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L. Koth, O. Solberg, Jeffrey Peng, N. Bhakta, Christine Nguyen, P. Woodruff (2011)
Sarcoidosis blood transcriptome reflects lung inflammation and overlaps with tuberculosis.American journal of respiratory and critical care medicine, 184 10
(World Health Organization. Global Tuberculosis Report 2020https://www.who.int/publications/i/item/9789240013131 (WHO, 2020).)
World Health Organization. Global Tuberculosis Report 2020https://www.who.int/publications/i/item/9789240013131 (WHO, 2020).World Health Organization. Global Tuberculosis Report 2020https://www.who.int/publications/i/item/9789240013131 (WHO, 2020)., World Health Organization. Global Tuberculosis Report 2020https://www.who.int/publications/i/item/9789240013131 (WHO, 2020).
Anthony Cadena, S. Fortune, J. Flynn (2017)
Heterogeneity in tuberculosisNature Reviews Immunology, 17
L. Tezera, M. Bielecka, P. Ogongo, N. Walker, M. Ellis, D. Garay-Baquero, Kristian Thomas, Michaela Reichmann, D. Johnston, K. Wilkinson, Mohamed Ahmed, S. Jogai, S. Jayasinghe, R. Wilkinson, S. Mansour, G. Thomas, C. Ottensmeier, A. Leslie, P. Elkington (2020)
Anti-PD-1 immunotherapy leads to tuberculosis reactivation via dysregulation of TNF-αeLife, 9
A. Green, Joshua Mattila, C. Bigbee, K. Bongers, P. Lin, J. Flynn (2010)
CD4(+) regulatory T cells in a cynomolgus macaque model of Mycobacterium tuberculosis infection.The Journal of infectious diseases, 202 4
(2003)
Sarcoidosis.Lancet, 361
Keith Kauffman, Michelle Sallin, Shunsuke Sakai, O. Kamenyeva, J. Kabat, Danielle Weiner, M. Sutphin, D. Schimel, L. Via, C. Barry, Temeri Wilder-Kofie, Ian Moore, Rashida Moore, D. Barber (2017)
Defective positioning in granulomas but not lung-homing limits CD4 T cell interactions with Mycobacterium tuberculosis infected macrophages in rhesus macaquesMucosal immunology, 11
H. Warsinske, R. Vashisht, P. Khatri (2019)
Host-response-based gene signatures for tuberculosis diagnosis: A systematic comparison of 16 signaturesPLoS Medicine, 16
(2019)
Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granulomaNat. Commun., 10
U. Gautam, Taylor Foreman, Allison Bucşan, Ashley Veatch, X. Alvarez, T. Adékambi, Nadia Golden, Kaylee Gentry, Lara Doyle-Meyers, K. Russell-Lodrigue, Peter Didier, James Blanchard, K. Kousoulas, Andrew Lackner, D. Kalman, Jyothi Rengarajan, S. Khader, D. Kaushal, S. Mehra (2017)
In vivo inhibition of tryptophan catabolism reorganizes the tuberculoma and augments immune-mediated control of Mycobacterium tuberculosisProceedings of the National Academy of Sciences of the United States of America, 115
Lei Shen, Yan Gao, Yuanyuan Liu, Bingyan Zhang, Qianqian Liu, Jing Wu, L. Fan, Qinfang Ou, Wenhong Zhang, L. Shao (2016)
PD-1/PD-L pathway inhibits M.tb-specific CD4+ T-cell functions and phagocytosis of macrophages in active tuberculosisScientific Reports, 6
(2017)
CD4 T cells promote rather than control CD4 T cells promote rather than control tuberculosis in the absence of PD-1–mediated inhibitionJ. Immunol., 6
M. Girvan, M. Newman (2001)
Community structure in social and biological networksProceedings of the National Academy of Sciences of the United States of America, 99
Stefan Oehlers, M. Cronan, N. Scott, Monica Thomas, Kazuhide Okuda, E. Walton, Rebecca Beerman, P. Crosier, D. Tobin (2014)
Interception of host angiogenic signalling limits mycobacterial growthNature, 517
S. Subbian, L. Tsenova, Mi‐jeong Kim, H. Wainwright, A. Visser, N. Bandyopadhyay, J. Bader, P. Karakousis, Gabriele Murrmann, L. Bekker, D. Russell, G. Kaplan (2015)
