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Status |
Public on Oct 27, 2020 |
Title |
A Single-Cell Tumor Immune Atlas for Precision Oncology |
Organisms |
Homo sapiens; Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
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 resolved tumor immune cell atlas, jointly analyzing >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 for a harmonized interpretation. To enable in situ mapping of immune populations for digital pathology, we developed SPOTlight, a computational tool that identified striking spatial immune cell patterns in tumor sections. We expect the atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification strategies for prognosis and immuno-therapy response.
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Overall design |
Single-cell RNA sequencing was performed on two human uveal melanoma cancers, one human ovarian cancer, one human uveal melanoma liver metastasis, one human non-small cell lung cancer brain metastasis (including TCR), two human head and neck cancers and two mice colorectal cancers (one full and one only T cells and TCR)
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Contributor(s) |
Nieto P, Heyn H |
Citation(s) |
34548323 |
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Paula Nieto, Marc Marc Elosua-Bayes, Juan Luis Trincado, Domenica Marchese, Ramon Massoni-Badosa, Maria Salvany, Ana Henriques, Elisabetta Mereu, Catia Moutinho, Sara Ruiz, Patricia Lorden, Vanessa Chin, Dominik Conrad Kaczorowski, Chia-Ling Chan, Richard Gallagher, Angela Chou, Ester Planas-Rigol, Carlota Rubio-Perez, Ivo Glynne Gut, Joseph Maria Piulats, Joan Seoane, Joseph Powell, Eduard Batlle, and Holger Heyn. A Single-Cell Tumor Immune Atlas for Precision Oncology. bioRxiv 2020.10.26.354829; doi:10.1101/2020.10.26.354829
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Submission date |
Sep 30, 2020 |
Last update date |
Oct 13, 2021 |
Contact name |
Paula Nieto |
E-mail(s) |
nietogarciapaula@gmail.com
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Organization name |
CNAG
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Department |
CNAG
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Lab |
Single-Cell Genomics
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Street address |
Barcelona, Barcelona Science Park - Tower I
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City |
Barcelona |
State/province |
Spain |
ZIP/Postal code |
08028 |
Country |
Spain |
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Platforms (2) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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Samples (10)
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Relations |
BioProject |
PRJNA666613 |
SRA |
SRP285894 |
Supplementary file |
Size |
Download |
File type/resource |
GSE158803_RAW.tar |
122.8 Mb |
(http)(custom) |
TAR (of CSV, MTX, TSV) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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