Abstract
Only a subset of cancer patients respond to T-cell checkpoint inhibitors, highlighting the need for alternative immunotherapeutics. We performed CRISPR-Cas9 screens in a leukemia cell line to identify perturbations that enhance natural killer effector functions. Our screens defined critical components of the tumor-immune synapse and highlighted the importance of cancer cell interferon-γ signaling in modulating NK activity. Surprisingly, disrupting the ubiquitin ligase substrate adaptor DCAF15 strongly sensitized cancer cells to NK-mediated clearance. DCAF15 disruption induced an inflamed state in leukemic cells, including increased expression of lymphocyte costimulatory molecules. Proteomic and biochemical analysis revealed that cohesin complex members were endogenous client substrates of DCAF15. Genetic disruption of DCAF15 was phenocopied by treatment with indisulam, an anticancer drug that functions through DCAF15 engagement. In AML patients, reduced DCAF15 expression was associated with improved survival. These findings suggest that DCAF15 inhibition may have useful immunomodulatory properties in the treatment of myeloid neoplasms.
Highlights
28 29 Major advances in tumor control have recently been achieved by targeting immune inhibitory signaling pathways
Disruption of the protein tyrosine phosphatases PTPN2 and PTPN1 were 128 the #2 and #5 ranked natural killer (NK)-92 -sensitizing mechanisms, respectively. These proteins suppress IFNg-induced immunomodulation by dephosphorylating STAT and JAK proteins, as has been reported in CRISPR screens using T-cell coculture systems or syngeneic tumor models 9,10. Taken together, these findings indicate that our in vitro functional genomics screens effectively revealed known components of physiologically-relevant immune synapse and cytokine pathways. 134 Prospective identification of novel genes affecting sensitization to NK cells 135 136 Mechanisms of NK-92 sensitization identified in the screen were diverse, revealing many strongly137 scoring genes not previously linked to either interferon signaling or NK cell biology (Figure 1). Most surprisingly, the top-ranked mechanism for promoting NK-92 mediated clearance was disruption of DCAF15, an uncharacterized substrate adaptor for CRL4 ubiquitin E3 ligases
As with most substrate adaptors, the normal client repertoire of DCAF15 is undefined, and relatively little is known about the biological function of DCAF15. 147 We noted that disruption of two cohesin-related genes, STAG2 and HDAC8, scored as NK148 92 sensitization factors
Summary
28 29 Major advances in tumor control have recently been achieved by targeting immune inhibitory signaling pathways. B2M and JAK1/2 mutations have been identified in melanoma patients with acquired resistance to checkpoint inhibitors 6,7 These mutations impair recognition of the tumor by the adaptive immune system, either by directly disrupting antigen presentation or by rendering the cells insensitive to IFNg, an important inducer of MHC-I expression. Even treatment-naïve tumors can be highly immuno-edited, presenting with IFNg pathway mutations, reduced MHC-I expression and loss of the peptide sequences that can serve as antigens 12-15. Together, these findings highlight a critical need for therapies that can either increase MHC expression or work in a MHC-independent fashion. NK cells are cytotoxic lymphocytes capable of mounting rapid responses to damaged, infected, or stressed cells, including cancer cells
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