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The purpose of this resource is to enable you to: (1) reproduce the key results of our recent study of immune resistance in melanoma (Jerby-Arnon et al.); and (2) apply our approach to other single-cell cohorts to explore cell-cell interactions in cancer.
- R (tested in R version 3.4.0 (2017-04-21) -- "You Stupid Darkness").
- R libraries: scde, matrixStats, plotrix, plyr, ppcor, survival, ROCR, Hmisc, rms, mixtools, lme4, lmerTest
The data is provided in the Single Cell Portal (ImmRes_Rfiles.zip).
In the Portal you will also find the processed single-cell gene expression of the clinical cohort and experimental data, as well as interactive views.
To reproduce the results reported in Jerby-Arnon et al. download ImmRes_Rfiles.zip from the Single Cell Portal. Unzip the file and move the resulting Data directory to the ImmuneResistance directory.
In R go to the Code directory and run master.code() which is provided in ImmRes_master.R. The master.code() will walk you through the different stages of the study, divided into six main analyses:
(1-2) First, analyzing the single-cell data to generate various gene signatures that characterize different cell subtypes and immune resistant cell states. For more information see I. Mapping immune resistance in melanoma
(3-5) Next, analyzing independent cohorts obtained from bulk melanoma tumors to explore and test the immune resistance program. For more details see II. Predicting immunotherapy resistance.
(6) Lastly, performing a pan-cancer analysis to identify drugs that could repress the immune resistance program in cancer cells.
The ImmRes_master.R file reproduces the key results of the study. It also reproduces the study figures and table, which could then be found in Output/Tables/ and Output/Figures/, respectively. The code follows the analyses that were performed in the study in a sequential manner. As the results are already provided in the Results directory, it is possible to run only some parts of the code and focus on specific analyses, or apply the approach to other datasets.
Please use the following citation:
Jerby-Arnon L et al. Single-cell RNA-seq of melanoma ecosystems reveals sources of T cell exclusion linked to immunotherapy clinical outcomes.