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Johnson MS, Venkataram S, Kryazhimskiy S. Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes. J Mol Evol 2023; 91:263-280. [PMID: 36651964 PMCID: PMC10276077 DOI: 10.1007/s00239-022-10083-z] [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: 09/08/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023]
Abstract
Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.
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Affiliation(s)
- Milo S Johnson
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Sandeep Venkataram
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, 92093, USA.
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2
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Look A, Burns D, Tews I, Roghanian A, Mansour S. Towards a better understanding of human iNKT cell subpopulations for improved clinical outcomes. Front Immunol 2023; 14:1176724. [PMID: 37153585 PMCID: PMC10154573 DOI: 10.3389/fimmu.2023.1176724] [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: 02/28/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023] Open
Abstract
Invariant natural killer T (iNKT) cells are a unique T lymphocyte population expressing semi-invariant T cell receptors (TCRs) that recognise lipid antigens presented by CD1d. iNKT cells exhibit potent anti-tumour activity through direct killing mechanisms and indirectly through triggering the activation of other anti-tumour immune cells. Because of their ability to induce potent anti-tumour responses, particularly when activated by the strong iNKT agonist αGalCer, they have been the subject of intense research to harness iNKT cell-targeted immunotherapies for cancer treatment. However, despite potent anti-tumour efficacy in pre-clinical models, the translation of iNKT cell immunotherapy into human cancer patients has been less successful. This review provides an overview of iNKT cell biology and why they are of interest within the context of cancer immunology. We focus on the iNKT anti-tumour response, the seminal studies that first reported iNKT cytotoxicity, their anti-tumour mechanisms, and the various described subsets within the iNKT cell repertoire. Finally, we discuss several barriers to the successful utilisation of iNKT cells in human cancer immunotherapy, what is required for a better understanding of human iNKT cells, and the future perspectives facilitating their exploitation for improved clinical outcomes.
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Affiliation(s)
- Alex Look
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Daniel Burns
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ivo Tews
- Biological Sciences, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Ali Roghanian
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Salah Mansour
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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3
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Kretschmer L, Busch DH, Buchholz VR. A Single-Cell Perspective on Memory T-Cell Differentiation. Cold Spring Harb Perspect Biol 2021; 13:a038067. [PMID: 33903160 PMCID: PMC8411955 DOI: 10.1101/cshperspect.a038067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Memory differentiation of CD4 and CD8 T-cell populations has been extensively studied and many key molecular players and transcriptional networks have been identified. But how regulatory principles, identified on this population level, translate to immune responses that originate from single antigen-specific T cells is only now being elucidated. Here, we provide a short summary of the approaches used for mapping the fate of individual T cells and their progeny in vivo. We then highlight which major questions, with respect to memory T-cell differentiation, have been addressed by studying the development of single-cell-derived T-cell families during infection or vaccination. We discuss how fate decisions of single T cells are modulated by the affinity of their TCR and further shaped through a coregulation of T-cell differentiation and T-cell proliferation. These current findings indicate the early segregation into slowly dividing T central memory precursors (CMPs) and rapidly dividing non-CMPs, as a key event that separates the developmental paths of long- and short-lived T cells.
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Affiliation(s)
- Lorenz Kretschmer
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), Munich 81675 , Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), Munich 81675 , Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich 81675, Germany
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), Munich 81675 , Germany
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4
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Dujardin P, Baginska AK, Urban S, Grüner BM. Unraveling Tumor Heterogeneity by Using DNA Barcoding Technologies to Develop Personalized Treatment Strategies in Advanced-Stage PDAC. Cancers (Basel) 2021; 13:4187. [PMID: 34439341 PMCID: PMC8394487 DOI: 10.3390/cancers13164187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/12/2021] [Accepted: 08/14/2021] [Indexed: 12/14/2022] Open
Abstract
Tumor heterogeneity is a hallmark of many solid tumors, including pancreatic ductal adenocarcinoma (PDAC), and an inherent consequence of the clonal evolution of cancers. As such, it is considered the underlying concept of many characteristics of the disease, including the ability to metastasize, adapt to different microenvironments, and to develop therapy resistance. Undoubtedly, the high mortality of PDAC can be attributed to a high extent to these properties. Despite its apparent importance, studying tumor heterogeneity has been a challenging task, mainly due to its complexity and lack of appropriate methods. However, in recent years molecular DNA barcoding has emerged as a sophisticated tool that allows mapping of individual cells or subpopulations in a cell pool to study heterogeneity and thus devise new personalized treatment strategies. In this review, we provide an overview of genetic and non-genetic inter- and intra-tumor heterogeneity and its impact on (personalized) treatment strategies in PDAC and address how DNA barcoding technologies work and can be applied to study this clinically highly relevant question.
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Affiliation(s)
- Philip Dujardin
- West German Cancer Center, Department of Medical Oncology, University Hospital Essen at the University Duisburg-Essen, 45147 Essen, Germany; (A.K.B.); (S.U.)
| | - Anna K. Baginska
- West German Cancer Center, Department of Medical Oncology, University Hospital Essen at the University Duisburg-Essen, 45147 Essen, Germany; (A.K.B.); (S.U.)
| | - Sebastian Urban
- West German Cancer Center, Department of Medical Oncology, University Hospital Essen at the University Duisburg-Essen, 45147 Essen, Germany; (A.K.B.); (S.U.)
| | - Barbara M. Grüner
- West German Cancer Center, Department of Medical Oncology, University Hospital Essen at the University Duisburg-Essen, 45147 Essen, Germany; (A.K.B.); (S.U.)
- German Cancer Consortium (DKTK) Partner Site Essen/Düsseldorf, 45147 Essen, Germany
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5
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Lafouresse F, Jugele R, Müller S, Doineau M, Duplan-Eche V, Espinosa E, Puisségur MP, Gadat S, Valitutti S. Stochastic asymmetric repartition of lytic machinery in dividing CD8 + T cells generates heterogeneous killing behavior. eLife 2021; 10:62691. [PMID: 33427199 PMCID: PMC7867409 DOI: 10.7554/elife.62691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/08/2021] [Indexed: 12/27/2022] Open
Abstract
Cytotoxic immune cells are endowed with a high degree of heterogeneity in their lytic function, but how this heterogeneity is generated is still an open question. We therefore investigated if human CD8+ T cells could segregate their lytic components during telophase, using imaging flow cytometry, confocal microscopy, and live-cell imaging. We show that CD107a+-intracellular vesicles, perforin, and granzyme B unevenly segregate in a constant fraction of telophasic cells during each division round. Mathematical modeling posits that unequal lytic molecule inheritance by daughter cells results from the random distribution of lytic granules on the two sides of the cleavage furrow. Finally, we establish that the level of lytic compartment in individual cytotoxic T lymphocyte (CTL) dictates CTL killing capacity.
