by fresh tissue processing. Profiling sequentially collected melanoma samples from a patient treated in the KEYNOTE-001 trial12, we resolved cellular, genomic, spatial and clonotype dynamics that represent molecular patterns of heterogeneous intralesional evolution during anti-programmed cell death protein 1 therapy. To demonstrate applicability to banked biospecimens of rare diseases13, we generated a single-cell atlas of uveal melanoma liver metastasis with matched WGS data. These results show that single-cell genomics from archival, clinical specimens is feasible and provides a framework for translating these methods more broadly to the clinical arena.
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Affiliation(s)
- Yiping Wang
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Program for Mathematical Genomics, Columbia University, New York, NY, USA
| | - Joy Linyue Fan
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yohanna Georgis
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Patricia Ho
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Somnath Tagore
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Gabriel Abril-Rodríguez
- Department of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Siyu He
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Yinuo Jin
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Program for Mathematical Genomics, Columbia University, New York, NY, USA
| | - Matan Hofree
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lindsay Caprio
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Simon Berhe
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Shaheer A Khan
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Brian S Henick
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Antoni Ribas
- Department of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Alison M Taylor
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Gary K Schwartz
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Richard D Carvajal
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Elham Azizi
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA.
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Systems Biology, Program for Mathematical Genomics, Columbia University, New York, NY, USA.
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA.
- Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
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11
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Millar-Wilson A, Ward Ó, Duffy E, Hardiman G. Multiscale modeling in the framework of biological systems and its potential for spaceflight biology studies. iScience 2022; 25:105421. [DOI: 10.1016/j.isci.2022.105421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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12
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Quintana JF, Chandrasegaran P, Sinton MC, Briggs EM, Otto TD, Heslop R, Bentley-Abbot C, Loney C, de Lecea L, Mabbott NA, MacLeod A. Single cell and spatial transcriptomic analyses reveal microglia-plasma cell crosstalk in the brain during Trypanosoma brucei infection. Nat Commun 2022; 13:5752. [PMID: 36180478 PMCID: PMC9525673 DOI: 10.1038/s41467-022-33542-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/21/2022] [Indexed: 11/08/2022] Open
Abstract
Human African trypanosomiasis, or sleeping sickness, is caused by the protozoan parasite Trypanosoma brucei and induces profound reactivity of glial cells and neuroinflammation when the parasites colonise the central nervous system. However, the transcriptional and functional responses of the brain to chronic T. brucei infection remain poorly understood. By integrating single cell and spatial transcriptomics of the mouse brain, we identify that glial responses triggered by infection are readily detected in the proximity to the circumventricular organs, including the lateral and 3rd ventricle. This coincides with the spatial localisation of both slender and stumpy forms of T. brucei. Furthermore, in silico predictions and functional validations led us to identify a previously unknown crosstalk between homeostatic microglia and Cd138+ plasma cells mediated by IL-10 and B cell activating factor (BAFF) signalling. This study provides important insights and resources to improve understanding of the molecular and cellular responses in the brain during infection with African trypanosomes.
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Affiliation(s)
- Juan F Quintana
- Wellcome Centre for Integrative Parasitology (WCIP), University of Glasgow, Glasgow, UK.
- School of Biodiversity, One Health, and Veterinary Medicine (SBOHVM), MVLS, University of Glasgow, Glasgow, UK.