Lesion-Specific Immune Response in Granulomas of Patients with Pulmonary Tuberculosis: A Pilot StudyPLoS ONE, 10
Roshni Chowdhury, Francesco Vallania, Qianting Yang, C. Angel, F. Darboe, A. Penn-Nicholson, V. Rozot, E. Nemes, S. Malherbe, K. Ronacher, G. Walzl, W. Hanekom, Mark Davis, Jill Winter, Xinchun Chen, T. Scriba, P. Khatri, Y. Chien (2018)
A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomesNature, 560
K. Mulder, Amit Patel, Wan Kong, Cécile Piot, Evelyn Halitzki, G. Dunsmore, Shabnam Khalilnezhad, S. Irac, A. Dubuisson, Marion Chevrier, Xiao Zhang, J. Tam, T. Lim, R. Wong, Rhea Pai, A. Khalil, P. Chow, Suny Wu, Ghamdan Al-Eryani, D. Roden, A. Swarbrick, J. Chan, S. Albani, L. Derosa, L. Zitvogel, Ankur Sharma, Jinmiao Chen, Aymeric Silvin, A. Bertoletti, Camille Blériot, C. Dutertre, F. Ginhoux (2021)
Cross-tissue single-cell landscape of human monocytes and macrophages in health and disease.Immunity
(Hartmann, F. J., et al. Multiplexed single-cell metabolic profiles organize the spectrum of cytotoxic human T cells. Preprint at bioRxiv10.1101/2020.01.17.909796 (2020).)
Hartmann, F. J., et al. Multiplexed single-cell metabolic profiles organize the spectrum of cytotoxic human T cells. Preprint at bioRxiv10.1101/2020.01.17.909796 (2020).Hartmann, F. J., et al. Multiplexed single-cell metabolic profiles organize the spectrum of cytotoxic human T cells. Preprint at bioRxiv10.1101/2020.01.17.909796 (2020)., Hartmann, F. J., et al. Multiplexed single-cell metabolic profiles organize the spectrum of cytotoxic human T cells. Preprint at bioRxiv10.1101/2020.01.17.909796 (2020).
B. Gern, Kristin Adams, C. Plumlee, C. Stoltzfus, Laila Shehata, Albanus Moguche, K. Busman-Sahay, S. Hansen, M. Axthelm, L. Picker, J. Estes, K. Urdahl, Michael Gerner (2021)
TGFβ restricts expansion, survival, and function of T cells within the tuberculous granuloma.Cell host & microbe
T. Sweeney, W. Haynes, Francesco Vallania, J. Ioannidis, P. Khatri (2016)
Methods to increase reproducibility in differential gene expression via meta-analysisNucleic Acids Research, 45
John Wherry, M. Kurachi (2015)
Molecular and cellular insights into T cell exhaustionNature Reviews Immunology, 15
(2018)
Myeloid-derived suppressor cells coming of age review-article
(2016)
Persisting positron emission tomography lesion activity and Mycobacterium tuberculosis mRNA after tuberculosis cureNat. Med., 22
E. Wong, Louis Joslyn, N. Grant, E. Klein, P. Lin, D. Kirschner, J. Flynn (2018)
Low Levels of T Cell Exhaustion in Tuberculous Lung GranulomasInfection and Immunity, 86
C. Martin, Anthony Cadena, Vivian Leung, P. Lin, Pauline Maiello, Nathan Hicks, M. Chase, J. Flynn, S. Fortune (2017)
Digitally Barcoding Mycobacterium tuberculosis Reveals In Vivo Infection Dynamics in the Macaque Model of TuberculosismBio, 8
S. Gassen, Britt Callebaut, M. Helden, B. Lambrecht, P. Demeester, T. Dhaene, Y. Saeys (2015)
FlowSOM: Using self‐organizing maps for visualization and interpretation of cytometry dataCytometry Part A, 87
J. Scott-Browne, S. Shafiani, G. Tucker-Heard, Kumiko Ishida-Tsubota, J. Fontenot, A. Rudensky, M. Bevan, K. Urdahl (2007)
Expansion and function of Foxp3-expressing T regulatory cells during tuberculosisThe Journal of Experimental Medicine, 204
G. Rossi, O. Sacco, E. Cosulich, A. Risso, B. Balbi, C. Ravazzoni (1986)
Helper T-lymphocytes in pulmonary sarcoidosis. Functional analysis of a lung T-cell subpopulation in patients with active disease.The American review of respiratory disease, 133 6
D. Barber, Shunsuke Sakai, R. Kudchadkar, S. Fling, T. Day, Julie Vergara, D. Ashkin, Jonathan Cheng, Lisa Lundgren, V. Raabe, C. Kraft, J. Nieva, M. Cheever, P. Nghiem, E. Sharon (2019)