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Affiliation(s)
- Fanny Lafouresse
- INSERM U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, Toulouse, France
| | - Romain Jugele
- INSERM U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, Toulouse, France
| | - Sabina Müller
- INSERM U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, Toulouse, France
| | - Marine Doineau
- Toulouse School of Economics, CNRS UMR 5314, Université Toulouse 1 Capitole, France and Institut Universitaire de France, Toulouse, France
| | - Valérie Duplan-Eche
- INSERM, UMR1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France
| | - Eric Espinosa
- INSERM U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, Toulouse, France
| | - Marie-Pierre Puisségur
- INSERM U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, Toulouse, France
| | - Sébastien Gadat
- Toulouse School of Economics, CNRS UMR 5314, Université Toulouse 1 Capitole, France and Institut Universitaire de France, Toulouse, France
| | - Salvatore Valitutti
- INSERM U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, Toulouse, France.,Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
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6
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Al Khabouri S, Gerlach C. T cell fate mapping and lineage tracing technologies probing clonal aspects underlying the generation of CD8 T cell subsets. Scand J Immunol 2020; 92:e12983. [PMID: 33037653 PMCID: PMC7757170 DOI: 10.1111/sji.12983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/18/2022]
Abstract
T cells responding to acute infections generally provide two key functions to protect the host: (1) active contribution to pathogen elimination and (2) providing long‐lived cells that are poised to rapidly respond to renewed infection, thus ensuring long‐lasting protection against the particular pathogen. Extensive work has established an astonishing amount of additional diversity among T cells actively contributing to pathogen elimination, as well as among resting, long‐lived antigen‐experienced T cells. This led to the description of a variety of functionally distinct T cell ‘subsets’. Understanding how this heterogeneity develops among T cells responding to the same antigen is currently an active area of research, since knowledge of such mechanisms may have implications for the development of vaccines and immunotherapy. The number of naïve T cells specific to a given antigen span a great range. Considering this, one mechanistic angle focusses on how individual naïve T cells contribute to the development of the distinct T cell subsets. In this review, we highlight the current technologies that enable one to address the contributions of individual naïve T cells to different T cell subsets, with a focus on CD8 T cell subsets generated in the context of acute infections. Moreover, we discuss the requirements of new technologies to further our understanding of the mechanisms that help generate long‐lasting immunity.
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Affiliation(s)
- Shaima Al Khabouri
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Carmen Gerlach
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
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7
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CD38: T Cell Immuno-Metabolic Modulator. Cells 2020; 9:cells9071716. [PMID: 32709019 PMCID: PMC7408359 DOI: 10.3390/cells9071716] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/22/2022] Open
Abstract
Activation and subsequent differentiation of T cells following antigenic stimulation are triggered by highly coordinated signaling events that lead to instilling cells with a discrete metabolic and transcriptional feature. Compelling studies indicate that intracellular nicotinamide adenine dinucleotide (NAD+) levels have profound influence on diverse signaling and metabolic pathways of T cells, and hence dictate their functional fate. CD38, a major mammalian NAD+ glycohydrolase (NADase), expresses on T cells following activation and appears to be an essential modulator of intracellular NAD+ levels. The enzymatic activity of CD38 in the process of generating the second messenger cADPR utilizes intracellular NAD+, and thus limits its availability to different NAD+ consuming enzymes (PARP, ART, and sirtuins) inside the cells. The present review discusses how the CD38-NAD+ axis affects T cell activation and differentiation through interfering with their signaling and metabolic processes. We also describe the pivotal role of the CD38-NAD+ axis in influencing the chromatin remodeling and rewiring T cell response. Overall, this review emphasizes the crucial contribution of the CD38-NAD+ axis in altering T cell response in various pathophysiological conditions.
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8
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TCR sequencing paired with massively parallel 3' RNA-seq reveals clonotypic T cell signatures. Nat Immunol 2019; 20:1692-1699. [PMID: 31745340 DOI: 10.1038/s41590-019-0544-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/21/2019] [Indexed: 01/14/2023]
Abstract
High-throughput 3' single-cell RNA-sequencing (scRNA-seq) allows cost-effective, detailed characterization of individual immune cells from tissues. Current techniques, however, are limited in their ability to elucidate essential immune cell features, including variable sequences of T cell antigen receptors (TCRs) that confer antigen specificity. Here, we present a strategy that enables simultaneous analysis of TCR sequences and corresponding full transcriptomes from 3'-barcoded scRNA-seq samples. This approach is compatible with common 3' scRNA-seq methods, and adaptable to processed samples post hoc. We applied the technique to identify transcriptional signatures associated with T cells sharing common TCRs from immunized mice and from patients with food allergy. We observed preferential phenotypes among subsets of expanded clonotypes, including type 2 helper CD4+ T cell (TH2) states associated with food allergy. These results demonstrate the utility of our method when studying diseases in which clonotype-driven responses are critical to understanding the underlying biology.
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9
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Chevrier N. Decoding the Body Language of Immunity: Tackling the Immune System at the Organism Level. ACTA ACUST UNITED AC 2019; 18:19-26. [PMID: 32490290 DOI: 10.1016/j.coisb.2019.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The immune system is a dynamic mesh of molecules, cells and tissues spanning the entire organism. Despite a wealth of knowledge about the components of the immune system, little is known about the general rules governing the organismal circuitry of immunity. Deciphering the immune system at the scale of the whole organism is crucial to understanding fundamental problems in immunobiology and physiology, and to manipulate immunity for maintaining health and preventing disease. Here I discuss the emerging principles of inter-organ communications during immune responses by focusing on three common themes that are the regulation of the (i) composition, (ii) condition and (iii) coordination of communicating organs by molecular and cellular factors. Based on these common principles, I emphasize fundamental gaps in our knowledge of organismal immune processes and the outlook to tackle immunity at the scale of the whole organism.
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Affiliation(s)
- Nicolas Chevrier
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
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10
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Xu F, He D, Ning R, Zeng B, Thompson CW, Li Y, Wang D, Li Y. Genetic diversity of chemokine XCL1 and its receptor XCR1 in murine rodents. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 98:80-88. [PMID: 31026469 DOI: 10.1016/j.dci.2019.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/21/2019] [Accepted: 04/21/2019] [Indexed: 06/09/2023]
Abstract
The chemokine ligand XCL1 plays critical roles in immune responses with diverse physiological and pathological implications through interactions with a cognate G protein-coupled receptor XCR1. To shed insight into their versatile nature, we analyzed genetic variations of XCL1 and XCR1 in murine rodents, including commonly-used model organisms Mus musculus (house mouse) and Rattus norvegicus (Norway rat). Our results showed that adaptive selection has contributed to the genetic diversification of these proteins in murine lineage. Moreover, in both M. musculus and R. norvegicus, the chemokine and its receptor exhibit similar signs of selective sweeps resulting from positive selection. In light of currently available structural and interaction information for chemokines and their receptors, the similarity of XCL1/XCR1 evolutionary patterns among murine species and the parallels of their evolutionary footprints within individual species suggest that interplay could exist between the adaptively selected changes, or between the domains on which the identified changes are located, and consequently preserve the physiological interaction of XCL1 and XCR1.
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Affiliation(s)
- Feifei Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Dan He
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Ruihong Ning
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Bo Zeng
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Cody W Thompson
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, USA
| | - Ying Li
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Dawei Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China.
