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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.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.issn 1088-9051
dc.identifier.uri http://hdl.handle.net/10230/52297
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.language.iso eng
dc.publisher Cold Spring Harbor Laboratory Press (CSHL Press)
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.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.identifier.doi http://dx.doi.org/10.1101/gr.273300.120
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/810287
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/SAF2017-89109-P
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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