B-ALL-CAR-T

Single-cell profiling identifies pre-existing CD19-negative subclones in a B-ALL patient with CD19-negative relapse after CAR-T therapy

Authors: Tracy Rabilloud†, Delphine Potier†, Saran Pankaew, Mathis Nozais, Marie Loosveld*, Dominique Payet-Bornet*

†These authors contributed equally ; * Corresponding authors

link to the article (to come)

Overview

This repository contains the instructions and material to reproduce the analysis reported in the article. Source code is available in the github repository. Required data and builded Docker/singularity images are available respectively in SRA/GEO and Zenodo. Intructions to reproduce the analysis are provided in the different subdirectories:

• Fastq preprocessing is described in the "fastq_pre-processing" directory
• Seurat analysis is described in the "Seurat_analysis" directory
• SCENIC analysis is described in the "SCENIC_analysis" directory
• CaSpER analysis is described in the "CaSpER_analysis" directory

Data availability

Fastq preprocessing

• 4 fastq files are available in SRA under the accession ID SRP269742:
  • 2 fastq files containing paired-end reads sequenced from the mRNA library
  • 2 fastq files containing paired-end reads sequenced from the HTO library
• Cellranger output and CITE-seq-count output that can be load in seurat are available in GEO (GSE153697) respectively under accession number GSM4649255 and GSM4649254 :
  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4649255
  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4649254

Seurat analysis

• Filtered expression matrices (raw and normalized) as well as metadata are available in GEO (GSE153697) :
  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE153697
• Seurat html report containing figures generated in R from article can be download here :
  • https://github.com/Delphine-Potier/B-ALL-CAR-T/blob/master/1_Seurat_analysis/analysis/analysis_CarT_paper_V2.html
  and the Rmd script used to produce it can be seen here :
  • https://github.com/Delphine-Potier/B-ALL-CAR-T/blob/master/1_Seurat_analysis/scripts/analysis_CarT_paper_V2.Rmd

SCENIC analysis

SCENIC analysis output is available here : https://zenodo.org/record/4114854/files/SCENIC_output.tar.gz?download=1

The ipython notebook to reproduce the analysis is available here : https://github.com/Delphine-Potier/B-ALL-CAR-T/tree/master/2_SCENIC_analysis/script

The docker container with all tools is available here : https://zenodo.org/record/4114854/files/jupyscenic2.tar?download=1

Explanations to reproduce the analysis are given here : https://github.com/Delphine-Potier/B-ALL-CAR-T/tree/master/2_SCENIC_analysis/

CASPER analysis

CASPER analysis output is available here : https://zenodo.org/record/4114854/files/final_CaSpER_object.Robj?download=1

Full explanations to reproduce the analysis are given here : https://github.com/Delphine-Potier/B-ALL-CAR-T/tree/master/3_CaSpER_analysis

The Rmd script to reproduce the R part of analysis is available here : https://github.com/Delphine-Potier/B-ALL-CAR-T/tree/master/3_CaSpER_analysis/script

The docker container with all tools are available here : https://zenodo.org/record/4114854/files/BAFExtract.tar?download=1 and https://zenodo.org/record/4114854/files/casperseurat315.tar?download=1

Docker/Singularity images

Singularity/Docker images are all availabe in Zenodo : https://doi.org/10.5281/zenodo.4114854