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11
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Grassmann S, Pachmayr LO, Leube J, Mihatsch L, Andrae I, Flommersfeld S, Oduro J, Cicin-Sain L, Schiemann M, Flossdorf M, Buchholz VR. Distinct Surface Expression of Activating Receptor Ly49H Drives Differential Expansion of NK Cell Clones upon Murine Cytomegalovirus Infection. Immunity 2019; 50:1391-1400.e4. [DOI: 10.1016/j.immuni.2019.04.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 03/08/2019] [Accepted: 04/25/2019] [Indexed: 12/25/2022]
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12
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Li Q, Wang B, Mu K, Zhang J. The pathogenesis of thyroid autoimmune diseases: New T lymphocytes – Cytokines circuits beyond the Th1−Th2 paradigm. J Cell Physiol 2018; 234:2204-2216. [PMID: 30246383 DOI: 10.1002/jcp.27180] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 05/22/2018] [Accepted: 07/17/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Qian Li
- Department of EndocrinologyJinshan Hospital of Fudan UniversityShanghai China
| | - Bin Wang
- Department of EndocrinologyJinshan Hospital of Fudan UniversityShanghai China
| | - Kaida Mu
- Department of EndocrinologyShanghai University of Medicine & Health Sciences Affiliated Zhoupu HospitalShanghai China
| | - Jin‐An Zhang
- Department of EndocrinologyShanghai University of Medicine & Health Sciences Affiliated Zhoupu HospitalShanghai China
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13
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Hu Z, Zou Q, Su B. Regulation of T cell immunity by cellular metabolism. Front Med 2018; 12:463-472. [PMID: 30112717 DOI: 10.1007/s11684-018-0668-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/17/2018] [Indexed: 12/14/2022]
Abstract
T cells are an important adaptive immune response arm that mediates cell-mediated immunity. T cell metabolism plays a central role in T cell activation, proliferation, differentiation, and effector function. Specific metabolic programs are tightly controlled to mediate T cell immune responses, and alterations in T cell metabolism may result in many immunological disorders. In this review, we will summarize the main T cell metabolic pathways and the important factors participating in T cell metabolic programming during T cell homeostasis, differentiation, and function.
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Affiliation(s)
- Zhilin Hu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qiang Zou
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Bing Su
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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14
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15
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Wang J, Li Z, Gao L, Qi Y, Zhu H, Qin X. The regulation effect of AMPK in immune related diseases. SCIENCE CHINA-LIFE SCIENCES 2017; 61:523-533. [DOI: 10.1007/s11427-017-9169-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/28/2017] [Indexed: 12/12/2022]
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16
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Gabel M, Regoes RR, Graw F. More or less-On the influence of labelling strategies to infer cell population dynamics. PLoS One 2017; 12:e0185523. [PMID: 29045427 PMCID: PMC5646766 DOI: 10.1371/journal.pone.0185523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/14/2017] [Indexed: 11/18/2022] Open
Abstract
The adoptive transfer of labelled cell populations has been an essential tool to determine and quantify cellular dynamics. The experimental methods to label and track cells over time range from fluorescent dyes over congenic markers towards single-cell labelling techniques, such as genetic barcodes. While these methods have been widely used to quantify cell differentiation and division dynamics, the extent to which the applied labelling strategy actually affects the quantification of the dynamics has not been determined so far. This is especially important in situations where measurements can only be obtained at a single time point, as e.g. due to organ harvest. To this end, we studied the appropriateness of various labelling strategies as characterised by the number of different labels and the initial number of cells per label to quantify cellular dynamics. We simulated adoptive transfer experiments in systems of various complexity that assumed either homoeostatic cellular turnover or cell expansion dynamics involving various steps of cell differentiation and proliferation. Re-sampling cells at a single time point, we determined the ability of different labelling strategies to recover the underlying kinetics. Our results indicate that cell transition and expansion rates are differently affected by experimental shortcomings, such as loss of cells during transfer or sampling, dependent on the labelling strategy used. Furthermore, uniformly distributed labels in the transferred population generally lead to more robust and less biased results than non-equal label sizes. In addition, our analysis indicates that certain labelling approaches incorporate a systematic bias for the identification of complex cell expansion dynamics.
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Affiliation(s)
- Michael Gabel
- Center for Modelling and Simulation in the Biosciences, BioQuant-Center, Heidelberg University, 69120 Heidelberg, Germany
- * E-mail: (MG); (FG)
| | - Roland R. Regoes
- Institute for Integrative Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Frederik Graw
- Center for Modelling and Simulation in the Biosciences, BioQuant-Center, Heidelberg University, 69120 Heidelberg, Germany
- * E-mail: (MG); (FG)
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Ahn SB, Lee SB, Singh TD, Cho SJ, Kim SK, Lee IK, Jeong SY, Ahn BC, Lee J, Lee SW, Jeon YH. Multimodality Imaging of Bone Marrow-Derived Dendritic Cell Migration and Antitumor Immunity. Transl Oncol 2017; 10:262-270. [PMID: 28214774 PMCID: PMC5314440 DOI: 10.1016/j.tranon.2017.01.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/11/2017] [Accepted: 01/13/2017] [Indexed: 11/17/2022] Open
Abstract
Here, we sought to monitor bone marrow-derived dendritic cell (BMDC) migration and antitumor effects using a multimodal reporter imaging strategy in living mice. BMDCs were transduced with retroviral vector harboring human sodium iodide symporter (hNIS, nuclear imaging reporter), firefly luc2 (optical imaging reporter), and thy1.1 (surrogate marker of NIS and luc2) genes (BMDC/NF cells). No significant differences in biological functions, including cell proliferation, antigen uptake, phenotype expression, and migration ability, were observed between BMDC and BMDC/NF cells. Combined bioluminescence imaging and I-124 positron emission tomography/computed tomography clearly revealed the migration of BMDC/NF cells to draining popliteal lymph nodes at day 7 postinjection. Interestingly, marked tumor protection was observed in mice immunized with TC-1 lysate-pulsed BMDC/NF cells. Our findings suggested that multimodal reporter gene imaging of NIS and luciferase could provide insights into the biological behaviors of dendritic cells in living organisms and could be a useful tool for the optimization of DC-based immunotherapy protocols.
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Affiliation(s)
- Su-Bi Ahn
- Department of Nuclear Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Sang Bong Lee
- Department of Nuclear Medicine, Kyungpook National University Hospital, Daegu, South Korea; Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, South Korea
| | - Thoudam Debraj Singh
- Department of Nuclear Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Sung Jin Cho
- Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, South Korea; New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, South Korea
| | - Sang Kyoon Kim
- Department of Nuclear Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - In-Kyu Lee
- Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, South Korea; Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Shin Young Jeong
- Department of Nuclear Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Byeong-Cheol Ahn
- Department of Nuclear Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Jaetae Lee
- Department of Nuclear Medicine, Kyungpook National University Hospital, Daegu, South Korea; Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, South Korea
| | - Sang-Woo Lee
- Department of Nuclear Medicine, Kyungpook National University Hospital, Daegu, South Korea; Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, South Korea.
| | - Yong Hyun Jeon
- Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, South Korea; Laboratory Animal Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea.