| | - Praveena Chandrasegaran
- Wellcome Centre for Integrative Parasitology (WCIP), University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health, and Veterinary Medicine (SBOHVM), MVLS, University of Glasgow, Glasgow, UK
| | - Matthew C Sinton
- Wellcome Centre for Integrative Parasitology (WCIP), University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health, and Veterinary Medicine (SBOHVM), MVLS, University of Glasgow, Glasgow, UK
| | - Emma M Briggs
- Wellcome Centre for Integrative Parasitology (WCIP), University of Glasgow, Glasgow, UK
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Thomas D Otto
- Wellcome Centre for Integrative Parasitology (WCIP), University of Glasgow, Glasgow, UK
- School of Infection and Immunity, MVLS, University of Glasgow, Glasgow, UK
| | - Rhiannon Heslop
- Wellcome Centre for Integrative Parasitology (WCIP), University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health, and Veterinary Medicine (SBOHVM), MVLS, University of Glasgow, Glasgow, UK
| | - Calum Bentley-Abbot
- Wellcome Centre for Integrative Parasitology (WCIP), University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health, and Veterinary Medicine (SBOHVM), MVLS, University of Glasgow, Glasgow, UK
| | - Colin Loney
- School of Infection and Immunity, MVLS, University of Glasgow, Glasgow, UK
- MRC Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Luis de Lecea
- Stanford University School of Medicine, Stanford, CA, USA
| | - Neil A Mabbott
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Annette MacLeod
- Wellcome Centre for Integrative Parasitology (WCIP), University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health, and Veterinary Medicine (SBOHVM), MVLS, University of Glasgow, Glasgow, UK
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13
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Andreatta M, Tjitropranoto A, Sherman Z, Kelly MC, Ciucci T, Carmona SJ. A CD4 + T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections. eLife 2022; 11:76339. [PMID: 35829695 PMCID: PMC9323004 DOI: 10.7554/elife.76339] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
CD4+ T cells are critical orchestrators of immune responses against a large variety of pathogens, including viruses. While multiple CD4+ T cell subtypes and their key transcriptional regulators have been identified, there is a lack of consistent definition for CD4+ T cell transcriptional states. In addition, the progressive changes affecting CD4+ T cell subtypes during and after immune responses remain poorly defined. Using single-cell transcriptomics, we characterized the diversity of CD4+ T cells responding to self-resolving and chronic viral infections in mice. We built a comprehensive map of virus-specific CD4+ T cells and their evolution over time, and identified six major cell states consistently observed in acute and chronic infections. During the course of acute infections, T cell composition progressively changed from effector to memory states, with subtype-specific gene modules and kinetics. Conversely, in persistent infections T cells acquired distinct, chronicity-associated programs. By single-cell T cell receptor (TCR) analysis, we characterized the clonal structure of virus-specific CD4+ T cells across individuals. Virus-specific CD4+ T cell responses were essentially private across individuals and most T cells differentiated into both Tfh and Th1 subtypes irrespective of their TCR. Finally, we showed that our CD4+ T cell map can be used as a reference to accurately interpret cell states in external single-cell datasets across tissues and disease models. Overall, this study describes a previously unappreciated level of adaptation of the transcriptional states of CD4+ T cells responding to viruses and provides a new computational resource for CD4+ T cell analysis.
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Affiliation(s)
- Massimo Andreatta
- Agora Cancer Research Center, University of Lausanne, Lausanne, Switzerland
| | - Ariel Tjitropranoto
- Department of Microbiology and Immunology, University of Rochester, Rochester, United States
| | - Zachary Sherman
- Department of Microbiology and Immunology, University of Rochester, Rochester, United States
| | - Michael C Kelly
- Frederick National Laboratory for Cancer Research, Fregerick, United States
| | - Thomas Ciucci
- Department of Microbiology and Immunology, University of Rochester, Rochester, United States
| | - Santiago J Carmona
- Agora Cancer Research Center, University of Lausanne, Lausanne, Switzerland
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14
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Biermann J, Melms JC, Amin AD, Wang Y, Caprio LA, Karz A, Tagore S, Barrera I, Ibarra-Arellano MA, Andreatta M, Fullerton BT, Gretarsson KH, Sahu V, Mangipudy VS, Nguyen TTT, Nair A, Rogava M, Ho P, Koch PD, Banu M, Humala N, Mahajan A, Walsh ZH, Shah SB, Vaccaro DH, Caldwell B, Mu M, Wünnemann F, Chazotte M, Berhe S, Luoma AM, Driver J, Ingham M, Khan SA, Rapisuwon S, Slingluff CL, Eigentler T, Röcken M, Carvajal R, Atkins MB, Davies MA, Agustinus A, Bakhoum SF, Azizi E, Siegelin M, Lu C, Carmona SJ, Hibshoosh H, Ribas A, Canoll P, Bruce JN, Bi WL, Agrawal P, Schapiro D, Hernando E, Macosko EZ, Chen F, Schwartz GK, Izar B. Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. Cell 2022; 185:2591-2608.e30. [PMID: 35803246 PMCID: PMC9677434 DOI: 10.1016/j.cell.2022.06.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/08/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022]
Abstract
