ArticleImmunity2024
An atlas of cells in the human tonsil.
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Article in Immunity, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 papers.
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108citing papers in PubMed
30.3field-weighted citation impact, top 1% of its field
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Who cites it
108 citing papers in PubMed, 133 citations in OpenAlex.
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- Different primary thyroid B-cell lymphomas show overlapping mutation profiles, suggesting involvement of a common pathogenic process.Haematologica · 2026Article
- Tumor-infiltrating plasma cell profiling after PD-1 blockade reveals tumor-specific antibodies.Cancer cell · 2026Article
- Analysis of multicellular anatomical structures from spatial omics data using sosta.PLoS computational biology · 2026Article
- Data-driven identification of cell subtypes for single-cell transcriptomic data with Subtypist.Briefings in bioinformatics · 2026Article
- A bispecific CD3×CD19 antibody for systemic lupus erythematosus: a phase 1 trial.Nature medicine · 2026Article
- DPAS-Graph: adaptive spatial-feature relation learning for spatial RNA-to-protein prediction and virtual protein profiling.Briefings in bioinformatics · 2026Article
- CD9Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Clonal sharing and plasticity of follicular CD4 + T cells across lymph nodes and tumors in non-small cell lung cancer.Nature communications · 2026Article
- Follicular Lymphoma Transformation is Characterized by Cytokine-associated Remodeling of Stromal and Macrophage Compartments.Cancer discovery · 2026Article
- Malignant B-cell States Orchestrate Spatially Organized Immune Ecosystems in B-cell Lymphomas.Research square · 2026Article
- SPEN Loss Drives Extrafollicular Diffuse Large B-cell Lymphoma with Female-Specific Lethality and Therapeutic Vulnerabilities.Cancer discovery · 2026Article
- Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment.Cancer discovery · 2026Article
- On or within: spatial determinants of antigen handling in the nasal turbinates.Current opinion in immunology · 2026Review
- Nanomaterials for the Prevention, Detection, and Treatment of Pharyngeal Human Papillomavirus Infection: A Translational Roadmap.Materials (Basel, Switzerland) · 2026Review
- A 3D genome atlas of human tonsil and the role of loop extrusion in B cell somatic hypermutation.Science (New York, N.Y.) · 2026Article
- Simultaneous Quantification of Multiple Immune Checkpoint Interactions in Melanoma.Journal of clinical medicine · 2026Article
- A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation.Nature communications · 2026Article
- A spatial multi-omics atlas of immunosenescence reveals germinal-center B cell dysfunction in human lymph nodes.Cell press blue · 2026Article
48 more citing papers are in PubMed but not listed here.
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Authors and funding
49 authors at 20 institutions in 8 countries.
Ramon Massoni-BadosaCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain. Electronic address: ram4025@med.cornell.edu.
Sergio Aguilar-FernándezCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Juan C NietoCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Paula Soler-VilaInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
Marc Elosua-BayesCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Domenica MarcheseCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Marta KulisInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
Amaia Vilas-ZornozaHemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.
Marco Matteo BühlerInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain.
Sonal RashmiCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Clara AlsinetCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Ginevra CaratùCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Catia MoutinhoCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Sara RuizCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Patricia LordenCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Giulia LunazziCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Dolors ColomerInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain.
Gerard FrigolaHematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain.
Will BlevinsCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.
Lucia Romero-RiveroInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
Víctor Jiménez-MartínezInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
Anna VidalInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
Judith Mateos-JaimezInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
Alba Maiques-DiazInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
Sara OvejeroDepartment of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France.
Jérôme MoreauxDepartment of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France; Department of Clinical Hematology, CHU Montpellier, Montpellier, France.
Sara PalominoTranslational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain.
David Gomez-CabreroTranslational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia.
Xabier AgirreHemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.
Marc A WenigerInstitute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany.
Hamish W KingEpigenetics and Development Division, Walter and Eliza Hall Institute, Parkville, Australia.
Lucy C GarnerTranslational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
Federico MariniInstitute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany; Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
Francisco Javier Cervera-PazDepartment of Otorhinolaryngology, University of Navarra, Pamplona, Spain.
Peter M BaptistaDepartment of Otorhinolaryngology, University of Navarra, Pamplona, Spain.
Isabel VilasecaOtorhinolaryngology Head-Neck Surgery Department, Hospital Clínic, IDIBAPS Universitat de Barcelona, Barcelona, Spain.
Cecilia RosalesInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
Silvia Ruiz-GaspàInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
Benjamin TalksBiosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Department of Otolaryngology, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK.
Keval SidhpuraBiosciences Institute, Newcastle University, Newcastle Upon Tyne, UK.
Anna Pascual-ReguantDepartment of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany.
Anja E HauserDepartment of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany.
Muzlifah HaniffaBiosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK.
Felipe ProsperHemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Departamento de Hematología, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain.
Ralf KüppersInstitute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany.
Ivo Glynne GutCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Elias CampoInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain.
José Ignacio Martin-SuberoInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain. Electronic address: imartins@recerca.clinic.cat.
Holger HeynCentro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain. Electronic address: holger.heyn@cnag.eu.
Centro Nacional de Análisis Genómico · ESConsorci Institut D'Investigacions Biomediques August Pi I Sunyer · ESHospital Clínic de Barcelona · ESCentre National de la Recherche Scientifique · FRCentro de Investigación Biomédica en Red de Cáncer · ESGerman Rheumatism Research Centre · DENavarrabiomed · ESUniversidad de Navarra · ESUniversitat Pompeu Fabra · ESUniversity of Duisburg-Essen · DEClinica Universidad de Navarra · ESCornell University · USInstitució Catalana de Recerca i Estudis Avançats · ESJohannes Gutenberg University Mainz · DENewcastle University · GBNewcastle upon Tyne Hospitals NHS Foundation Trust · GBUniversity Hospital of Zurich · CHUniversity of Oxford · GBWalter and Eliza Hall Institute of Medical Research · AUWellcome Sanger Institute · GB
Funding
European Research Council 810287Wellcome TrustWellcome Trust 223092/Z/21/Z
Abstract
Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas of the human tonsil composed of >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well as spatial transcriptomics. This census identified 121 cell types and states, defined developmental trajectories, and enabled an understanding of the functional units of the tonsil. Exemplarily, we stratified myeloid slan-like subtypes, established a BCL6 enhancer as locally active in follicle-associated T and B cells, and identified SIX5 as putative transcriptional regulator of plasma cell maturation. Analyses of a validation cohort confirmed the presence, annotation, and markers of tonsillar cell types and provided evidence of age-related compositional shifts. We demonstrate the value of this resource by annotating cells from B cell-derived mantle cell lymphomas, linking transcriptional heterogeneity to normal B cell differentiation states of the human tonsil.
Indexed as
B-LymphocytesPalatine TonsilAdultHumansadaptive immunityagingHuman Cell Atlashuman tonsilinnate immunitymantle cell lymphomasecondary lymphoid organssingle-cell genomicsspatial transcriptomics
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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.