Tuberculosis following PD-1 blockade for cancer immunotherapyScience Translational Medicine, 11
L. Ramakrishnan (2012)
Revisiting the role of the granuloma in tuberculosisNature Reviews Immunology, 12
T. Ulrichs, G. Kosmiadi, V. Trusov, S. Jörg, L. Pradl, Marina Titukhina, V. Mishenko, N. Gushina, S. Kaufmann (2004)
Human tuberculous granulomas induce peripheral lymphoid follicle‐like structures to orchestrate local host defence in the lungThe Journal of Pathology, 204
Nitya Krishnan, B. Robertson, G. Thwaites (2010)
The mechanisms and consequences of the extra-pulmonary dissemination of Mycobacterium tuberculosis.Tuberculosis, 90 6
Robert DiFazio, Joshua Mattila, E. Klein, L. Cirrincione, Mondraya Howard, E. Wong, J. Flynn (2016)
Active transforming growth factor-β is associated with phenotypic changes in granulomas after drug treatment in pulmonary tuberculosisFibrogenesis & Tissue Repair, 9
Andrea Wolf, Beth Linas, G. Trevejo-Nuñez, Eleanor Kincaid, T. Tamura, K. Takatsu, J. Ernst (2007)
Mycobacterium tuberculosis Infects Dendritic Cells with High Frequency and Impairs Their Function In Vivo1The Journal of Immunology, 179
D. Barber, K. Mayer-Barber, C. Feng, A. Sharpe, A. Sher (2011)
CD4 T Cells Promote Rather than Control Tuberculosis in the Absence of PD-1–Mediated InhibitionThe Journal of Immunology, 186
M. Kanamori, Hiroko Nakatsukasa, M. Okada, Q. Lu, A. Yoshimura (2016)
Induced Regulatory T Cells: Their Development, Stability, and Applications.Trends in immunology, 37 11
M. Newman (2006)
Finding community structure in networks using the eigenvectors of matrices.Physical review. E, Statistical, nonlinear, and soft matter physics, 74 3 Pt 2
V. Guyot-Revol, J. Innes, S. Hackforth, T. Hinks, A. Lalvani (2006)
Regulatory T cells are expanded in blood and disease sites in patients with tuberculosis.American journal of respiratory and critical care medicine, 173 7
(2016)
Mast cell: a multi-functional master cellFront. Oncol., 6
Sara Cohen, B. Gern, Jared Delahaye, Kristin Adams, C. Plumlee, Jessica Winkler, D. Sherman, Michael Gerner, K. Urdahl (2018)
Alveolar Macrophages Provide an Early Mycobacterium tuberculosis Niche and Initiate Dissemination.Cell host & microbe, 24 3
Dylan Bannon, Erick Moen, Morgan Schwartz, Enrico Borba, Takamasa Kudo, N. Greenwald, Vibha Vijayakumar, B. Chang, Edward Pao, Erik Osterman, William Graf, David Valen (2021)
DeepCell Kiosk: scaling deep learning–enabled cellular image analysis with KubernetesNature Methods, 18
J. Havel, D. Chowell, T. Chan (2019)
The evolving landscape of biomarkers for checkpoint inhibitor immunotherapyNature Reviews Cancer, 19
P. Bankhead, M. Loughrey, José Fernández, Yvonne Dombrowski, D. McArt, P. Dunne, S. McQuaid, R. Gray, L. Murray, H. Coleman, J. James, M. Salto‐Tellez, P. Hamilton (2017)
QuPath: Open source software for digital pathology image analysisScientific Reports, 7
E. Wong, S. Evans, Carolyn Kraus, Kathleen Engelman, Pauline Maiello, Walter Flores, Anthony Cadena, E. Klein, Kayla Thomas, Alexander White, Chelsea Causgrove, Brianne Stein, Jaime Tomko, Joshua Mattila, H. Gideon, P. Lin, Keith Reimann, Denise Kirschner, J. Flynn (2019)
IL-10 Impairs Local Immune Response in Lung Granulomas and Lymph Nodes during Early Mycobacterium tuberculosis InfectionThe Journal of Immunology, 204
(Rossi, G. A. et al. Helper T-lymphocytes in pulmonary sarcoidosis: functional analysis of a lung T-cell subpopulation in patients with active disease. Am. Rev. Respir. Dis.133, 1086–1090 (1986).)