Melanoma brain metastasis (MBM) frequently occurs in patients with advanced melanoma; yet, our understanding of the underlying salient biology is rudimentary. Here, we performed single-cell/nucleus RNA-seq in 22 treatment-naive MBMs and 10 extracranial melanoma metastases (ECMs) and matched spatial single-cell transcriptomics and T cell receptor (TCR)-seq. Cancer cells from MBM were more chromosomally unstable, adopted a neuronal-like cell state, and enriched for spatially variably expressed metabolic pathways. Key observations were validated in independent patient cohorts, patient-derived MBM/ECM xenograft models, RNA/ATAC-seq, proteomics, and multiplexed imaging. Integrated spatial analyses revealed distinct geography of putative cancer immune evasion and evidence for more abundant intra-tumoral B to plasma cell differentiation in lymphoid aggregates in MBM. MBM harbored larger fractions of monocyte-derived macrophages and dysfunctional TOX+CD8+ T cells with distinct expression of immune checkpoints. This work provides comprehensive insights into MBM biology and serves as a foundational resource for further discovery and therapeutic exploration.
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Affiliation(s)
- Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA
| | - Lindsay A Caprio
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alcida Karz
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Somnath Tagore
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Irving Barrera
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Miguel A Ibarra-Arellano
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | - Massimo Andreatta
- Department of Oncology UNIL CHUV, Lausanne Branch, Ludwig Institute for Cancer Research Lausanne, CHUV and University of Lausanne, Lausanne, 1066 Épalinges, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Benjamin T Fullerton
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kristjan H Gretarsson
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Varun Sahu
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Vaibhav S Mangipudy
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Trang T T Nguyen
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Ajay Nair
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patricia Ho
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter D Koch
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Matei Banu
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nelson Humala
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aayushi Mahajan
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zachary H Walsh
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shivem B Shah
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Daniel H Vaccaro
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Blake Caldwell
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Michael Mu
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Florian Wünnemann
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | - Margot Chazotte
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | - Simon Berhe
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA
| | - Joseph Driver
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Ingham
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shaheer A Khan
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Suthee Rapisuwon
- Division of Hematology/Oncology, Medstar Washington Cancer Institute, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Craig L Slingluff
- Department of Surgery, University of Virginia, Charlottesville, VA, USA
| | - Thomas Eigentler
- Department of Dermatology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Dermatology, Venereology and Allergology, 10117, Berlin, Germany
| | - Martin Röcken
- Department of Dermatology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Richard Carvajal
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michael B Atkins
- Georgetown-Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Albert Agustinus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pharmacology, Weill Cornell Graduate School, New York, NY 10065, USA
| | - Samuel F Bakhoum
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elham Azizi
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
| | - Markus Siegelin
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Santiago J Carmona
- Department of Oncology UNIL CHUV, Lausanne Branch, Ludwig Institute for Cancer Research Lausanne, CHUV and University of Lausanne, Lausanne, 1066 Épalinges, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Antoni Ribas
- Department of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90024, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Jeffrey N Bruce
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Praveen Agrawal
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Denis Schapiro
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Eva Hernando
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gary K Schwartz
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
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15
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Briggs EM, Rojas F, McCulloch R, Matthews KR, Otto TD. Single-cell transcriptomic analysis of bloodstream Trypanosoma brucei reconstructs cell cycle progression and developmental quorum sensing. Nat Commun 2021; 12:5268. [PMID: 34489460 DOI: 10.1038/s41467-021-25607-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Developmental steps in the trypanosome life-cycle involve transition between replicative and non-replicative forms specialised for survival in, and transmission between, mammalian and tsetse fly hosts. Here, using oligopeptide-induced differentiation in vitro, we model the progressive development of replicative 'slender' to transmissible 'stumpy' bloodstream form Trypanosoma brucei and capture the transcriptomes of 8,599 parasites using single cell transcriptomics (scRNA-seq). Using this framework, we detail the relative order of biological events during asynchronous development, profile dynamic gene expression patterns and identify putative regulators. We additionally map the cell cycle of proliferating parasites and position stumpy cell-cycle exit at early G1 before progression to a distinct G0 state. A null mutant for one transiently elevated developmental regulator, ZC3H20 is further analysed by scRNA-seq, identifying its point of failure in the developmental atlas. This approach provides a paradigm for the dissection of differentiation events in parasites, relevant to diverse transitions in pathogen biology.
