Besides acute infection, CX3CR1+ effector-like CD8 T cells also appear in chronic infection and cancer. Whether there is a central transcriptional regulator of the effector fate is unclear.
Here, using joint single-cell profiling of the transcriptome and epigenome of chimeric antigen receptor (CAR) T cells, we identified KLF2 as a hub transcription factor in the gene regulatory network of effector-like CAR T cells.
KLF2 deficiency abolished effector-like differentiation in both CAR T cells and antiviral CD8 T cells. KLF2 deficiency also impaired the differentiation of the stem-like subset. In both chronic viral infection and cancer, KLF2 deficiency impaired CD8 T cell infiltration to non-lymphoid tissues. However, unlike CAR T cells, KLF2-deficient antiviral CD8 T cells showed a greater expansion in the lymphoid tissue. Single-cell transcriptomics analysis revealed that KLF2-deficient CD8 T cells upregulated the transcriptional signature of terminally exhausted T cells and downregulated the signature of effector-like T cells, suggesting a central role of KLF2 in regulating the bifurcation of effector versus terminal exhaustion cell fates. In addition, the TOX-controlled transcriptional program was upregulated in KLF2-deficient CD8 T cells. KLF2 deficiency downregulated multiple genes associated with T cell migration including S1pr1. S1PR1 deficiency impaired the effector-like subset, whereas deficiency of CD69, a negative regulator of S1PR1, increased the effector-like subset. Notably, aging downregulated KLF2 in antigen-specific CD8 T cells, impaired the differentiation of the CX3CR1+ subset, and upregulated the TOX-mediated transcriptional program.
Thus, our study demonstrates KLF2 as a central regulator of the effector fate and migration of CD8 T cells.
NIH, CRI, AFAR, V Foundation
Immune Response Regulation: Molecular Mechanisms (IRM)
Tuoqi Wu, Ziang Zhu, Ying Luo et al.· Journal of Immunology· 0 citations
Self-renewing stem-like T cells promote the efficacy of cancer immunotherapy and are a heterogeneous population with sub-lineages demonstrating different degrees of stemness. At the apex of this hierarchy are long-term (LT) stem-like T cells with the highest capacity of persistence, repopulation and response to immune checkpoint inhibitors (ICI). However, the pathway that establishes the hierarchy of stemness in chimeric antigen receptor (CAR) T cells and its role in anti-tumor efficacy of CAR T cells are unclear.
We analyzed CAR T cell infusion products from both humans and mice, examining epigenetic, transcriptional, and functional correlates of stem-like subsets. We deleted BACH2 to assess its role in LT stem-like differentiation and antitumor potency. In a GD2 CAR T model prone to exhaustion, we used small-molecule modulation to fine-tune BACH2 protein levels and temporally activate BACH2 during CAR T manufacture, followed by in vivo efficacy testing in solid tumor models.
We demonstrate that BACH2 regulates LT stem-like CAR T cell differentiation and antitumor immunity in a dose-dependent manner. Pre-infusion LT stem-like CAR T cells displayed epigenetic activation of BACH2 and correlated with more robust antitumor responses in both mice and humans. After tumor clearance in vivo, LT stem-like cells emerged that transcriptionally and epigenetically upregulated BACH2 and downregulated TOX. Loss of BACH2 impaired antitumor efficacy and disrupted the LT stem-like transcriptional program. In GD2 CAR T cells, quantitative control of BACH2 via a small molecule adjusted the balance between stemness and exhaustion. Temporal induction of BACH2 during CAR T manufacturing enhanced antitumor immunity in solid tumor models compared to unmodified cells.
Together, we show that BACH2 dosage establishes the hierarchy of stem-like CAR T cells and can be temporally and tunably controlled in CAR T cells to optimize differentiation and antitumor immunity.
AI154450 from National Institutes of Health, RR210035 from Cancer Prevention and Research Institute of Texas, HT94252310801 from Department of Defense to C. Yao; AI158294, AG083398, AG056524 from National Institutes of Health, Clinic & Laboratory Integrat
Tumor Immunology: Checkpoints, Prevention, and Treatment (TIPT)
Chen Yao· Journal of Immunology· 0 citations
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