Despite the clinical success of cancer immunotherapies, the majority of patients fail to respond or develop resistance through disruption of pathways that promote neo-antigen presentation on MHC I ...molecules. Here, we conducted a series of unbiased, genome-wide CRISPR/Cas9 screens to identify genes that limit natural killer (NK) cell anti-tumor activity. We identified that genes associated with antigen presentation and/or interferon-γ (IFN-γ) signaling protect tumor cells from NK cell killing. Indeed, Jak1-deficient melanoma cells were sensitized to NK cell killing through attenuated NK cell-derived IFN-γ-driven transcriptional events that regulate MHC I expression. Importantly, tumor cells that became resistant to T cell killing through enrichment of MHC I-deficient clones were highly sensitive to NK cell killing. Taken together, we reveal the genes targeted by tumor cells to drive checkpoint blockade resistance but simultaneously increase their vulnerability to NK cells, unveiling NK cell-based immunotherapies as a strategy to antagonize tumor immune escape.
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•CRISPR screening allows discovery of tumor genes that limit NK cell effector function•Disruption of IFN-γ signaling and/or MHC-I triggers sensitivity to NK cells•Evasion of T cell immunity promotes tumor vulnerability to NK cells•NK cell-targeted immunotherapies may antagonize tumor immune evasion from T cells
Freeman et al. use a series of genome-wide loss-of-function genetic screens to identify genes that limit tumor sensitivity to killing by natural killer cells. The findings highlight that natural killer cells can suppress tumor immune evasion from T cells, identifying a potential strategy to overcome resistance to checkpoint blockade therapy.
The mitochondrial enzyme dihydroorotate dehydrogenase (DHODH) catalyzes one of the rate‐limiting steps in de novo pyrimidine biosynthesis, a pathway that provides essential metabolic precursors for ...nucleic acids, glycoproteins, and phospholipids. DHODH inhibitors (DHODHi) are clinically used for autoimmune diseases and are emerging as a novel class of anticancer agents, especially in acute myeloid leukemia (AML) where pyrimidine starvation was recently shown to reverse the characteristic differentiation block in AML cells. Herein, we show that DHODH blockade rapidly shuts down protein translation in leukemic stem cells (LSCs) and has potent and selective activity against multiple AML subtypes. Moreover, we find that ablation of CDK5, a gene that is recurrently deleted in AML and related disorders, increases the sensitivity of AML cells to DHODHi. Our studies provide important molecular insights and identify a potential biomarker for an emerging strategy to target AML.
Synopsis
This study reports that AG636, an inhibitor of the metabolic enzyme DHODH, has excellent potency against acute myeloid leukemia (AML) in pre‐clinical models.
AG636 exhibits potent activity against different AML subtypes in vivo, promoting a combination of cell death and differentiation and effectively reducing leukemic stem cells.
DHODH inhibition has a moderate impact on normal blood development, but the effects are temporary with hematopoietic populations recovering after treatment cessation.
Pyrimidine starvation limits nascent protein synthesis, in part through downregulating YY1.
Loss of CDK5, a gene recurrently deleted in a subset of patients with aggressive disease, alters the molecular response of leukemic cells to AG636 and increases their sensitivity to drug treatment.
This study reports that AG636, an inhibitor of the metabolic enzyme DHODH, has excellent potency against acute myeloid leukemia (AML) in pre‐clinical models.
Cancer immunotherapies have demonstrated remarkable success; however, the majority of patients do not respond or develop resistance. Here, we conduct epigenetic gene-targeted CRISPR-Cas9 screens to ...identify epigenomic factors that limit CD8+ T cell-mediated anti-tumor immunity. We identify that PRMT1 suppresses interferon gamma (Ifnγ)-induced MHC-I expression, thus dampening CD8+ T cell-mediated killing. Indeed, PRMT1 knockout or pharmacological targeting of type I PRMT with the clinical inhibitor GSK3368715 enhances Ifnγ-induced MHC-I expression through elevated STAT1 expression and activation, while re-introduction of PRMT1 in PRMT1-deficient cells reverses this effect. Importantly, loss of PRMT1 enhances the efficacy of anti-PD-1 immunotherapy, and The Cancer Genome Atlas analysis reveals that PRMT1 expression in human melanoma is inversely correlated with expression of human leukocyte antigen molecules, infiltration of CD8+ T cells, and overall survival. Taken together, we identify PRMT1 as a negative regulator of anti-tumor immunity, unveiling clinical type I PRMT inhibitors as immunotherapeutic agents or as adjuncts to existing immunotherapies.
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•CRISPR screens identify PRMT1 as a negative regulator of tumor cell killing by CD8+ T cells•PRMT1 negatively regulates STAT1-driven MHC-I expression•Loss of PRMT1 augments the efficacy of anti-PD-1 immunotherapy
PRMT1 negatively regulates STAT1-driven MHC-I expression and can be targeted to enhance the efficacy of cancer immunotherapy.
To separate causal effects of histone acetylation on chromatin accessibility and transcriptional output, we used integrated epigenomic and transcriptomic analyses following acute inhibition of major ...cellular lysine acetyltransferases P300 and CBP in hematological malignancies. We found that catalytic P300/CBP inhibition dynamically perturbs steady-state acetylation kinetics and suppresses oncogenic transcriptional networks in the absence of changes to chromatin accessibility. CRISPR-Cas9 screening identified NCOR1 and HDAC3 transcriptional co-repressors as the principal antagonists of P300/CBP by counteracting acetylation turnover kinetics. Finally, deacetylation of H3K27 provides nucleation sites for reciprocal methylation switching, a feature that can be exploited therapeutically by concomitant KDM6A and P300/CBP inhibition. Overall, this study indicates that the steady-state histone acetylation-methylation equilibrium functions as a molecular rheostat governing cellular transcription that is amenable to therapeutic exploitation as an anti-cancer regimen.
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•Persistent P300/CBP KAT activity is required to maintain oncogenic gene expression•P300/CBP inhibition modulates transcription independently of DNA accessibility•Compensatory loss of NCoR/SMRT complexes overcomes catalytic P300/CBP inhibition•Histone methylation switching imparts stable transcriptional suppression
Hogg et al. use multimodal genomics to explore the acute epigenetic and transcriptional effects of therapies targeting histone acetyltransferases P300/CBP in cancer. Catalytic P300/CBP inhibition selectively impairs expression of key oncogenic transcription factors, leading to robust anti-tumor responses, but remains inherently reversible prior to compensatory histone methylation switching.
Multimodal single-cell RNA sequencing enables the precise mapping of transcriptional and phenotypic features of cellular differentiation states but does not allow for simultaneous integration of ...critical posttranslational modification data. Here, we describe SUrface-protein Glycan And RNA-seq (SUGAR-seq), a method that enables detection and analysis of N-linked glycosylation, extracellular epitopes, and the transcriptome at the single-cell level. Integrated SUGAR-seq and glycoproteome analysis identified tumor-infiltrating T cells with unique surface glycan properties that report their epigenetic and functional state.
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