Dorrance, Adrienne M.

Abstract Background: Partial tandem duplications of the histone methyltransferase KMT2Agene(KMT2A-PTD) are the most common KMT2A-aberration in adult acute myeloid leukemia (AML). KMT2A-PTD AML represents a high-risk disease subset with a poor prognosis. However, KMT2A-PTD leukemia is under studied, likely due to a lack of experimental models, and therefore the underlying mechanisms of leukemogenesis remain elusive. Since KMT2A-PTD leukemias possess high-level expression of HOXAgenes, similar to KMT2A-rearranged (KMT2A-r) and NPM1c AML, patients with this type of AML are currently enrolled into several phase I/II trials assessing menin inhibitors (MIs). However, mechanistic or clinical evidence for treatment response is lacking. To date, no targeted therapeutic approaches for KMT2A-PTD leukemia are available. Results: To better understand KMT2A-PTD mediated leukemogenesis, we endogenously tagged the KMT2A-PTD or KMT2A-wildtype (WT) allele in EOL-1 cells with a dTAG that can be degraded with PROTACs. Targeted protein degradation showed that the KMT2A-PTD, but not the KMT2A-WT protein, is critical to maintain leukemia cell growth. We identified KMT2A-PTD specific genome-wide chromatin binding sites and direct target genes as assessed by changes in nascent RNA production that started to occur within 30 minutes of KMT2A-PTD degradation. KMT2A-PTD target genes identified in this study included HOXA9, HMX2, HMX3, CDKN2C, MYC and CDK6 among others. Having defined the KMT2A-PTD target gene program, we assessed the effect of MI on KMT2A-PTD function. In KMT2A-PTD cell lines, PDXs and cells from a published murine KMT2A-PTD/FLT3-ITD knockin model, we observed intrinsic resistance to revumenib characterized by retained chromatin binding of KMT2A-PTD, but not KMT2A-WT after MI treatment. We next defined critical domains for KMT2A-PTD function via a KMT2A domain scan. This revealed the CXXC domain and AT hooks as critical dependencies in EOL-1 cells. Overexpression of KMT2A or mutants with duplicated domains in 293T cells showed that a duplication of the CXXC domain or the AT hooks is sufficient to mediate retained KMT2A chromatin binding under MI. Therefore, the resistance to MIs is likely due to the duplicated protein of KMT2A subverting menin function at critical target loci. Given that KMT2A-PTD remains chromatin-bound upon menin inhibition, we focused on ENL as a potential regulator of leukemia gene expression programs. In KMT2A-r and NPM1c leukemia, the ENL protein has been shown to be a critical dependency as it associates with acetyl lysine via its YEATS domain. ENL/AF9 YEATS inhibitors reverse ENL-dependent gene expression including HOXA9 and MYC. Using the small molecules TDI-11055 and TM-7, we show that YEATS inhibition leads to loss of members of the super-elongation complex and DOT1L from KMT2A-PTD driven loci and downregulation of target gene expression. Treatment of KMT2A-PTD PDXs with YEATS inhibitors induced differentiation and significantly reduced leukemia burden in vivo. Interestingly, we show that in contrast to previous findings in KMT2A-r leukemia, loss of ENL alone is insufficient to abrogate leukemic proliferation of EOL-1 cells. Instead, by combining ENL degradation with CRISPR-Cas9 mediated knockdown of AF9, we find that both YEATS proteins, ENL and its paralogue AF9, support aberrant gene expression in KMT2A-PTD leukemia. Finally, we show that the novel combination of MI and YEATS inhibition (revumenib plus TDI-11055) synergistically affects proliferation and induces differentiation in cell line and PDX models of KMT2A-PTD leukemia, which in turn prolongs survival of mice with KMT2A-PTD leukemia. Conclusions: KMT2A-PTD leukemia is dependent on the mutated, but not the WT KMT2A allele. It is characterized by a relative, intrinsic resistance to MI monotherapy, which is mediated by a duplication of the CXXC domain and AT hooks of KMT2A. Targeting both, the ENL and AF9 YEATS domain, is a possible treatment strategy and when combined with revumenib, YEATS inhibition has synergistic effects and overcomes intrinsic MI resistance. However, based on our studies, MI monotherapy may not be effective for most patients with KMT2A-PTD leukemia. Given that numerous compounds targeting the ENL (and AF9) YEATS domain are under study and MIs have recently obtained FDA approval, the combination of MI and YEATS inhibition could be translated into clinical trials for patients with KMT2A-PTD leukemia in the relatively near future.

Significance In this work we report on the previously uncharacterized clinical and biological role for EGFL7 in acute myeloid leukemia (AML). Patients with increased EGFL7 mRNA expression had lower complete remission rates and shorter overall and event-free survival, demonstrating the clinical relevance of EGFL7 expression in cytogenetically normal AML. Our results show that AML blasts are able to synthesize and secrete EGFL7 protein, promoting autocrine blast cell growth. Inhibition of EGFL7 results in decreased proliferation and induces apoptosis of AML cells. Taken together, our data provide the rationale for targeting EGFL7 using blocking antibodies as a therapy for patients with AML.

AbstractRecently, we showed that increased miR-181a expression was associated with improved outcomes in cytogenetically normal acute myeloid leukemia (CN-AML). Interestingly, miR-181a expression was increased in CN-AML patients harboring CEBPA mutations, which are usually biallelic and associate with better prognosis. CEBPA encodes the C/EBPα transcription factor. We demonstrate here that the presence of N-terminal CEBPA mutations and miR-181a expression are linked. Indeed, the truncated C/EBPα-p30 isoform, which is produced from the N-terminal mutant CEBPA gene or from the differential translation of wild-type CEBPA mRNA and is commonly believed to have no transactivation activity, binds to the miR-181a-1 promoter and up-regulates the microRNA expression. Furthermore, we show that lenalidomide, a drug approved for myelodysplastic syndromes and multiple myeloma, enhances translation of the C/EBPα-p30 isoform, resulting in higher miR-181a levels. In xenograft mouse models, ectopic miR-181a expression inhibits tumor growth. Similarly, lenalidomide exhibits antitumorigenic activity paralleled by increased miR-181a expression. This regulatory pathway may explain an increased sensitivity to apoptosis-inducing chemotherapy in subsets of AML patients. Altogether, our data provide a potential explanation for the improved clinical outcomes observed in CEBPA-mutated CN-AML patients, and suggest that lenalidomide treatment enhancing the C/EBPα-p30 protein levels and in turn miR-181a may sensitize AML blasts to chemotherapy.