In vivo CD8+ T cell CRISPR screening reveals control by Fli1 in infection and cancer

Single-Cell Transcriptomics Reveals Core Regulatory Programs That Determine the Heterogeneity of Circulating and Tissue-Resident Memory CD8+ T Cells

“…In addition, we also found TRM-enriched regulons that have previously been reported to regulate T-cell differentiation and function in broader settings, but whose roles in TRM cells specifically have not been determined. These included Trp53 [36], Nr3c1 [37], and Fli1 [38]. In summary, we identified known and unknown TFs that may contribute to the phenotypic heterogeneity of memory CD8 + T cells during viral infection.…”

“…Cish is a member of the suppressor of cytokine signaling (SOCS) family, which has been shown to silence TCR signaling and suppress T-cell expansion, effector function, and cytokine polyfunctionality in CD8 + T cells [43]. Fli1 has been reported to function as a repressor of effector-cell differentiation during acute and chronic infection [38]. Therefore, Elf2 and Elf4 might be key TFs that regulate the quiescence of the memory-like TRM subset.…”

Genome-wide fitness gene identification reveals Roquin as a potent suppressor of CD8 T cell expansion and anti-tumor immunity

“…Known tumor suppressors Trp53 and Pten were among top hits suppressing CD8 T cell expansion, confirming fidelity of our screening. However, unlike 10-to 100-fold enrichment of negative regulators of T cell expansion in focused screens (Chen et al, 2021;Wei et al, 2019), even these strong tumor suppressors showed only 2-to 3-fold enrichment in our genome-wide screens (Figures 3A and 3B; Tables S1 and S2). This is likely due to large library size and/or low input cell number.…”

“…Initial genome-wide CRISPR screens in T cells performed in vitro demonstrated the feasibility of pooled screens in primary T cells (Henriksson et al, 2019;Shifrut et al, 2018). Due to coverage issues, most in vivo CRISPR screens performed in T cells in later studies used libraries focused on transcription factors or metabolism (Chen et al, 2021;Huang et al, 2021;Wei et al, 2019). These studies were optimized for positive selections (enrichment of cells), and few novel essential genes were discovered, suggesting drop-out screens in vivo are still difficult due to random loss of cells.…”

The architectural design of CD8+ T cell responses in acute and chronic infection: Parallel structures with divergent fates

“…Even though T cell exhaustion is a progressive process that occurs over several weeks to months, the effector differentiation programs begin to diverge between acute and chronic infection within the first week of infection ( Wherry et al, 2007 ; Ahmadzadeh et al, 2009 ; Sen et al, 2016 ; Chen et al, 2019b , 2021 ; Yao et al, 2019 ; Zhang et al, 2019 ). More specifically, the effector cells in both acute and chronic LCMV infection are transcriptionally similar up to day 4.5 after infection ( Yao et al, 2019 ), but a significant transcriptional and epigenetic divergence begins a couple of days later and then continues for several more weeks ( Wherry et al, 2007 ; Ahmadzadeh et al, 2009 ; Sen et al, 2016 ; Philip et al, 2017 ; Chen et al, 2019b , 2021 ; Yao et al, 2019 ; Zhang et al, 2019 ). This time period coincides exactly with changes in the expression of the TF TOX, as it dwindles in antigen-specific CD8 + T cells in acute infection but becomes amplified in chronic infection and tumors ( Page et al, 2018 ; Yao et al, 2019 ; Khan et al, 2019 ).…”