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A single-cell tumor immune atlas for precision oncology

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 i...

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Autores principales: Nieto, Paula, Elosua-Bayes, Marc, Trincado, Juan L., Marchese, Domenica, Massoni-Badosa, Ramon, Salvany, Maria, Henriques, Ana, Nieto, Juan, Aguilar-Fernández, Sergio, Mereu, Elisabetta, Moutinho, Catia, Ruiz, Sara, Lorden, Patricia, Chin, Vanessa T., Kaczorowski, Dominik, Chan, Chia-Ling, Gallagher, Richard, Chou, Angela, Planas-Rigol, Ester, Rubio-Perez, Carlota, Gut, Ivo, Piulats, Josep M., Seoane, Joan, Powell, Joseph E., Batlle, Eduard, Heyn, Holger
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8494216/
https://www.ncbi.nlm.nih.gov/pubmed/34548323
http://dx.doi.org/10.1101/gr.273300.120
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author Nieto, Paula
Elosua-Bayes, Marc
Trincado, Juan L.
Marchese, Domenica
Massoni-Badosa, Ramon
Salvany, Maria
Henriques, Ana
Nieto, Juan
Aguilar-Fernández, Sergio
Mereu, Elisabetta
Moutinho, Catia
Ruiz, Sara
Lorden, Patricia
Chin, Vanessa T.
Kaczorowski, Dominik
Chan, Chia-Ling
Gallagher, Richard
Chou, Angela
Planas-Rigol, Ester
Rubio-Perez, Carlota
Gut, Ivo
Piulats, Josep M.
Seoane, Joan
Powell, Joseph E.
Batlle, Eduard
Heyn, Holger
author_facet Nieto, Paula
Elosua-Bayes, Marc
Trincado, Juan L.
Marchese, Domenica
Massoni-Badosa, Ramon
Salvany, Maria
Henriques, Ana
Nieto, Juan
Aguilar-Fernández, Sergio
Mereu, Elisabetta
Moutinho, Catia
Ruiz, Sara
Lorden, Patricia
Chin, Vanessa T.
Kaczorowski, Dominik
Chan, Chia-Ling
Gallagher, Richard
Chou, Angela
Planas-Rigol, Ester
Rubio-Perez, Carlota
Gut, Ivo
Piulats, Josep M.
Seoane, Joan
Powell, Joseph E.
Batlle, Eduard
Heyn, Holger
author_sort Nieto, Paula
collection PubMed
description 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.
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spelling pubmed-84942162021-10-07 A single-cell tumor immune atlas for precision oncology Nieto, Paula Elosua-Bayes, Marc Trincado, Juan L. Marchese, Domenica Massoni-Badosa, Ramon Salvany, Maria Henriques, Ana Nieto, Juan Aguilar-Fernández, Sergio Mereu, Elisabetta Moutinho, Catia Ruiz, Sara Lorden, Patricia Chin, Vanessa T. Kaczorowski, Dominik Chan, Chia-Ling Gallagher, Richard Chou, Angela Planas-Rigol, Ester Rubio-Perez, Carlota Gut, Ivo Piulats, Josep M. Seoane, Joan Powell, Joseph E. Batlle, Eduard Heyn, Holger Genome Res Resource 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. Cold Spring Harbor Laboratory Press 2021-10 /pmc/articles/PMC8494216/ /pubmed/34548323 http://dx.doi.org/10.1101/gr.273300.120 Text en © 2021 Nieto et al.; Published by Cold Spring Harbor Laboratory Press https://creativecommons.org/licenses/by-nc/4.0/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/ (https://creativecommons.org/licenses/by-nc/4.0/) .
spellingShingle Resource
Nieto, Paula
Elosua-Bayes, Marc
Trincado, Juan L.
Marchese, Domenica
Massoni-Badosa, Ramon
Salvany, Maria
Henriques, Ana
Nieto, Juan
Aguilar-Fernández, Sergio
Mereu, Elisabetta
Moutinho, Catia
Ruiz, Sara
Lorden, Patricia
Chin, Vanessa T.
Kaczorowski, Dominik
Chan, Chia-Ling
Gallagher, Richard
Chou, Angela
Planas-Rigol, Ester
Rubio-Perez, Carlota
Gut, Ivo
Piulats, Josep M.
Seoane, Joan
Powell, Joseph E.
Batlle, Eduard
Heyn, Holger
A single-cell tumor immune atlas for precision oncology
title A single-cell tumor immune atlas for precision oncology
title_full A single-cell tumor immune atlas for precision oncology
title_fullStr A single-cell tumor immune atlas for precision oncology
title_full_unstemmed A single-cell tumor immune atlas for precision oncology
title_short A single-cell tumor immune atlas for precision oncology
title_sort single-cell tumor immune atlas for precision oncology
topic Resource
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8494216/
https://www.ncbi.nlm.nih.gov/pubmed/34548323
http://dx.doi.org/10.1101/gr.273300.120
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