Rossi, G. A. et al. Helper T-lymphocytes in pulmonary sarcoidosis: functional analysis of a lung T-cell subpopulation in patients with active disease. Am. Rev. Respir. Dis.133, 1086–1090 (1986).Rossi, G. A. et al. Helper T-lymphocytes in pulmonary sarcoidosis: functional analysis of a lung T-cell subpopulation in patients with active disease. Am. Rev. Respir. Dis.133, 1086–1090 (1986)., Rossi, G. A. et al. Helper T-lymphocytes in pulmonary sarcoidosis: functional analysis of a lung T-cell subpopulation in patients with active disease. Am. Rev. Respir. Dis.133, 1086–1090 (1986).
Zicheng Hu, Chethan Jujjavarapu, J. Hughey, Sandra Andorf, Hao-Chih Lee, P. Gherardini, M. Spitzer, Cristel Thomas, John Campbell, P. Dunn, Jeffery Wiser, B. Kidd, J. Dudley, G. Nolan, S. Bhattacharya, A. Butte (2018)
MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data.Cell reports, 24 5
D. Munn, A. Mellor (2016)
IDO in the Tumor Microenvironment: Inflammation, Counter-Regulation, and Tolerance.Trends in immunology, 37 3
J. Jurado, I. Alvarez, V. Pasquinelli, G. Martinez, M. Quiroga, E. Abbate, R. Musella, H. Chuluyan, V. García (2008)
Programmed Death (PD)-1:PD-Ligand 1/PD-Ligand 2 Pathway Inhibits T Cell Effector Functions during Human Tuberculosis1The Journal of Immunology, 181
J. Ernst, A. Cornelius, L. Desvignes, J. Tavs, Brian Norris (2018)
Limited Antimycobacterial Efficacy of Epitope Peptide Administration Despite Enhanced Antigen-Specific CD4 T-Cell ActivationThe Journal of Infectious Diseases, 218
M. Coleman, Pauline Maiello, Jaime Tomko, L. Frye, Daniel Fillmore, Christopher Janssen, E. Klein, P. Lin (2014)
Early Changes by 18Fluorodeoxyglucose Positron Emission Tomography Coregistered with Computed Tomography Predict Outcome after Mycobacterium tuberculosis Infection in Cynomolgus MacaquesInfection and Immunity, 82
J. Collins, Amnah Siddiqa, Dean Jones, Ken Liu, R. Kempker, A. Nizam, N. Shah, N. Ismail, S. Ouma, N. Tukvadze, Shuzhao Li, C. Day, Jyothi Rengarajan, J. Brust, N. Gandhi, J. Ernst, H. Blumberg, T. Ziegler (2020)
Tryptophan catabolism reflects disease activity in human tuberculosis.JCI insight
K. Anand, G. Sahu, E. Burns, Allyne Ensor, J. Ensor, S. Pingali, V. Subbiah, S. Iyer (2020)
Mycobacterial infections due to PD-1 and PD-L1 checkpoint inhibitorsESMO Open, 5
D. Zak, A. Penn-Nicholson, T. Scriba, E. Thompson, S. Suliman, L. Amon, H. Mahomed, Mzwandile Erasmus, Wendy Whatney, G. Hussey, D. Abrahams, F. Kafaar, T. Hawkridge, S. Verver, E. Hughes, M. Ota, J. Sutherland, R. Howe, H. Dockrell, W. Boom, B. Thiel, T. Ottenhoff, H. Mayanja-Kizza, A. Crampin, K. Downing, M. Hatherill, Joe Valvo, Smitha Shankar, S. Parida, S. Kaufmann, G. Walzl, A. Aderem, W. Hanekom (2016)
A prospective blood RNA signature for tuberculosis disease riskLancet (London, England), 387
J. Bagaitkar (2014)
Cellular dynamics of resolving inflammation.Blood, 124 11
(Gideon, H. P. et al. Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte. Preprint at bioRxiv10.1101/2020.10.24.352492 (2020).)
