A single-cell tumor immune atlas for precision oncology

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• dc.contributor.author Nieto, Paula
• dc.contributor.author Elosua-Bayés, Marc
• dc.contributor.author Trincado Alonso, Juan Luis, 1987-
• dc.contributor.author Marchese, Domenica, 1986-
• dc.contributor.author Massoni-Badosa, Ramon
• dc.contributor.author Nieto, Juan C.
• dc.contributor.author Aguilar-Fernández, Sergio
• dc.contributor.author Mereu, Elisabetta
• dc.contributor.author Moutinho, Catia
• dc.contributor.author Ruiz, Sara
• dc.contributor.author Lorden, Patricia
• dc.contributor.author Gut, Ivo Glynne
• dc.contributor.author Heyn, Holger
• dc.date.accessioned 2022-01-24T12:21:26Z
• dc.date.available 2022-01-24T12:21:26Z
• dc.date.issued 2021
• dc.description.abstract The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients, and biomarkers for prognosis and treatment response lack precision. A comprehensive compendium of tumor immune cells is required to pinpoint predictive cellular states and their spatial localization. We generated a single-cell tumor immune atlas, jointly analyzing published data sets of >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system. To enable in situ mapping of immune populations for digital pathology, we applied SPOTlight, combining single-cell and spatial transcriptomics data and identifying colocalization patterns of immune, stromal, and cancer cells in tumor sections. We expect the tumor immune cell atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification approaches for prognosis and immunotherapy.
• dc.description.sponsorship This publication is part of a project (BCLLATLAS) that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 810287). This work has received funding from the Ministerio de Ciencia, Innovación y Universidades (SAF2017-89109-P; AEI/FEDER, UE) and the Fundació La Marató de TV3 (201903-30-31-32).We further acknowledge funding from the St. Vincent’s Clinic Foundation (V.T.C.) and the National Health and Medical Research Council Investigator Grant (APP1175781, J.E.P.), the Fundación Asociación Española contra el Cáncer (AECC), FERO (EDM), Ramón Areces Foundation, Cellex Foundation, BBVA (CAIMI), the ISCIII, FIS (PI16/01278), Juan de la Cierva formación fellowship (C.R.-P.) and Sara Borrell fellowship (E.P.-R.). Core funding is from the ISCIII and the Generalitat de Catalunya. We acknowledge support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, the Centro de Excelencia Severo Ochoa, the CERCA Programme / Generalitat de Catalunya, the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) through the nstituto de Salud Carlos III and the Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement. We also acknowledge the cofinancing by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) with funds from the European Regional Development Fund (ERDF) corresponding to the 2014–2020 Smart Growth Operating Program
• dc.format.mimetype application/pdf
• dc.identifier.citation Nieto P, Elosua-Bayes M, Trincado JL, Marchese D, Massoni-Badosa, R, Salvany M et al. Genome Res. 2021 Oct;31(10):1913-1926. DOI: 10.1101/gr.273300.120
• dc.identifier.doi http://dx.doi.org/10.1101/gr.273300.120
• dc.identifier.issn 1088-9051
• dc.identifier.uri http://hdl.handle.net/10230/52297
• dc.language.iso eng
• dc.publisher Cold Spring Harbor Laboratory Press (CSHL Press)
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/810287
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/SAF2017-89109-P
• dc.rights © 2021 Paula Nieto et al.; Published by Cold Spring Harbor Laboratory Press. This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.other Càncer
• dc.subject.other Tumors
• dc.subject.other Genètica
• dc.subject.other Oncologia
• dc.subject.other Immunitat
• dc.title A single-cell tumor immune atlas for precision oncology
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion