Transcriptional Regulation of Cytotoxic T-Cell Responses in Acute Myeloid Leukemia
Authors: Chen Xufeng , Sun Zhengxi , Elegast Jana , Zhou Hua , Lee Soobeom , Nicolet Deedra , Lu Qiao , Wang Kun , Wang Jun , Al-Santli Wafa , Eisfeld Ann-Kathrin , Stegmaier Kimberly , Aifantis Iannis , Austin Rebecca 
Published: December 2024

Acute Myeloid Leukemia (AML) is an aggressive clonal hematopoietic neoplasm with an increased incidence in aged adults, a patient population who is often unfit to receive intensive cytotoxic induction chemotherapy and even alternative approved frontline regimes such as BH3 mimetics are often associated with high morbidity. Unfortunately, neither ICBs nor T cell-based cellular therapies are FDA-approved for treating AML. Recently, several TCR-T cells have shown moderate clinical activity in patients with AML. In such TCR-T studies, some patients do not respond and others develop acquired resistance. One potential reason for the low efficacy of immunotherapies in AML is that AML cells harbor a low mutational burden, which makes them less immunogenic. Moreover, AML can actively inhibit the MHC-I antigen presentation (AP) pathway, which determines recognition by CD8+ T cells and is essential for their activation and proliferation. Through hijacking this essential pathway, AML cells reduce their immunogenicity and avoid immune surveillance. These data are supported by clinical evidence that AML cells express low levels of the antigen presentation machinery (APM), especially at the time of relapse after conventional chemotherapies. In addition, several studies have demonstrated that AML cells may evade T-cell recognition by disrupting key pathways that modulate T-cell cytotoxicity, such as immune checkpoints and autophagy. However, the major contributors to the suppression of AML-associated T-cell cytotoxicity remain unknown. AML is also highly heterogeneous and aggressive, highlighting the difficulty of targeting this disease with a single therapeutic option. Combining or sequentially applying targeted therapy and immunotherapy might be a potential future strategy that could bypass mechanisms of resistance. Therefore, it is imperative to identify AML-specific regulators that potentiate T-cell cytotoxicity which could be combined with frontline therapies to offer more effective treatments to patients with AML.

To systematically identify AML-associated regulators that suppress the efficacy of T-cell-based cellular therapies, we performed transcriptional regulator-focused CRISPR-Cas9 screens in two OVA-expressing mouse AML cell lines co-cultured with OT-I T cells engineered to express TCRs recognizing the H-2Kb:OVA complex presented on AML cells. We started with a CRISPR library targeting regulators of transcription for the following reasons: 1) changes in the transcriptional landscape are associated with resistance to both small-molecule targeted therapies and immunotherapies, 2) transcriptional regulators are highly evolutionarily conserved, indicating the potential for extending their mechanisms to other cancer types. Through these screens, we uncovered positive and negative transcriptional regulatory networks of AML responsiveness to T-cell-based cellular therapies. Notably, we identified IRF2BP2 as a potent suppressor of T-cell immunosurveillance, as its ablation potentiated T-cell cytotoxicity against AML cells. Consistently, IRF2BP2 depletion enhanced in vivo T-cell-mediated immune surveillance, which was evidenced by increased T-cell infiltration and enhanced T-cell killing to suppress AML progression and prolong animal survival. Moreover, we found that high expression of IRF2BP2 led to blunted immune surveillance of cytotoxic T cells in patients with AML. Notably, we confirmed that IRF2BP2 potently suppressed MHC-I AP in AML cells. Therefore, ablation of IRF2BP2 enhanced the immunogenicity of AML cells by restoring their MHC-I AP, thus facilitating their recognition by T cells and eliciting subsequent T-cell-mediated elimination of AML. Mechanistically, IRF2BP2 modulated AML AP by repressing the expression of genes involved in the interferon-alpha (IFNa) signaling pathway. These findings advance our understanding of AML-associated immune recognition and evasion mechanisms and provide promising candidates for the next-generation immunotherapy for AML.