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18
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Gnanaprakasam JNR, Wang R. MYC in Regulating Immunity: Metabolism and Beyond. Genes (Basel) 2017; 8:E88. [PMID: 28245597 PMCID: PMC5368692 DOI: 10.3390/genes8030088] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 02/09/2017] [Accepted: 02/16/2017] [Indexed: 12/28/2022] Open
Abstract
Myelocytomatosis oncogene (MYC) family members, including cellular MYC (c-Myc), neuroblastoma derived MYC (MYCN), and lung carcinoma derived MYC (MYCL), have all been implicated as key oncogenic drivers in a broad range of human cancers. Beyond cancer, MYC plays an important role in other physiological and pathological processes, namely immunity and immunological diseases. MYC largely functions as a transcription factor that promotes the expression of numerous target genes to coordinate death, proliferation, and metabolism at the cellular, tissue, and organismal levels. It has been shown that the expression of MYC family members is tightly regulated in immune cells during development or upon immune stimulations. Emerging evidence suggests that MYC family members play essential roles in regulating the development, differentiation and activation of immune cells. Through driving the expression of a broad range of metabolic genes in immune cells, MYC family members coordinate metabolic programs to support immune functions. Here, we discuss our understanding of MYC biology in immune system and how modulation of MYC impacts immune metabolism and responses.
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Affiliation(s)
- J N Rashida Gnanaprakasam
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, The Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH 43205, USA.
| | - Ruoning Wang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, The Research Institute at Nationwide Children's Hospital, Ohio State University, Columbus, OH 43205, USA.
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19
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Oh SG, Li X, Lee HW, Singh TD, Lee SB, Ji HD, Yoon G, Cho SJ, Lee IK, Jeong SY, Ahn BC, Lee J, Chang HW, Lee SW, Jeon YH. Non-invasive visualization of mast cell recruitment and its effects in lung cancer by optical reporter gene imaging and glucose metabolism monitoring. Biomaterials 2017; 112:192-203. [DOI: 10.1016/j.biomaterials.2016.10.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/11/2016] [Accepted: 10/11/2016] [Indexed: 12/20/2022]
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20
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Metabolic pathways in T cell activation and lineage differentiation. Semin Immunol 2016; 28:514-524. [PMID: 27825556 DOI: 10.1016/j.smim.2016.10.009] [Citation(s) in RCA: 299] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/07/2016] [Accepted: 10/14/2016] [Indexed: 12/13/2022]
Abstract
Recent advances in the field of immunometabolism support the concept that fundamental processes in T cell biology, such as TCR-mediated activation and T helper lineage differentiation, are closely linked to changes in the cellular metabolic programs. Although the major task of the intermediate metabolism is to provide the cell with a constant supply of energy and molecular precursors for the production of biomolecules, the dynamic regulation of metabolic pathways also plays an active role in shaping T cell responses. Key metabolic processes such as glycolysis, fatty acid and mitochondrial metabolism are now recognized as crucial players in T cell activation and differentiation, and their modulation can differentially affect the development of T helper cell lineages. In this review, we describe the diverse metabolic processes that T cells engage during their life cycle from naïve towards effector and memory T cells. We consider in particular how the cellular metabolism may actively support the function of T cells in their different states. Moreover, we discuss how molecular regulators such as mTOR or AMPK link environmental changes to adaptations in the cellular metabolism and elucidate the consequences on T cell differentiation and function.
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21
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Affiliation(s)
- Veit R. Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 München, Germany; ,
| | - Ton N.M. Schumacher
- Division of Immunology, The Netherlands Cancer Institute (NKI), 1066 CX Amsterdam, The Netherlands;
| | - Dirk H. Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 München, Germany; ,
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22
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Perié L, Duffy KR, Kok L, de Boer RJ, Schumacher TN. The Branching Point in Erythro-Myeloid Differentiation. Cell 2016; 163:1655-62. [PMID: 26687356 DOI: 10.1016/j.cell.2015.11.059] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/18/2015] [Accepted: 11/28/2015] [Indexed: 12/17/2022]
Abstract
Development of mature blood cell progenies from hematopoietic stem cells involves the transition through lineage-restricted progenitors. The first branching point along this developmental process is thought to separate the erythro-myeloid and lymphoid lineage fate by yielding two intermediate progenitors, the common myeloid and the common lymphoid progenitors (CMPs and CLPs). Here, we use single-cell lineage tracing to demonstrate that so-called CMPs are highly heterogeneous with respect to cellular output, with most individual CMPs yielding either only erythrocytes or only myeloid cells after transplantation. Furthermore, based on the labeling of earlier progenitors, we show that the divergence between the myeloid and erythroid lineage develops within multipotent progenitors (MPP). These data provide evidence for a model of hematopoietic branching in which multiple distinct lineage commitments occur in parallel within the MPP pool.
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Affiliation(s)
- Leïla Perié
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Institut Curie, PSL Research University, CNRS UMR168, 26 rue d'Ulm, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 4 place Jussieu, 75005 Paris, France.
| | - Ken R Duffy
- Hamilton Institute, Maynooth University, Maynooth, Co Kildare, Ireland
| | - Lianne Kok
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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23
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Beltman JB, Urbanus J, Velds A, van Rooij N, Rohr JC, Naik SH, Schumacher TN. Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells. BMC Bioinformatics 2016; 17:151. [PMID: 27038897 PMCID: PMC4818877 DOI: 10.1186/s12859-016-0999-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/23/2016] [Indexed: 12/31/2022] Open
Abstract
Background Next generation sequencing (NGS) of amplified DNA is a powerful tool to describe genetic heterogeneity within cell populations that can both be used to investigate the clonal structure of cell populations and to perform genetic lineage tracing. For applications in which both abundant and rare sequences are biologically relevant, the relatively high error rate of NGS techniques complicates data analysis, as it is difficult to distinguish rare true sequences from spurious sequences that are generated by PCR or sequencing errors. This issue, for instance, applies to cellular barcoding strategies that aim to follow the amount and type of offspring of single cells, by supplying these with unique heritable DNA tags. Results Here, we use genetic barcoding data from the Illumina HiSeq platform to show that straightforward read threshold-based filtering of data is typically insufficient to filter out spurious barcodes. Importantly, we demonstrate that specific sequencing errors occur at an approximately constant rate across different samples that are sequenced in parallel. We exploit this observation by developing a novel approach to filter out spurious sequences. Conclusions Application of our new method demonstrates its value in the identification of true sequences amongst spurious sequences in biological data sets. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0999-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joost B Beltman
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. .,Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC, Leiden, The Netherlands.
| | - Jos Urbanus
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Arno Velds
- Genomics Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Nienke van Rooij
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jan C Rohr
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Shalin H Naik
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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24
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Han F, Li G, Dai S, Huang J. Genome-wide metabolic model to improve understanding of CD4+ T cell metabolism, immunometabolism and application in drug design. MOLECULAR BIOSYSTEMS 2016; 12:431-43. [DOI: 10.1039/c5mb00480b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Model-based investigation of the metabolism and immunometabolism of CD4+ T cells (CD4T1670) and the application of CD4T1670 in drug development.
