KLF2 maintains lineage fidelity and suppresses CD8 T cell exhaustion during acute LCMV infection (PerturbSeq Data)

Naïve CD8 T cells have the potential to differentiate into a variety of functional states during an immune response. How these developmental decisions are made and what mechanisms exist to suppress differentiation towards alternative fates remains unclear. We employed in vivo CRISPR/Cas9-based perturbation sequencing to assess the role of ~40 transcription factors (TFs) and epigenetic modulators (EMs) in T cell fate decisions. Unexpectedly, we found that knockout of TF Klf2 resulted in aberrant differentiation to exhausted-like CD8 T cells during acute infection. KLF2 was required to suppress the exhaustion-promoting TF TOX and to enable TBET to drive effector differentiation. KLF2 was also necessary to maintain tumor-specific progenitor-exhausted T cells. Thus, KLF2 provides effector CD8 T cell lineage fidelity and suppresses the exhaustion program.

Methods
This dataset contains scRNA-sequencing of endogenous H2Db-gp33 specific CD8 T cells in acute and chronic LCMV infection at days 4,8,28, and 40 post-infection (linked Dryad submission). There is also scRNA sequencing with CRISPR features (perturbSeq) of P14 Cas9 T cells in acute infection with a sgRNA library targeting ~40 transcription factors and epigenetic modulators (this Dryad submission). In addition, there is bulk atac-seq data of WT and KLF2 KO P14 T cells from day 8 of acute and chronic infection (linked Dryad submission). Finally data from Connolly et al, Science Immunology 2021 was reanalyzed and an rds object is uploaded here. This data is scRNA of H2Db-gp33 specific CD8s from KP-NINJA autochthonous lung tumor and tdLN. 

Raw sequencing files are included of all data in addition to bigwig files of atac data and rds objects of single cell data. Dryad_data_key.xls contains details on all samples for this and linked upload.