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16
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Briggs EM, Warren FSL, Matthews KR, McCulloch R, Otto TD. Application of single-cell transcriptomics to kinetoplastid research. Parasitology 2021; 148:1223-1236. [PMID: 33678213 PMCID: PMC8311972 DOI: 10.1017/s003118202100041x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/13/2022]
Abstract
Kinetoplastid parasites are responsible for both human and animal diseases across the globe where they have a great impact on health and economic well-being. Many species and life cycle stages are difficult to study due to limitations in isolation and culture, as well as to their existence as heterogeneous populations in hosts and vectors. Single-cell transcriptomics (scRNA-seq) has the capacity to overcome many of these difficulties, and can be leveraged to disentangle heterogeneous populations, highlight genes crucial for propagation through the life cycle, and enable detailed analysis of host–parasite interactions. Here, we provide a review of studies that have applied scRNA-seq to protozoan parasites so far. In addition, we provide an overview of sample preparation and technology choice considerations when planning scRNA-seq experiments, as well as challenges faced when analysing the large amounts of data generated. Finally, we highlight areas of kinetoplastid research that could benefit from scRNA-seq technologies.
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Affiliation(s)
- Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Felix S. L. Warren
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Keith R. Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Richard McCulloch
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Thomas D. Otto
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
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Andreatta M, Corria-Osorio J, Müller S, Cubas R, Coukos G, Carmona SJ. Interpretation of T cell states from single-cell transcriptomics data using reference atlases. Nat Commun 2021; 12:2965. [PMID: 34017005 PMCID: PMC8137700 DOI: 10.1038/s41467-021-23324-4] [Citation(s) in RCA: 175] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/22/2021] [Indexed: 02/07/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has revealed an unprecedented degree of immune cell diversity. However, consistent definition of cell subtypes and cell states across studies and diseases remains a major challenge. Here we generate reference T cell atlases for cancer and viral infection by multi-study integration, and develop ProjecTILs, an algorithm for reference atlas projection. In contrast to other methods, ProjecTILs allows not only accurate embedding of new scRNA-seq data into a reference without altering its structure, but also characterizing previously unknown cell states that "deviate" from the reference. ProjecTILs accurately predicts the effects of cell perturbations and identifies gene programs that are altered in different conditions and tissues. A meta-analysis of tumor-infiltrating T cells from several cohorts reveals a strong conservation of T cell subtypes between human and mouse, providing a consistent basis to describe T cell heterogeneity across studies, diseases, and species.
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Affiliation(s)
- Massimo Andreatta
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, Lausanne, Epalinges, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jesus Corria-Osorio
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, Lausanne, Epalinges, Switzerland
| | - Sören Müller
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA
| | - Rafael Cubas
- Department of Translational Oncology, Genentech, South San Francisco, CA, USA
| | - George Coukos
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, Lausanne, Epalinges, Switzerland
| | - Santiago J Carmona
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, Lausanne, Epalinges, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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