SynthesisNature immunology2022
The immunoregulatory landscape of human tuberculosis granulomas.
Erratum issuedOpen access · hybridAbstract readMeta-Analysis
In one paragraph
Synthesis in Nature immunology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 217 papers.
0numbers the graph read from it
0cells of the map it votes in
217citing papers in PubMed
25.9field-weighted citation impact, top 1% of its field
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
217 citing papers in PubMed, 280 citations in OpenAlex.
- Temporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition in metastatic TNBC.Nature cancer · 2026Trial
- Article
- Host-pathogen interactions in tuberculosis: from immunological mechanisms to translational applications.Cell insight · 2026Review
- Pembrolizumab and reactivation of TB: is there a link?IJTLD open · 2026Article
- Early immune dysregulation iniScience · 2026Article
- Identification of a spatially organized TREM2-associated permissive macrophage niche in human pulmonary tuberculosis alveolar pneumonia.Nature communications · 2026Article
- Therapeutic remodeling of the tuberculosis granuloma with 1-methyl-D-tryptophan enhances CD8Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The Kynurenine Pathway in Tuberculosis: Focus on Immunometabolic Regulation, Compartment-Specific Biology, and Therapeutic Potential.Life (Basel, Switzerland) · 2026Review
- Direct bacterial transcript visualization illuminates spatiotemporal environmental adaptation ofScience advances · 2026Article
- Monocytic niches escape T cell surveillance and promote Mycobacterium tuberculosis persistence in lymph nodes.Immunity · 2026Article
- γδ T Cells at the Crossroads of Tuberculosis and COPD: From Early Immunity to Tissue Remodeling.International journal of molecular sciences · 2026Review
- Data modeling the interplay between single-cell shape, single-cell protein expression, and tissue state.Cell reports methods · 2026Article
- Macrophage-derived oxysterols organize T helper 2 cells to suppress type 1 inflammation during pulmonary fungal infection.Science immunology · 2026Article
- IFN𝛾 and IFN𝛾 mimetics prevent IFN-I-mediated TB susceptibility by regulating iron metabolism and lipid peroxidation.bioRxiv : the preprint server for biology · 2026Article
- Infection dose shapes granuloma phenotypes in a humanized mouse model of tuberculosis.Research square · 2026Article
- Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis.bioRxiv : the preprint server for biology · 2026Article
- Sertraline Enhances Bacterial Control without Adversely Affecting the Pharmacodynamic-Pharmacokinetic Properties of Frontline Tuberculosis Drugs.ACS pharmacology & translational science · 2026Article
- Compositional and interpretable representation of histology using AI foundation models and sparse autoencoders.bioRxiv : the preprint server for biology · 2026Article
- Lipid accumulation in tuberculosis granulomas inhibits macrophage-CD4Nature microbiology · 2026Article
- Immune endotypes in tuberculosis: Keys to decoding disease complexity.Journal of internal medicine · 2026Review
157 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
28 authors at 11 institutions in 3 countries.
Erin F McCaffreyDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-7241-1798
Michele DonatoDepartment of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-9968-6027
Leeat KerenDepartment of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
Zhenghao ChenCalico Life Sciences LLC, South San Francisco, CA, USA.
Alea DelmastroDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-7959-3165
Megan B FitzpatrickDepartment of Pathology, University of Wisconsin, Madison, WI, USA.ORCID http://orcid.org/0000-0001-7040-8018
Sanjana GuptaDepartment of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA.
Noah F GreenwaldDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-7836-4379
Alex BaranskiDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
William GrafDivision of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA.ORCID http://orcid.org/0000-0002-4264-9479
Rashmi KumarDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Marc BosseDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Christine Camacho FullawayDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-4924-591X
Pratista K RamdialAfrica Health Research Institute, University of KwaZulu-Natal, Durban, South Africa.
Erna ForgóDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Vladimir JojicCalico Life Sciences LLC, South San Francisco, CA, USA.
David Van ValenDivision of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA.ORCID http://orcid.org/0000-0001-7534-7621
Smriti MehraTexas Biomedical Research Institute, San Antonio, TX, USA.
Shabaana A KhaderDepartment of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.ORCID http://orcid.org/0000-0002-9545-4982
Sean C BendallDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-1341-2453
Matt van de RijnDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Daniel KalmanDepartment of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
Deepak KaushalSouthwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA.ORCID http://orcid.org/0000-0003-3521-1257
Robert L HunterDepartment of Pathology and Laboratory Medicine, University of Texas Health Sciences Center at Houston, Houston, TX, USA.
