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      Tissue-resident-like CD4 + T cells secreting IL-17 control Mycobacterium tuberculosis in the human lung

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      1 , 2 , 3 , 4 , 5 , 6 , 1 , 2 , 1 , 2 , 1 , 1 , 1 , 1 , 1 , 1 , 7 , 8 , 8 , 8 , 9 , 9 , 10 , 11 , 1 , 12 , 13 , 7 , 1 , 6 , 14 , 4 , 5 , 1 , 2 , 6 ,
      The Journal of Clinical Investigation
      American Society for Clinical Investigation
      Immunology, Infectious disease, Bacterial infections, T cells

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          Abstract

          T cell immunity is essential for the control of tuberculosis (TB), an important disease of the lung, and is generally studied in humans using peripheral blood cells. Mounting evidence, however, indicates that tissue-resident memory T cells (Trms) are superior at controlling many pathogens, including Mycobacterium tuberculosis ( M. tuberculosis), and can be quite different from those in circulation. Using freshly resected lung tissue, from individuals with active or previous TB, we identified distinct CD4 + and CD8 + Trm-like clusters within TB-diseased lung tissue that were functional and enriched for IL-17–producing cells. M. tuberculosis–specific CD4 + T cells producing TNF-α, IL-2, and IL-17 were highly expanded in the lung compared with matched blood samples, in which IL-17 + cells were largely absent. Strikingly, the frequency of M. tuberculosis–specific lung T cells making IL-17, but not other cytokines, inversely correlated with the plasma IL-1β levels, suggesting a potential link with disease severity. Using a human granuloma model, we showed the addition of either exogenous IL-17 or IL-2 enhanced immune control of M. tuberculosis and was associated with increased NO production. Taken together, these data support an important role for M. tuberculosis–specific Trm-like, IL-17–producing cells in the immune control of M. tuberculosis in the human lung.

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          Most cited references99

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          Dimensionality reduction for visualizing single-cell data using UMAP

          Advances in single-cell technologies have enabled high-resolution dissection of tissue composition. Several tools for dimensionality reduction are available to analyze the large number of parameters generated in single-cell studies. Recently, a nonlinear dimensionality-reduction technique, uniform manifold approximation and projection (UMAP), was developed for the analysis of any type of high-dimensional data. Here we apply it to biological data, using three well-characterized mass cytometry and single-cell RNA sequencing datasets. Comparing the performance of UMAP with five other tools, we find that UMAP provides the fastest run times, highest reproducibility and the most meaningful organization of cell clusters. The work highlights the use of UMAP for improved visualization and interpretation of single-cell data.
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            Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.

            Acute myeloid leukemia (AML) manifests as phenotypically and functionally diverse cells, often within the same patient. Intratumor phenotypic and functional heterogeneity have been linked primarily by physical sorting experiments, which assume that functionally distinct subpopulations can be prospectively isolated by surface phenotypes. This assumption has proven problematic, and we therefore developed a data-driven approach. Using mass cytometry, we profiled surface and intracellular signaling proteins simultaneously in millions of healthy and leukemic cells. We developed PhenoGraph, which algorithmically defines phenotypes in high-dimensional single-cell data. PhenoGraph revealed that the surface phenotypes of leukemic blasts do not necessarily reflect their intracellular state. Using hematopoietic progenitors, we defined a signaling-based measure of cellular phenotype, which led to isolation of a gene expression signature that was predictive of survival in independent cohorts. This study presents new methods for large-scale analysis of single-cell heterogeneity and demonstrates their utility, yielding insights into AML pathophysiology.
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              Two subsets of memory T lymphocytes with distinct homing potentials and effector functions.

              Naive T lymphocytes travel to T-cell areas of secondary lymphoid organs in search of antigen presented by dendritic cells. Once activated, they proliferate vigorously, generating effector cells that can migrate to B-cell areas or to inflamed tissues. A fraction of primed T lymphocytes persists as circulating memory cells that can confer protection and give, upon secondary challenge, a qualitatively different and quantitatively enhanced response. The nature of the cells that mediate the different facets of immunological memory remains unresolved. Here we show that expression of CCR7, a chemokine receptor that controls homing to secondary lymphoid organs, divides human memory T cells into two functionally distinct subsets. CCR7- memory cells express receptors for migration to inflamed tissues and display immediate effector function. In contrast, CCR7+ memory cells express lymph-node homing receptors and lack immediate effector function, but efficiently stimulate dendritic cells and differentiate into CCR7- effector cells upon secondary stimulation. The CCR7+ and CCR7- T cells, which we have named central memory (TCM) and effector memory (TEM), differentiate in a step-wise fashion from naive T cells, persist for years after immunization and allow a division of labour in the memory response.
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                Author and article information

                Contributors
                Journal
                J Clin Invest
                J Clin Invest
                J Clin Invest
                The Journal of Clinical Investigation
                American Society for Clinical Investigation
                0021-9738
                1558-8238
                17 May 2021
                17 May 2021
                17 May 2021
                17 May 2021
                : 131
                : 10
                : e142014
                Affiliations
                [1 ]Africa Health Research Institute, Durban, South Africa.
                [2 ]School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
                [3 ]Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya.
                [4 ]National Institute for Health Research Southampton Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, and
                [5 ]Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.
                [6 ]Division of Infection and Immunity, University College London, London, United Kingdom.
                [7 ]Department of Cardiothoracic Surgery, Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
                [8 ]ImmunoScape Pte Ltd, Singapore, Singapore.
                [9 ]La Jolla Institute for Immunology, La Jolla, California, USA.
                [10 ]Department of Medicine, University of California, San Diego, La Jolla, California, USA.
                [11 ]Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
                [12 ]Department of Microbiology and
                [13 ]Center for AIDS Research and Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA.
                [14 ]Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
                Author notes
                Address correspondence to: Alasdair Leslie, K-RITH Tower, Nelson Mandela School of Medicine, 719 Umbilo Road, Congella, Durban, South Africa, 4001. Phone: 27.31. 2604186; Email: al.leslie@ 123456ahri.org .
                Author information
                http://orcid.org/0000-0002-0093-5768
                http://orcid.org/0000-0002-7898-6709
                http://orcid.org/0000-0002-0384-8408
                http://orcid.org/0000-0001-7302-8002
                http://orcid.org/0000-0002-3374-6699
                http://orcid.org/0000-0001-9177-8827
                http://orcid.org/0000-0003-0390-0613
                http://orcid.org/0000-0003-2538-6467
                Article
                142014
                10.1172/JCI142014
                8121523
                33848273
                4d3174a5-33c6-4fcd-922a-88333704ad08
                © 2021 Ogongo et al.

                This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 6 July 2020
                : 8 April 2021
                Funding
                Funded by: BMGF and The Wellcome Trust
                Award ID: OPP1137006,210662/Z/18/Z
                Categories
                Research Article

                immunology,infectious disease,bacterial infections,t cells

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