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Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens
Sean R McCutcheon1,2, Adam M Swartz3, Michael C Brown4
1Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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.
Insights
Overexpressing BATF3 in T cells promotes memory phenotypes and enhances CAR T cell therapy efficacy against tumors. This discovery offers a new strategy to improve adoptive T cell therapies and clinical outcomes.
Area of Science:
- Immunology
- Molecular Biology
- Gene Regulation
Background:
- Clinical success in adoptive T cell therapy depends on the specific gene expression and epigenetic profiles of therapeutic T cells.
- Identifying regulators of T cell gene networks is crucial for enhancing T cell therapy effectiveness.
Purpose of the Study:
- To systematically investigate the impact of 120 transcriptional and epigenetic regulators on human CD8+ T cell states using pooled epigenetic CRISPR screening.
- To identify novel regulators that can improve T cell function and therapeutic potential.
Main Methods:
- Developed pooled, epigenetic CRISPR screening to assess the effects of activating or repressing 120 regulators in human CD8+ T cells.
- Utilized in vitro and in vivo tumor models to evaluate the therapeutic potential of identified regulators, specifically BATF3.
- Conducted CRISPR knockout screens to elucidate downstream effectors and cofactors of the BATF3 gene network.
Main Results:
- Overexpression of BATF3 promoted memory T cell characteristics while reducing gene programs linked to cytotoxicity, regulatory T cell function, and exhaustion.
- BATF3 mitigated phenotypic and epigenetic signs of T cell exhaustion under chronic antigen stimulation.
- BATF3 enhanced the efficacy of CAR T cells in preclinical tumor models and correlated with favorable clinical responses in patients.
Conclusions:
- BATF3 acts as a key regulator that can reprogram T cells towards a more potent and less exhausted state, improving their therapeutic function.
- The findings provide a foundation for engineering T cells with enhanced properties for improved adoptive T cell therapies.
- Understanding the BATF3 gene network offers new avenues for targeting T cell function in cancer immunotherapy.