Niaz BanaeiDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Adrie J C SteynAfrica Health Research Institute, University of KwaZulu-Natal, Durban, South Africa.
Purvesh KhatriDepartment of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-4143-4708
Michael AngeloDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA. mangelo0@stanford.edu.ORCID http://orcid.org/0000-0003-1531-5067
Stanford University · USCalifornia Institute of Technology · USTexas Biomedical Research Institute · USAfrica Health Research Institute · ZAEmory University · USStanford Medicine · USThe University of Texas Health Science Center at Houston · USUniversity of Alabama at Birmingham · USUniversity of Wisconsin–Madison · USWashington University in St. Louis · USWeizmann Institute of Science · IL
Funding
The Southwest National Primate Research Center Supplement- Infrastructure improvements of ABSL2 holding areasP51OD011133 · OD · TEXAS BIOMEDICAL RESEARCH INSTITUTE · PI Larry S. Schlesinger · 2012 to 2026
$129.7MUsing a tonsil organoid system to probe conditions for the induction of protective antibody and T cell responses to influenza.U19AI057229 · NIAID · STANFORD UNIVERSITY · PI Mark Morris Davis · 2003 to 2026
$88.5MTranslational Incubator CoreU19AI109662 · NIAID · STANFORD UNIVERSITY · PI GLENN, JEFFREY S · 2014 to 2019
$28.6MMOLECULAR &CELLULAR IMMUNOBIOLOGYT32AI007290 · NIAID · STANFORD UNIVERSITY · PI Sean Curtis Bendall, Olivia M Martinez · 1985 to 2026
$27.0MSystems biological assessment of T cell responses to vaccinationU19AI167903 · NIAID · STANFORD UNIVERSITY · PI BALI PULENDRAN · 2022 to 2026
$13.2MMyeloid and lymphoid immunity-specific mechanisms of IDO mediated immunosuppression and its reversal, during TBR01AI134245 · NIAID · TULANE UNIVERSITY OF LOUISIANA · PI Smriti Mehra · 2018 to 2026
$6.2MEmory/Georgia TB Research Advancement Center (TRAC)P30AI168386 · NIAID · EMORY UNIVERSITY · PI Cheryl Liane Day · 2022 to 2026
$5.8MGiant MagnetoResistive (GMR) Sensors for Measuring Influenza VaccineR01AI125197 · NIAID · STANFORD UNIVERSITY · PI UTZ, PAUL JOSEPH, WANG, SHAN X. · 2016 to 2021
$5.0MHydrogen Sulfide and Tuberculosis DiseaseR01AI134810 · NIAID · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI STEYN, ADRIE JC · 2018 to 2021
$2.2MMETABOLIC REPROGRAMMING OF T CELL ENERGY METABOLISM IN TUBERCULOSIS AND HIVR33AI138280 · NIAID · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI STEYN, ADRIE JC · 2020 to 2023
$2.0MPredicting response to anti-PD-1 therapy in triple negative breast cancer by comprehensive profiling of the tumor microenvironmentF31CA246880 · NCI · STANFORD UNIVERSITY · PI GREENWALD, NOAH · 2020 to 2021
$53kNCI NIH HHS F31 CA246880NIAID NIH HHS P30 AI168386NIAID NIH HHS R01 AI125197NIAID NIH HHS R01 AI134245NIAID NIH HHS R01 AI134810NIAID NIH HHS R33 AI138280NIAID NIH HHS T32 AI007290NIAID NIH HHS U19 AI057229NIAID NIH HHS U19 AI109662NIAID NIH HHS U19 AI167903NIH HHS P51 OD011133Wellcome Trust
Abstract
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
Indexed as
B7-H1 AntigenCells, CulturedCytokinesGene Expression ProfilingGranulomaHumansIndoleamine-Pyrrole 2,3,-DioxygenaseLungMycobacterium tuberculosisMyeloid CellsTuberculosisB7-H1 AntigenCytokinesIndoleamine-Pyrrole 2,3,-Dioxygenase
Identifiers
What OpenQuestion holds
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LicenceCC BY
Read underepoch 390
Registered trials
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.