Sharing our preprint on single-cell RNA-seq analysis of tumor-infiltrating CD8 lymphocytes in B16 murine melanoma tumors biorxiv.org/content/10.110…
We defined a transcriptomic map of CD8 TIL states, with unbiased identification of terminally exhausted (PD-1+ Tcf1-), memory-like / progenitor exhausted (PD-1+ Tcf1+), naïve and effector memory-like (EM-like) states, including clonality and tumor-specificity information
We describe novel surface markers for the EM-like population, including Ly6C and CXCR3. Re-analysis of public bulk and single-cell RNA-seq data suggests that EM-like cells expand upon Checkpoint Blockade
We built a novel predictor of CD8 TIL states for scRNA-seq data, TILPRED, that is available as an R package at github.com/carmonalab/TIL…
A reproducible R workflow using #Seurat to define our CD8 T cell clusters is available at gitlab.unil.ch/carmona/workfl… and data is available at ncbi.nlm.nih.gov/geo/query/acc.…
An #iSEE Shiny web tool to interact with these data is available at tilatlas.shinyapps.io/B16_CD8TIL_10X/ . Have fun!