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Affiliation(s)
- Feifei Han
- State Key Laboratory of Genetic Resources and Evolution
- Kunming Institute of Zoology
- Chinese Academy of Sciences
- Kunming
- China
| | - Gonghua Li
- State Key Laboratory of Genetic Resources and Evolution
- Kunming Institute of Zoology
- Chinese Academy of Sciences
- Kunming
- China
| | - Shaoxing Dai
- State Key Laboratory of Genetic Resources and Evolution
- Kunming Institute of Zoology
- Chinese Academy of Sciences
- Kunming
- China
| | - Jingfei Huang
- State Key Laboratory of Genetic Resources and Evolution
- Kunming Institute of Zoology
- Chinese Academy of Sciences
- Kunming
- China
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25
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Limited niche availability suppresses murine intrathymic dendritic-cell development from noncommitted progenitors. Blood 2014; 125:457-64. [PMID: 25411428 DOI: 10.1182/blood-2014-07-592667] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The origins of dendritic cells (DCs) and other myeloid cells in the thymus have remained controversial. In this study, we assessed developmental relationships between thymic dendritic cells and thymocytes, employing retrovirus-based cellular barcoding and reporter mice, as well as intrathymic transfers coupled with DC depletion. We demonstrated that a subset of early T-lineage progenitors expressed CX3CR1, a bona fide marker for DC progenitors. However, intrathymic transfers into nonmanipulated mice, as well as retroviral barcoding, indicated that thymic dendritic cells and thymocytes were largely of distinct developmental origin. In contrast, intrathymic transfers after in vivo depletion of DCs resulted in intrathymic development of non-T-lineage cells. In conclusion, our data support a model in which the adoption of T-lineage fate by noncommitted progenitors at steady state is enforced by signals from the thymic microenvironment unless niches promoting alternative lineage fates become available.
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26
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Graef P, Buchholz VR, Stemberger C, Flossdorf M, Henkel L, Schiemann M, Drexler I, Höfer T, Riddell SR, Busch DH. Serial transfer of single-cell-derived immunocompetence reveals stemness of CD8(+) central memory T cells. Immunity 2014; 41:116-26. [PMID: 25035956 DOI: 10.1016/j.immuni.2014.05.018] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 05/08/2014] [Indexed: 02/09/2023]
Abstract
Maintenance of immunological memory has been proposed to rely on stem-cell-like lymphocytes. However, data supporting this hypothesis are focused on the developmental potential of lymphocyte populations and are thus insufficient to establish the functional hallmarks of stemness. Here, we investigated self-renewal capacity and multipotency of individual memory lymphocytes by in vivo fate mapping of CD8(+) T cells and their descendants across three generations of serial single-cell adoptive transfer and infection-driven re-expansion. We found that immune responses derived from single naive T (Tn) cells, single primary, and single secondary central memory T (Tcm) cells reached similar size and phenotypic diversity, were subjected to comparable stochastic variation, and could ultimately reconstitute immunocompetence against an otherwise lethal infection with the bacterial pathogen Listeria monocytogenes. These observations establish that adult tissue stem cells reside within the CD62L(+) Tcm cell compartment and highlight the promising therapeutic potential of this immune cell subset.
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Affiliation(s)
- Patricia Graef
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich 81675, Germany
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich 81675, Germany
| | - Christian Stemberger
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich 81675, Germany; Focus Group "Clinical Cell Processing and Purification," Institute for Advanced Study, TUM, Munich 81675, Germany
| | - Michael Flossdorf
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; BioQuant Center, University of Heidelberg, Heidelberg 69120, Germany
| | - Lynette Henkel
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich 81675, Germany
| | - Matthias Schiemann
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich 81675, Germany; Clinical Cooperation Groups "Antigen-specific Immunotherapy" and "Immune-Monitoring," Helmholtz Center Munich (Neuherberg), TUM, Munich 81675, Germany
| | - Ingo Drexler
- Institute for Virology, Universitätsklinikum Düsseldorf (UKD), Heinrich-Heine Universität, Düsseldorf 40225, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; BioQuant Center, University of Heidelberg, Heidelberg 69120, Germany
| | - Stanley R Riddell
- Focus Group "Clinical Cell Processing and Purification," Institute for Advanced Study, TUM, Munich 81675, Germany; Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich 81675, Germany; Focus Group "Clinical Cell Processing and Purification," Institute for Advanced Study, TUM, Munich 81675, Germany; Clinical Cooperation Groups "Antigen-specific Immunotherapy" and "Immune-Monitoring," Helmholtz Center Munich (Neuherberg), TUM, Munich 81675, Germany; German Center for Infection Research (DZIF), Munich 81675, Germany.
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27
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Linnemann C, Mezzadra R, Schumacher TNM. TCR repertoires of intratumoral T-cell subsets. Immunol Rev 2014; 257:72-82. [PMID: 24329790 DOI: 10.1111/imr.12140] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The infiltration of human tumors by T cells is a common phenomenon, and over the past decades, it has become increasingly clear that the nature of such intratumoral T-cell populations can predict disease course. Furthermore, intratumoral T cells have been utilized therapeutically in clinical studies of adoptive T-cell therapy. In this review, we describe how novel methods that are either based on T-cell receptor (TCR) sequencing or on cancer exome analysis allow the analysis of the tumor reactivity and antigen-specificity of the intratumoral TCR repertoire with unprecedented detail. Furthermore, we discuss studies that have started to utilize these techniques to probe the link between cancer exomes and the intratumoral TCR pool. Based on the observation that both the cancer epitope repertoire and intratumoral TCR repertoire appear highly individual, we outline strategies, such as 'autologous TCR gene therapy', that exploit the tumor-resident TCR repertoire for the development of personalized immunotherapy.
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Affiliation(s)
- Carsten Linnemann
- Division of Immunology, The Netherlands Cancer Institute (NKI-AVL), Amsterdam, the Netherlands
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28
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Naik SH, Schumacher TN, Perié L. Cellular barcoding: a technical appraisal. Exp Hematol 2014; 42:598-608. [PMID: 24996012 DOI: 10.1016/j.exphem.2014.05.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 05/01/2014] [Accepted: 05/02/2014] [Indexed: 12/29/2022]
Abstract
Cellular barcoding involves the tagging of individual cells of interest with unique genetic heritable identifiers or barcodes and is emerging as a powerful tool to address individual cell fates on a large scale. However, as with many new technologies, diverse technical and analytical challenges have emerged. Here, we review those challenges and highlight both the power and limitations of cellular barcoding. We then illustrate the contribution of cellular barcoding to the understanding of hematopoiesis and outline the future potential of this technology.
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Affiliation(s)
- Shalin H Naik
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
| | - Ton N Schumacher
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Leïla Perié
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.
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29
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Rohr JC, Gerlach C, Kok L, Schumacher TN. Single cell behavior in T cell differentiation. Trends Immunol 2014; 35:170-7. [PMID: 24657362 DOI: 10.1016/j.it.2014.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 01/08/2023]
Abstract
Upon primary infection, naïve T cells that recognize their cognate antigen become activated, proliferate, and simultaneously differentiate into various subsets. A long-standing question in the field has been how this cellular diversification is achieved. Conceptually, diverse cellular output may either arise from every single cell or only from populations of naïve cells. Furthermore, such diversity may either be driven by cell-intrinsic heterogeneity or by external, niche-derived signals. In this review, we discuss how recently developed technologies have allowed the analysis of the mechanisms underlying T cell diversification at the single cell level. In addition, we outline the implications of this work on our understanding of the formation of immunological memory, and describe a number of unresolved key questions in this field.
