Thread by @paulanietog

So exciting to see our work at the @hoheyn lab published in @genomeresearch !!
"A single-cell tumor immune atlas for precision oncology"
genome.cshlp.org/content/early/…
And so my first #tweetorial begins (1/9)⬇️

#SingleCellCNAG #SingleCell

We created a single-cell atlas of the tumor immune microenvironment that contains over 300000 immune cells from 13 cancer types and over 200 patients. We were able to annotate over 25 immune populations.
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We were able to separate the patients into 6 different groups according to the predominant subtype of cells in their tumor immune microenvironments.
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Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system for both mouse and human samples.
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We applied #SPOTlight by @elosua_bayes (github.com/MarcElosua/SPO…) to enable in situ mapping of immune populations for digital pathology and found striking differences across tumor regions.
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This analysis allowed us to catalog tumor immune cells across a large patient cohort and to create a tumor immune cell atlas of human cancers. We envision the application of the atlas in multiple areas of precision
oncology.
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We provide a framework for an immune-based patient stratification, the posibility to integrate new single-cell data, and a toolbox to map immune cells directly in tumor sections.
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You can read the full paper here: genome.cshlp.org/content/early/…
Find all the code here: github.com/Single-Cell-Ge…
Get the atlas from Zenodo: zenodo.org/record/5186413…
And you can also use our app: …glecellgenomics-cnag-crg.shinyapps.io/TICA/
#SingleCellCNAG #SingleCell
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Of course this was a huge team effort, so shoutout to the whole @hoheyn lab, especially @elosua_bayes @rmassonix @trincadojl @JuanCNieto1 @saguilarfer and the @BatlleLab team! 🎉