CUL1: Novel Therapeutic Target in Myeloid Neoplasms Harboring -7/Del(7q)

Lenalidomide (LEN) has established a new paradigm of targeted therapy in MDS. The mechanistic underpinnings of LEN efficacy are related to the synthetic lethality of this agent through its ability to bind cereblon (CRBN). LEN induces degradation of CK1α, which is encoded by the CSNK1A1 gene located on the del(5q) CDR, whereby haploinsufficient levels of this gene allow for selective toxicity to deletion mutants. Another common cytogenetic abnormality present in patients with myeloid neoplasia (MN) is -7/del(7q). To date no selective therapies exist for -7/del(7q), an urgent unfulfilled need, given the poor prognosis associated with this cytogenetic abnormality. We were interested to explore if this same notion of selective toxicity may be possible in del(7q) myeloid patients and sought to screen drugs for this focused population.

From a large cohort of patients with MN (n=3,328), we found -7/del(7q) in 10% (n=316) of patients. We first identified a signature pattern of haploinsufficient genes on -7/del(7q) based on NGS. We then searched for haploinsufficient genes which, if targeted by investigational drugs, could provide a therapeutic window for selected MN subtypes in analogy to LEN in del(5q).

For the purpose of our analysis, haploinsufficient expression was defined as <25^th %tile of the mRNA levels seen in healthy individuals (Kerr, ASH 2019). Among others, we identified haploinsufficiency in CUL1 (7q36.1). CUL1 is a tumor suppressor gene, and is a well-characterized target of neddylation inhibitors. CUL1 had haploinsufficient mRNA levels in 92% of the patients compared to healthy individuals (n=64; log2 CPM 25^th %tile expression= 4.966; P<.0001). Similarly, in primary AML (Beat AML; n=37) CUL1 was haploinsufficient in 81% of the cases compared to healthy individuals (n=21; log2 CPM 25^th %tile expression= 6.182; P<.0001). Given that the 7q36.1 region involves CUL1 and EZH2, we investigated the interrelation between these 2 genes. Cases with overlapping microdeletions involving CUL1 and EZH2 have been previously described. A 25.4-kb microdeletion encompassing the last exon of EZH2 and the 3′ region of CUL1 has been found in Weaver syndrome, a congenital growth disorder caused by mutations in genes of the PRC2 complex (EED, SUZ12). Distinct from EZH2, CUL1 is rarely mutated in MN; only 2 mutations have been described (TCGAAML: N141S; E241D). Unexpectedly, in our cohort EZH2 had haploinsufficient expression in 97% of the patients compared to healthy individuals (n=64; log2 CPM 25^th %tile expression= 6.042; P<.0001). CUL1 and EZH2 low expressors had a significantly (P<.001) higher expression of CDKN1A (p21), another target of neddylation inhibitors. CUL1 low expressors had significantly increased expression of other key cell cycle control factors regulated by CUL1 e.g., p27 (P=.003), c-myc (P=.007), β-catenin (P<.0001), mTOR (P<.0001), as well as the ubiquitin promoter p-IκBα (P=.0017). We previously evaluated the global impact of impairing cullins-neddylation by using MLN4924 (Pevonedistat) on the AML proteome and established a rationale for its combination with azacytidine (AZA) in vivo. MLN4924 elicits an anti-proliferative effect (IC₅₀: 1 μM) in del(7q) AML cells KG-1; an effect that was doubled when MLN4924 was combined with AZA. Available databases of drug sensitivity (cancerrx) summarize the MLN4924 anti-proliferative effect on 721 cancer cells (0.02<IC₅₀ [μM]>97) with sensitivity levels of KG-1 in the lower μM ranges. Our analysis also identified changes in death box-RNA-helicases (DDX41, DDX24,DDX54) and DNA binding proteins (CHD3), opening the possibility that MLN4924 might lead to degradation of key proteins implicated in the pathogenesis of MDS/ AML. The therapeutic index was confirmed by the absence of toxicity to normal CD34⁺ cells which were unresponsive to MLN4924 because they lack the expression of NEDD8-activating enzyme (NAE) (major target of MLN4924). In contrast to normal cells, NAE is highly expressed in myeloid cancer cells. In an ongoing dose-escalation study of MLN4924 plus AZA, 1 patient with -7 had stable disease after 6 cycles of therapy and 2 patients with del(7q) achieved complete and partial remissions.

In sum, we propose that MN with -7/del(7q) abnormalities might represent a patient population genetically hypersensitive to synthetic lethality by neddylation inhibitors.