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

File Sets

151 items
AnalysisSet
knockout RNA-seq: transcriptome alignments
  • charles-gersbach:cd8-tcells-intermediate-analysis-rna-seq-cas-ko-gata3
Charles Gersbach, Duke
AuxiliarySet
gRNA sequencing for CRISPR activation FACS screen integrating a guide (sgRNA) library targeting transcription start sites in IL2RA
  • charles-gersbach:jurkats-auxiliary-set-crispra-vp64-il2ra-high-bin-rep3
Charles Gersbach, Duke
MeasurementSet
CRISPR knockout FACS screen 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: fold change over control, guide quantifications
  • charles-gersbach:cd8-tcells-analysis-set-crispra-ccr7
Charles Gersbach, Duke
AuxiliarySet
gRNA sequencing for CRISPR interference FACS screen integrating a guide (sgRNA) library targeting transcription start sites in B2M
  • charles-gersbach:cd8-tcells-auxiliary-set-crispri-b2m-high-bin-rep3
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 for CRISPR interference FACS screen integrating a guide (sgRNA) library targeting transcription start sites in CD2
  • 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
CRISPR activation FACS screen 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

Attribution