Gideon, H. P. et al. Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte. Preprint at bioRxiv10.1101/2020.10.24.352492 (2020).Gideon, H. P. et al. Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte. Preprint at bioRxiv10.1101/2020.10.24.352492 (2020)., Gideon, H. P. et al. Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte. Preprint at bioRxiv10.1101/2020.10.24.352492 (2020).
Finlay Mcnab, M. Berry, C. Graham, S. Bloch, T. Oni, K. Wilkinson, R. Wilkinson, O. Kon, J. Banchereau, D. Chaussabel, A. O’Garra (2011)
Programmed death ligand 1 is over-expressed by neutrophils in the blood of patients with active tuberculosisEuropean Journal of Immunology, 41
Leeat Keren, M. Bossé, S. Thompson, Tyler Risom, Kausalia Vijayaragavan, E. Mccaffrey, Diana Marquez, Roshan Angoshtari, N. Greenwald, Harris Fienberg, Jennifer Wang, N. Kambham, David Kirkwood, G. Nolan, T. Montine, S. Galli, Robert West, S. Bendall, Michael Angelo (2019)
MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structureScience Advances, 5
Mohlopheni Marakalala, Ravikiran Raju, K. Sharma, Y. Zhang, E. Eugenin, Brendan Prideaux, Isaac Daudelin, Pei-Yu Chen, M. Booty, Jin Kim, S. Eum, L. Via, S. Behar, C. Barry, M. Mann, V. Dartois, E. Rubin (2016)
Inflammatory signaling in human Tuberculosis granulomas is spatially organizedNature medicine, 22
S. Mehra, X. Alvarez, P. Didier, Lara Doyle, J. Blanchard, A. Lackner, D. Kaushal (2013)
Granuloma correlates of protection against tuberculosis and mechanisms of immune modulation by Mycobacterium tuberculosis.The Journal of infectious diseases, 207 7
F. Hartmann, Dunja Mrdjen, E. Mccaffrey, David Glass, N. Greenwald, Anusha Bharadwaj, Zumana Khair, Alex Baranski, Reema Baskar, Michael Angelo, S. Bendall (2020)
Multiplexed Single-cell Metabolic Profiles Organize the Spectrum of Cytotoxic Human T CellsbioRxiv
A. Jarnicki, J. Lysaght, S. Todryk, K. Mills (2006)
Suppression of Antitumor Immunity by IL-10 and TGF-β-Producing T Cells Infiltrating the Growing Tumor: Influence of Tumor Environment on the Induction of CD4+ and CD8+ Regulatory T Cells1The Journal of Immunology, 177
Zhenghao Chen, Ilya Soifer, H. Hilton, Leeat Keren, V. Jojic (2020)
Modeling Multiplexed Images with Spatial-LDA Reveals Novel Tissue MicroenvironmentsJournal of Computational Biology, 27
J. Maertzdorf, J. Weiner, H. Mollenkopf, TBornotTB Network, T. Bauer, A. Prasse, J. Müller‐Quernheim, S. Kaufmann (2012)
Common patterns and disease-related signatures in tuberculosis and sarcoidosisProceedings of the National Academy of Sciences, 109
Ming Li, Shomyseh Sanjabi, R. Flavell (2006)
Transforming Growth Factor-β Controls Development, Homeostasis, and Tolerance of T Cells by Regulatory T Cell-Dependent and -Independent MechanismsImmunity, 25
P. Elkington, A. Bateman, G. Thomas, C. Ottensmeier (2018)
Implications of Tuberculosis Reactivation after Immune Checkpoint Inhibition.American journal of respiratory and critical care medicine, 198 11
(Sweeney, T. E., Haynes, W. A., Vallania, F., Ioannidis, J. P. & Khatri, P. Methods to increase reproducibility in differential gene expression via meta-analysis. Nucleic Acids Res. (2017).)
