Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens

released
Title
Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens
Authors
Sean R McCutcheon, Adam M Swartz, Michael C Brown, Alejandro Barrera, Christian McRoberts Amador, Keith Siklenka, Lucas Humayun, Maria A Ter Weele, James M Isaacs, Timothy E Reddy, Andrew S Allen, Smita K Nair, Scott J Antonia, Charles A Gersbach
Citation
Sean R McCutcheon, Adam M Swartz, Michael C Brown, Alejandro Barrera, Christian McRoberts Amador, Keith Siklenka, Lucas Humayun, Maria A Ter Weele, James M Isaacs, Timothy E Reddy, Andrew S Allen, Smita K Nair, Scott J Antonia, Charles A Gersbach  Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens. Nature Genetics.  
Abstract
Clinical response to adoptive T cell therapies is associated with the transcriptional and epigenetic state of the cell product. Thus, discovery of regulators of T cell gene networks and their corresponding phenotypes has potential to improve T cell therapies. Here we developed pooled, epigenetic CRISPR screening approaches to systematically profile the effects of activating or repressing 120 transcriptional and epigenetic regulators on human CD8+ T cell state. We found that BATF3 overexpression promoted specific features of memory T cells and attenuated gene programs associated with cytotoxicity, regulatory T cell function, and exhaustion. Upon chronic antigen stimulation, BATF3 overexpression countered phenotypic and epigenetic signatures of T cell exhaustion. Moreover, BATF3 enhanced the potency of CAR T cells in both in vitro and in vivo tumor models and programmed a transcriptional profile that correlates with positive clinical response to adoptive T cell therapy. Finally, we performed CRISPR knockout screens that defined cofactors and downstream mediators of the BATF3 gene network.
Publication Identifiers

Samples

87 items
Sample Terms
Summary
PrimaryCell
Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)
PrimaryCell
Homo sapiens CD8-positive, alpha-beta memory T cell transduced (lentivirus) with a expression vector library
PrimaryCell
Homo sapiens CD8-positive, alpha-beta memory T cell transduced (lentivirus) with a expression vector library
PrimaryCell
Homo sapiens CD8-positive, alpha-beta memory T cell transduced (lentivirus) with a expression vector library
PrimaryCell
Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)
PrimaryCell
Homo sapiens CD8-positive, alpha-beta memory T cell (sorting details: FACS bin for 90-100% expression of IL7R) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)
PrimaryCell
Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)
PrimaryCell
Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)
PrimaryCell
Homo sapiens CD8-positive, alpha-beta memory T cell (sorting details: FACS bin for 0-10% expression of b2m) modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)
PrimaryCell
Homo sapiens CD8-positive, alpha-beta memory T cell (sorting details: FACS bin for 90-100% expression of CCR7) modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)

File Sets

106 items
MeasurementSet
low FACS signal CRISPR knockout FACS screen sorted on the expression of IL7R integrating a guide (sgRNA) library targeting transcription start sites in many genes
  • charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-low-bin-rep2
Charles Gersbach, Duke
MeasurementSet
CRISPR activation Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in 24 genes
  • charles-gersbach:cd8-tcells-perturb-seq-crispra-gex-rep3
Charles Gersbach, Duke
AnalysisSet
CRISPR activation FACS screen targeting CCR7: alignments, fold change over control, guide quantifications
  • charles-gersbach:cd8-tcells-analysis-set-crispra-ccr7
Charles Gersbach, Duke
MeasurementSet
CRISPR knockout RNA-seq integrating a guide (sgRNA) library targeting transcription start sites in GATA3
  • charles-gersbach:cd8-tcells-rna-seq-cas-ko-gata3-rep2
Charles Gersbach, Duke
AuxiliarySet
gRNA sequencing
  • charles-gersbach:cd8-tcells-auxiliary-set-crispri-cd2-low-bin-rep2
Charles Gersbach, Duke
AuxiliarySet
gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in 24 genes
  • charles-gersbach:cd8-tcells-perturb-seq-crispri-grna-rep3
Charles Gersbach, Duke
MeasurementSet
low FACS signal CRISPR activation FACS screen sorted on the expression of IL2RA integrating a guide (sgRNA) library targeting transcription start sites in IL2RA
  • charles-gersbach:jurkats-measurement-set-crispra-vp64-il2ra-low-bin-rep2
Charles Gersbach, Duke
MeasurementSet
CRISPR knockout RNA-seq integrating a guide (sgRNA) library targeting transcription start sites in GATA3
  • charles-gersbach:cd8-tcells-rna-seq-cas-ko-gata3-rep1
Charles Gersbach, Duke
MeasurementSet
RNA-seq integrating an expression vector library of BATF3
  • charles-gersbach:cd8-tcells-rna-seq-chronic-activation-batf3-rep1
Charles Gersbach, Duke
MeasurementSet
ATAC-seq integrating an expression vector library of BATF3
  • charles-gersbach:cd8-tcells-atac-seq-chronic-activation-batf3-rep1
Charles Gersbach, Duke

Attribution