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Affiliation(s)
- Jan C Rohr
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Carmen Gerlach
- Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Lianne Kok
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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30
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Nicolaou A, Mauro C, Urquhart P, Marelli-Berg F. Polyunsaturated Fatty Acid-derived lipid mediators and T cell function. Front Immunol 2014; 5:75. [PMID: 24611066 PMCID: PMC3933826 DOI: 10.3389/fimmu.2014.00075] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/11/2014] [Indexed: 01/10/2023] Open
Abstract
Fatty acids are involved in T cell biology both as nutrients important for energy production as well as signaling molecules. In particular, polyunsaturated fatty acids are known to exhibit a range of immunomodulatory properties that progress through T cell mediated events, although the molecular mechanisms of these actions have not yet been fully elucidated. Some of these immune activities are linked to polyunsaturated fatty acid-induced alteration of the composition of cellular membranes and the consequent changes in signaling pathways linked to membrane raft-associated proteins. However, significant aspects of the polyunsaturated fatty acid bioactivities are mediated through their transformation to specific lipid mediators, products of cyclooxygenase, lipoxygenase, or cytochrome P450 enzymatic reactions. Resulting bioactive metabolites including prostaglandins, leukotrienes, and endocannabinoids are produced by and/or act upon T leukocytes through cell surface receptors and have been shown to alter T cell activation and differentiation, proliferation, cytokine production, motility, and homing events. Detailed appreciation of the mode of action of these lipids presents opportunities for the design and development of therapeutic strategies aimed at regulating T cell function.
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Affiliation(s)
- Anna Nicolaou
- Manchester Pharmacy School, Faculty of Medical and Human Sciences, The University of Manchester , Manchester , UK
| | - Claudio Mauro
- Centre for Biochemical Pharmacology, William Harvey Research Institute, Queen Mary University of London , London , UK
| | - Paula Urquhart
- Manchester Pharmacy School, Faculty of Medical and Human Sciences, The University of Manchester , Manchester , UK
| | - Federica Marelli-Berg
- Centre for Biochemical Pharmacology, William Harvey Research Institute, Queen Mary University of London , London , UK
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31
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Maciolek JA, Pasternak JA, Wilson HL. Metabolism of activated T lymphocytes. Curr Opin Immunol 2014; 27:60-74. [PMID: 24556090 DOI: 10.1016/j.coi.2014.01.006] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/20/2013] [Accepted: 01/14/2014] [Indexed: 01/04/2023]
Abstract
Activated T cells undergo metabolic reprogramming which promotes glycolytic flux and lactate production as well as elevated production of lipids, proteins, nucleic acids and other carbohydrates (i.e. induction of biomass) even in the presence of oxygen. Activated T cells show induced expression of, among other things, Glucose Transporter 1 and several glycolytic enzymes, including ADP-Dependent Glucokinase and the low affinity isoform Pyruvate Kinase-M2 (which promote glycolytic flux), as well Glutamine Transporters and Glycerol-3-phosphate Dehydrogenase 2 which make available glutamate and glycerol-3-phosphate as mitochondrial energy sources. Intracellular leucine concentrations critically regulate mammalian target of rapamycin (mTOR) signaling to promote Th1, Th2, and Th17 CD4(+) T effector cell differentiation. In contrast, T regulatory (Treg) cells are generated when AMP-Activating Protein Kinase signaling is activated and mTOR activation is suppressed. Unlike effector CD4(+) and CD8(+) T cells, Tregs and memory T cells oxidize fatty acids for fuel. Effector and memory T cells perform different functions and thus show distinct metabolic profiles which are exquisitely controlled by cellular signaling. Upon activation, T cells express the insulin and leptin receptors on their surface and become sensitive to insulin signaling and nutrient availability and show changes in differentiation. Thus, metabolism and nutrient availability influence T cell activation and function.
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Affiliation(s)
- Jason A Maciolek
- Vaccine and Infectious Disease Organization (VIDO)-Home of the International Vaccine Centre (InterVac), University of Saskatchewan, 120 Veterinary Road, Saskatoon, S7N 5E3, Canada
| | - J Alex Pasternak
- Vaccine and Infectious Disease Organization (VIDO)-Home of the International Vaccine Centre (InterVac), University of Saskatchewan, 120 Veterinary Road, Saskatoon, S7N 5E3, Canada
| | - Heather L Wilson
- Vaccine and Infectious Disease Organization (VIDO)-Home of the International Vaccine Centre (InterVac), University of Saskatchewan, 120 Veterinary Road, Saskatoon, S7N 5E3, Canada.
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32
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Human cancer regression antigens. Curr Opin Immunol 2013; 25:284-90. [PMID: 23566921 DOI: 10.1016/j.coi.2013.03.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 02/08/2013] [Accepted: 03/12/2013] [Indexed: 12/13/2022]
Abstract
Cytotoxic T-cells can recognize antigens that are presented on the surface of human tumor cells and thereby mediate cancer regression. Importantly, those immune interventions that have thus far proven most successful in the clinic-i.e. checkpoint blockade and tumor-infiltrating lymphocyte (TIL) therapy-enhance T-cell activity without a deliberate focus on specific antigens. Thus, one major question remains unsolved: what is the nature of the antigens that need to be recognized on human cancer to result in tumor control? Here we discuss the repertoire of human tumor antigens by three main parameters. Firstly, the extent to which these antigens are shared by larger patient groups; secondly, the degree of tumor-restrictive expression; and finally, the likelihood of antigen loss the moment selection pressure is applied. Using this framework, we describe those classes of antigens that can be considered preferable targets in both active and passive T-cell based cancer immunotherapy.
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33
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Diverse and heritable lineage imprinting of early haematopoietic progenitors. Nature 2013; 496:229-32. [PMID: 23552896 DOI: 10.1038/nature12013] [Citation(s) in RCA: 294] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 02/14/2013] [Indexed: 12/24/2022]
Abstract
Haematopoietic stem cells (HSCs) and their subsequent progenitors produce blood cells, but the precise nature and kinetics of this production is a contentious issue. In one model, lymphoid and myeloid production branch after the lymphoid-primed multipotent progenitor (LMPP), with both branches subsequently producing dendritic cells. However, this model is based mainly on in vitro clonal assays and population-based tracking in vivo, which could miss in vivo single-cell complexity. Here we avoid these issues by using a new quantitative version of 'cellular barcoding' to trace the in vivo fate of hundreds of LMPPs and HSCs at the single-cell level. These data demonstrate that LMPPs are highly heterogeneous in the cell types that they produce, separating into combinations of lymphoid-, myeloid- and dendritic-cell-biased producers. Conversely, although we observe a known lineage bias of some HSCs, most cellular output is derived from a small number of HSCs that each generates all cell types. Crucially, in vivo analysis of the output of sibling cells derived from single LMPPs shows that they often share a similar fate, suggesting that the fate of these progenitors was imprinted. Furthermore, as this imprinting is also observed for dendritic-cell-biased LMPPs, dendritic cells may be considered a distinct lineage on the basis of separate ancestry. These data suggest a 'graded commitment' model of haematopoiesis, in which heritable and diverse lineage imprinting occurs earlier than previously thought.