Sweeney, T. E., Haynes, W. A., Vallania, F., Ioannidis, J. P. & Khatri, P. Methods to increase reproducibility in differential gene expression via meta-analysis. Nucleic Acids Res. (2017).Sweeney, T. E., Haynes, W. A., Vallania, F., Ioannidis, J. P. & Khatri, P. Methods to increase reproducibility in differential gene expression via meta-analysis. Nucleic Acids Res. (2017)., Sweeney, T. E., Haynes, W. A., Vallania, F., Ioannidis, J. P. & Khatri, P. Methods to increase reproducibility in differential gene expression via meta-analysis. Nucleic Acids Res. (2017).
Leland McInnes, John Healy (2018)
UMAP: Uniform Manifold Approximation and Projection for Dimension ReductionArXiv, abs/1802.03426
H. Polena, Frédéric Boudou, S. Tilleul, Nicolas Dubois-Colas, C. Lecointe, N. Rakotosamimanana, Mattia Pelizzola, S. Andriamandimby, V. Raharimanga, P. Charles, J. Herrmann, P. Ricciardi-Castagnoli, V. Rasolofo, B. Gicquel, L. Tailleux (2016)
Mycobacterium tuberculosis exploits the formation of new blood vessels for its disseminationScientific Reports, 6
A. Lalvani, R. Brookes, Robert, J., Wilkinson, Adam, Š., Malin, Ansar, Å., Pathan, P. Andersen, G. Pasvol, Adrián, S. V., Hill (1997)
Human cytolytic and interferon g-secreting CD 8 1 T lymphocytes specific for Mycobacterium tuberculosis
B. Carow, Thomas Hauling, Xiaoyan Qian, I. Kramnik, M. Nilsson, M. Rottenberg (2019)
Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granulomaNature Communications, 10
J. Flynn, M. Goldstein, K. Triebold, B. Koller, B. Bloom (1992)
Major histocompatibility complex class I-restricted T cells are required for resistance to Mycobacterium tuberculosis infection.Proceedings of the National Academy of Sciences of the United States of America, 89 24
(2020)
Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte
(2013)
Sterilization of granulomas is common in active and latent tuberculosis despite within-host variability in bacterial killing
(2016)
Active transforming growth factor-β is associated with phenotypic changes in granulomas after drug treatment in pulmonary tuberculosisDARU, J. Pharm. Sci., 24
Amalia Anastasopoulou, D. Ziogas, M. Samarkos, J. Kirkwood, H. Gogas (2019)
Reactivation of tuberculosis in cancer patients following administration of immune checkpoint inhibitors: current evidence and clinical practice recommendationsJournal for Immunotherapy of Cancer, 7
T. Scriba, A. Penn-Nicholson, Smitha Shankar, T. Hraha, E. Thompson, David Sterling, E. Nemes, F. Darboe, S. Suliman, Lynn Amon, H. Mahomed, Mzwandile Erasmus, Wendy Whatney, John Johnson, W. Boom, M. Hatherill, Joe Valvo, M. Groote, Urs Ochsner, A. Aderem, W. Hanekom, D. Zak (2017)
Sequential inflammatory processes define human progression from M. tuberculosis infection to tuberculosis diseasePLoS Pathogens, 13
D. Valen, Takamasa Kudo, Keara Lane, Derek Macklin, N. Quach, Mialy DeFelice, Inbal Maayan, Yu Tanouchi, E. Ashley, M. Covert (2016)
Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging ExperimentsPLoS Computational Biology, 12
(McInnes, L., Healy, J. & Melville, J. UMAP: uniform manifold approximation and projection for dimension reduction. Preprint at https://arxiv.org/abs/1802.03426 (2018).)
McInnes, L., Healy, J. & Melville, J. UMAP: uniform manifold approximation and projection for dimension reduction. Preprint at https://arxiv.org/abs/1802.03426 (2018).McInnes, L., Healy, J. & Melville, J. UMAP: uniform manifold approximation and projection for dimension reduction. Preprint at https://arxiv.org/abs/1802.03426 (2018)., McInnes, L., Healy, J. & Melville, J. UMAP: uniform manifold approximation and projection for dimension reduction. Preprint at https://arxiv.org/abs/1802.03426 (2018).
H. Gideon, Jiayao Phuah, Beth Junecko, Joshua Mattila (2019)
Neutrophils express pro- and anti-inflammatory cytokines in granulomas from Mycobacterium tuberculosis-infected cynomolgus macaquesMucosal immunology, 12
Melissa Krystel-Whittemore, K. Dileepan, J. Wood (2016)
Mast Cell: A Multi-Functional Master CellFrontiers in Immunology, 6
T. Bold, J. Ernst (2009)
Who Benefits from Granulomas, Mycobacteria or Host?Cell, 136
Leeat Keren, M. Bossé, Diana Marquez, Roshan Angoshtari, Samir Jain, S. Varma, Soo-Ryum Yang, A. Kurian, D. Valen, Robert West, S. Bendall, Michael Angelo (2018)
A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam ImagingCell, 174
M. Berry, C. Graham, Finlay Mcnab, Zhaohui Xu, S. Bloch, T. Oni, K. Wilkinson, R. Banchereau, Jason Skinner, R. Wilkinson, Charlie Quinn, D. Blankenship, R. Dhawan, J. Cush, A. Mejias, O. Ramilo, O. Kon, V. Pascual, J. Banchereau, D. Chaussabel, A. O’Garra (2010)
An Interferon-Inducible Neutrophil-Driven Blood Transcriptional Signature in Human TuberculosisNature, 466
S. Malherbe, S. Shenai, K. Ronacher, A. Loxton, G. Dolganov, M. Kriel, Tran Van, Ray Chen, J. Warwick, L. Via, T. Song, Myung‐hee Lee, G. Schoolnik, G. Tromp, D. Alland, C. Barry, Jill Winter, G. Walzl (2017)
Corrigendum: Persisting positron emission tomography lesion activity and Mycobacterium tuberculosis mRNA after tuberculosis cureNature Medicine, 23
J. Davis, L. Ramakrishnan (2009)
The Role of the Granuloma in Expansion and Dissemination of Early Tuberculous InfectionCell, 136
W. Haynes, Francesco Vallania, Charles Liu, Erika Bongen, Aurelie Tomczak, Marta Andres-Terrè, Shane Lofgren, Andrew Tam, C. Deisseroth, Matthew Li, T. Sweeney, P. Khatri (2016)
Empowering Multi-Cohort Gene Expression Analysis to Increase ReproducibilitybioRxiv
M. Facco, A. Cabrelle, A. Teramo, Valeria Olivieri, M. Gnoato, Sara Teolato, E. Ave, Cristina Gattazzo, G. Fadini, F. Calabrese, G. Semenzato, C. Agostini (2010)
Sarcoidosis is a Th1/Th17 multisystem disorderThorax, 66
Jingwen Shi, Shiyue Hou, Q. Fang, Xin Liu, Xiaolong Liu, Hai Qi (2018)
PD-1 Controls Follicular T Helper Cell Positioning and FunctionImmunity, 49
Tuberculosis (TB) in humans is characterized by formation of immune-rich granulomas in infected tissues, the architecture and composition of which are thought to affect disease outcome. However, our understanding of the spatial relationships that control human granulomas is limited. Here, we used multiplexed ion beam imaging by time of flight (MIBI-TOF) to image 37 proteins in tissues from patients with active TB. We constructed a comprehensive atlas that maps 19 cell subsets across 8 spatial microenvironments. This atlas shows an IFN-γ-depleted microenvironment enriched for TGF-β, regulatory T cells and IDO1+ PD-L1+ myeloid cells. In a further transcriptomic meta-analysis of peripheral blood from patients with TB, immunoregulatory trends mirror those identified by granuloma imaging. Notably, PD-L1 expression is associated with progression to active TB and treatment response. These data indicate that in TB granulomas, there are local spatially coordinated immunoregulatory programs with systemic manifestations that define active TB.
Nature Immunology – Springer Journals
Published: Feb 1, 2022
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