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34
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Gerlach C, Rohr JC, Perié L, van Rooij N, van Heijst JWJ, Velds A, Urbanus J, Naik SH, Jacobs H, Beltman JB, de Boer RJ, Schumacher TNM. Heterogeneous differentiation patterns of individual CD8+ T cells. Science 2013; 340:635-9. [PMID: 23493421 DOI: 10.1126/science.1235487] [Citation(s) in RCA: 276] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Upon infection, antigen-specific CD8(+) T lymphocyte responses display a highly reproducible pattern of expansion and contraction that is thought to reflect a uniform behavior of individual cells. We tracked the progeny of individual mouse CD8(+) T cells by in vivo lineage tracing and demonstrated that, even for T cells bearing identical T cell receptors, both clonal expansion and differentiation patterns are heterogeneous. As a consequence, individual naïve T lymphocytes contributed differentially to short- and long-term protection, as revealed by participation of their progeny during primary versus recall infections. The discordance in fate of individual naïve T cells argues against asymmetric division as a singular driver of CD8(+) T cell heterogeneity and demonstrates that reproducibility of CD8(+) T cell responses is achieved through population averaging.
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Affiliation(s)
- Carmen Gerlach
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
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35
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van Heijst JWJ, Ceberio I, Lipuma LB, Samilo DW, Wasilewski GD, Gonzales AMR, Nieves JL, van den Brink MRM, Perales MA, Pamer EG. Quantitative assessment of T cell repertoire recovery after hematopoietic stem cell transplantation. Nat Med 2013; 19:372-7. [PMID: 23435170 PMCID: PMC3594333 DOI: 10.1038/nm.3100] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 07/16/2012] [Indexed: 12/19/2022]
Abstract
Delayed T-cell recovery and restricted T-cell receptor (TCR) diversity after allogeneic hematopoietic stem cell transplantation (allo-HSCT) are associated with increased risks of infection and cancer relapse. Technical challenges have limited faithful measurement of TCR diversity following allo-HSCT. Here we combined 5′-RACE PCR with deep sequencing, to quantify TCR diversity in 28 allo-HSCT recipients using a single oligonucleotide pair. Analysis of duplicate blood samples confirmed that the frequency of individual TCRs was accurately determined. After 6 months, cord blood graft recipients approximated the TCR diversity of healthy individuals, whereas recipients of T-cell-depleted peripheral blood stem cell grafts had a 28-fold and 14-fold lower CD4+ and CD8+ T-cell diversity, respectively. After 12 months, these deficiencies had improved for the CD4+, but not the CD8+ T-cell compartment. Overall, this method provides unprecedented views of T-cell repertoire recovery after allo-HSCT and may identify patients at high risk of infection or relapse.
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Affiliation(s)
- Jeroen W J van Heijst
- Immunology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.
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36
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Buchholz VR, Gräf P, Busch DH. The smallest unit: effector and memory CD8(+) T cell differentiation on the single cell level. Front Immunol 2013; 4:31. [PMID: 23424063 PMCID: PMC3573211 DOI: 10.3389/fimmu.2013.00031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 01/26/2013] [Indexed: 12/16/2022] Open
Abstract
CD8+ T cell immune responses provide immediate protection against primary infection and durable memory capable of rapidly fighting off re-infection. Immediate protection and lasting memory are implemented by phenotypically and functionally distinct T cell subsets. While it is now widely accepted that these diverge from a common source of naïve T cells (Tn), the developmental relation and succession of effector and memory T cell subsets is still under intense debate. Recently, a distinct memory T cell subset has been suggested to possess stem cell-like features, sparking the hope to harness its capacity for self-renewal and diversification for successful therapy of chronic infections or malignant diseases. In this review we highlight current developmental models of memory generation, T cell subset diversification and T cell stemness. We discuss the importance of single cell monitoring techniques for adequately mapping these developmental processes and take a brief look at signaling components active in the putative stem cell-like memory T cell compartment.
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Affiliation(s)
- Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München Munich, Germany
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37
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Wensveen FM, van Gisbergen KPJM, Eldering E. The fourth dimension in immunological space: how the struggle for nutrients selects high-affinity lymphocytes. Immunol Rev 2013; 249:84-103. [PMID: 22889217 DOI: 10.1111/j.1600-065x.2012.01156.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lymphocyte activation via the antigen receptor is associated with radical shifts in metabolism and changes in requirements for nutrients and cytokines. Concomitantly, drastic changes occur in the expression of pro-and anti-apoptotic proteins that alter the sensitivity of lymphocytes to limiting concentrations of key survival factors. Antigen affinity is a primary determinant for the capacity of activated lymphocytes to access these vital resources. The shift in metabolic needs and the variable access to key survival factors is used by the immune system to eliminate activated low-affinity cells and to generate an optimal high-affinity response. In this review, we focus on the control of apoptosis regulators in activated lymphocytes by nutrients, cytokines, and costimulation. We propose that the struggle among individual clones that leads to the formation of high-affinity effector cell populations is in effect an 'invisible' fourth signal required for effective immune responses.
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Affiliation(s)
- Felix M Wensveen
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands
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38
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Alanio C, Bouvier I, Jusforgues-Saklani H, Albert ML. Tracking antigen-specific CD8⁺ T cells using MHC class I multimers. Methods Mol Biol 2013; 960:309-326. [PMID: 23329496 DOI: 10.1007/978-1-62703-218-6_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The tracking of epitope-specific T cells is a useful approach for the study of adaptive immune responses. This protocol describes how Major Histocompatibility Complex Class I (MHC-I) multimers can be used to stain, enrich, and enumerate (rare) populations of CD8(+) T cells specific for a given antigen. It provides the detailed steps for multimer labeling, magnetic enrichment, and cytometric analysis. Additionally, it provides informations for multiplexing experiments in order to achieve simultaneous detection of multiple antigenic specificities, and strategies for coupling the protocol with functional assays (e.g., intracellular cytokine staining). Future developments in cytometric systems (e.g., mass spectroscopy-based cytometry) and gene expression studies (e.g., single cell PCR) will extend these approaches and provide an unprecedented assessment of the immune repertoire.
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Affiliation(s)
- Cécile Alanio
- Immunobiologie des cellules dendritiques, Unité Mixte Pasteur/Inserm U818, Institut Pasteur and Centre d'Immunologie Humaine, Institut Pasteur, Paris, France
| | - Isabelle Bouvier
- Immunobiologie des cellules dendritiques, Unité Mixte Pasteur/Inserm U818, Institut Pasteur and Centre d'Immunologie Humaine, Institut Pasteur, Paris, France
| | - Hélène Jusforgues-Saklani
- Immunobiologie des cellules dendritiques, Unité Mixte Pasteur/Inserm U818, Institut Pasteur and Centre d'Immunologie Humaine, Institut Pasteur, Paris, France
| | - Matthew L Albert
- Immunobiologie des cellules dendritiques, Unité Mixte Pasteur/Inserm U818, Institut Pasteur and Centre d'Immunologie Humaine, Institut Pasteur, Paris, France.
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39
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Abstract
Activated T cells have classically been thought to progress unidirectionally through discrete phenotypic states and differentiate into static lineages. It is increasingly evident, however, that T cells exhibit much more complex and flexible dynamic behaviors than initially appreciated, and that these behaviors influence the efficacy of T cell responses to immunological challenges. In this review, we discuss how new technologies for monitoring the dynamics of T cells are enhancing the resolution of the fine phenotypic and functional heterogeneity within populations of T cells and revealing how individual T cells transition among a continuum of states. Such insights into the dynamic properties of T cells should improve immune monitoring and inform strategies for therapeutic interventions.
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Affiliation(s)
- Yvonne J Yamanaka
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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40
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Abstract
The immunological process of clonal selection requires a rapid burst in lymphocyte proliferation, and this involves a metabolic shift to provide energy and the building blocks of new cells. After activation, naive and memory T cells switch from the oxidation of free fatty acids to glycolysis and glutaminolysis to meet these demands. Beyond this, however, the availability of specific metabolites and the pathways that process them interconnect with signaling events in the cell to influence cell cycle, differentiation, cell death and immunological function. Here we define 'metabolic checkpoints' that represent such interconnections and provide examples of how these checkpoints sense metabolic status and transduce signals to affect T lymphocyte responses.
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Affiliation(s)
- Ruoning Wang
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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41
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Weber K, Thomaschewski M, Benten D, Fehse B. RGB marking with lentiviral vectors for multicolor clonal cell tracking. Nat Protoc 2012; 7:839-49. [PMID: 22481527 DOI: 10.1038/nprot.2012.026] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells transduced with lentiviral vectors are individually marked by a highly characteristic pattern of insertion sites inherited by all their progeny. We have recently extended this principle of clonal cell marking by introducing the method of RGB marking, which makes use of the simultaneous transduction of target cells with three lentiviral gene ontology (LeGO) vectors encoding red, green or blue fluorescent proteins. In accordance with the additive color model, individual RGB-marked cells display a large variety of unique and highly specific colors. Color codes remain stable after cell division and can thus be used for clonal tracking in vivo and in vitro. Our protocol for efficient RGB marking is based on established methods of lentiviral vector production (3-4 d) and titration (3 d). The final RGB-marking step requires concurrent transduction with the three RGB vectors at equalized multiplicities of infection (1-12 h). The initial efficiency of RGB marking can be assessed after 2-4 d by flow cytometry and/or fluorescence microscopy.
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Affiliation(s)
- Kristoffer Weber
- Research Department Cell and Gene Therapy, Clinic for Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Germany
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42
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The transcription factor Myc controls metabolic reprogramming upon T lymphocyte activation. Immunity 2012; 35:871-82. [PMID: 22195744 DOI: 10.1016/j.immuni.2011.09.021] [Citation(s) in RCA: 1520] [Impact Index Per Article: 126.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/21/2011] [Accepted: 09/16/2011] [Indexed: 12/13/2022]
Abstract
To fulfill the bioenergetic and biosynthetic demand of proliferation, T cells reprogram their metabolic pathways from fatty acid β-oxidation and pyruvate oxidation via the TCA cycle to the glycolytic, pentose-phosphate, and glutaminolytic pathways. Two of the top-ranked candidate transcription factors potentially responsible for the activation-induced T cell metabolic transcriptome, HIF1α and Myc, were induced upon T cell activation, but only the acute deletion of Myc markedly inhibited activation-induced glycolysis and glutaminolysis in T cells. Glutamine deprivation compromised activation-induced T cell growth and proliferation, and this was partially replaced by nucleotides and polyamines, implicating glutamine as an important source for biosynthetic precursors in active T cells. Metabolic tracer analysis revealed a Myc-dependent metabolic pathway linking glutaminolysis to the biosynthesis of polyamines. Therefore, a Myc-dependent global metabolic transcriptome drives metabolic reprogramming in activated, primary T lymphocytes. This may represent a general mechanism for metabolic reprogramming under patho-physiological conditions.
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Abstract
As Nature Reviews Immunology reaches its 10(th) anniversary, the authors of one of the top-cited articles from each year take a trip down memory lane. We've asked them to look back on the state of research at the time their Review was published, to consider why the article has had the impact it has and to discuss the future directions of their field. This Viewpoint article provides an interesting snapshot of some of the fundamental advances in immunology over the past 10 years. Highlights include our improved understanding of Toll-like receptor signalling, and of immune regulation mediated by regulatory T cells, indoleamine 2,3-dioxygenase, myeloid-derived suppressor cells and interleukin-10. The complexities in the development and heterogeneity of macrophages, dendritic cells and T helper cells continue to engage immunologists, as do the immune processes involved in diseases such as atherosclerosis. We look forward to what the next 10 years of immunology research may bring.
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44
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Sun JC, Lanier LL. NK cell development, homeostasis and function: parallels with CD8⁺ T cells. Nat Rev Immunol 2011; 11:645-57. [PMID: 21869816 DOI: 10.1038/nri3044] [Citation(s) in RCA: 484] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Natural killer (NK) cells survey host tissues for signs of infection, transformation or stress and, true to their name, kill target cells that have become useless or are detrimental to the host. For decades, NK cells have been classified as a component of the innate immune system. However, accumulating evidence in mice and humans suggests that, like the B and T cells of the adaptive immune system, NK cells are educated during development, possess antigen-specific receptors, undergo clonal expansion during infection and generate long-lived memory cells. In this Review, we highlight the many stages that an NK cell progresses through during its remarkable lifetime, discussing similarities and differences with its close relative, the cytotoxic CD8(+) T cell.
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Affiliation(s)
- Joseph C Sun
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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45
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Piccaluga PP, Agostinelli C, Tripodo C, Gazzola A, Bacci F, Sabattini E, Pileri SA. Peripheral T-cell lymphoma classification: the matter of cellular derivation. Expert Rev Hematol 2011; 4:415-425. [PMID: 21801133 DOI: 10.1586/ehm.11.37] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Peripheral T-cell lymphomas (PTCLs) represent approximately 12% of all non-Hodgkin's lymphomas in Western countries. They are quite heterogeneous as far as morphology and phenotype are concerned. Furthermore, until now, PTCLs could not be referred to specific normal counterparts, in contrast to B-cell-derived non-Hodgkin's lymphomas. In particular, in the last edition of the WHO classification of Tumors of the Hematopoietic and Lymphoid Tissues, for the majority of nodal PTCLs (including the not otherwise specified type and anaplastic large-cell lymphoma), the postulated cell of origin remained undefined. However, in the last few years, high-throughput genomic techniques, especially gene-expression profiling, have allowed us to better define the relationship between some entities and the different T-cell subpopulations. Consequently, it has become possible to clearly define, for example, the association between angioimmunoblastic T-cell lymphoma and T-follicular helper cells. In addition, within PTCLs/not otherwise specified, different subgroups were identified based on their similarity to different cellular counterparts, including T-helper, T-cytotoxic and T-follicular helper cells. In this article, based on their own experience as well as up-to-date literature, the authors revise the concept of PTCL classification by specially focusing on their cellular counterparts and discuss the possible clinical relevance of such an approach.
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Abstract
Our T cell repertoire is shaped by antigen encounter. From a naive T cell pool that contains millions of different T cells with unknown specificities, pathogen infection leads to selection of those T cells that can detect pathogen-derived antigens. Following clearance of infection, a population of memory T cells remains and protects the individual from severe reinfection. A central question in the field has been how the generation of long-lived memory T cells, versus short-lived ("terminally differentiated") T cells, is controlled. In this review we discuss the models that have been put forward to explain the generation of memory T cells after infection and the experimental evidence supporting these hypotheses. Based on the available data we propose a new model that stipulates that during immune responses T cells do not acquire different fates that determine their subsequent long-term survival but rather T cells assume different states that simply reflect the likelihood of future survival, states that can still be modulated by external signals.
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Affiliation(s)
- Carmen Gerlach
- The Netherlands Cancer Institute, Department of Immunology, Amsterdam, The Netherlands
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