Loss of all or part of chromosome 7 [-7/del(7q)] is recurrent in myeloid neoplasms and associated with a poor response to chemotherapy. Chromosome 7-encoded genes driving drug resistance and the consequences of combinatorial 7q tumor suppressor gene loss have remained unclear, the latter question largely because of the challenges of modeling aneuploidy. Here, we use in silico data mining to uncover 7q genes involved in chemotherapy resistance. We establish murine models of del(7q) clonal hematopoiesis and drug resistance with multiplex CRISPR-Cas9 (CRISPR-associated protein 9)-mediated inactivation of 4 genes, Cux1, Ezh2, Kmt2c, and Kmt2e. Postgenotoxic exposure, combined deficiency of Cux1 and Ezh2 preferentially promotes clonal myeloid expansion in vivo, with compounding defects in DNA damage recognition and repair. Human acute myeloid leukemia cell lines similarly illustrate central roles for CUX1 and EZH2 loss in survival and DNA damage resolution after chemotherapy exposure. Transcriptome analysis reveals combined Cux1 and Ezh2 loss recapitulates gene signatures of -7 patients and defective DNA damage response pathways, to a greater extent than single gene loss. This work reveals a genetic interaction between CUX1 and EZH2, and sheds light on how -7/del(7q) contributes to leukemogenesis and drug resistance characteristic of these adverse-risk neoplasms. These data support the concept of 7q as a contiguous gene syndrome region, in which combined loss of multiple gene drives pathogenesis. Furthermore, our CRISPR-based approach may serve as a framework for interrogating other recurrent aneuploid events in cancer.

Monosomy 7 (-7) and deletions of chromosome arm 7q (del(7q)) are prevalent high-risk cytogenetic abnormalities that often co-occur with del(17p) (harboring TP53). To identify novel targeted therapies based on specific vulnerabilities in high-risk myeloid malignancies, we investigated druggable, chromosome 7-encoded essential genes that are monoallelically deleted in the context of -7/del(7q), that is, collateral lethal genes. By mining genome-wide CRISPR-Cas9 screen data sets, we identified nicotinamide phosphoribosyltransferase (NAMPT) on 7q22.3 as a specific susceptibility in 81.5% of -7/del(7q) malignancies. Human acute myeloid leukemia (AML) cell lines with partial loss of NAMPT and primary samples from patients with -7 AML demonstrated heightened sensitivity to the NAMPT inhibitor KPT-9274 compared to control samples. Notably, NAMPT inhibitors were equally effective in NAMPT-deficient samples with TP53 loss. Furthermore, combining NAMPT and poly (ADP-ribose) polymerase (PARP) inhibitors, which augment DNA damage, resulted in synergistic therapeutic effects in NAMPT-deficient AML cells. These findings indicate that NAMPT heterozygosity is a therapeutic vulnerability in high-risk myeloid malignancies with -7/del(7q) and recommend NAMPT levels as a biomarker for NAMPT inhibitor sensitivity. This study also establishes a data-driven framework for identifying collateral lethal genes in cancers with recurrent chromosomal deletions.

Acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) with cytogenetic abnormalities of chromosome 7 have dismal survival outcomes. Monosomy 7 or deletion of 7q (-7/del7q) are adverse-risk cytogenetic features found in up to 12% of MDS/AML patients and are further enriched in therapy-related MDS/AML. Despite significant scientific effort, no targeted therapy is available for patients with -7/del7q MDS/AML. Several genes are associated with -7/del7q leukemogenesis. Cut-like homeobox 1 (CUX1) is a gene encoding a context-dependent transcription factor required for several molecular pathways, including epigenetic signaling. CUX1 is deleted in -7/del7q MDS/AML and somatically mutated in 2-4% of MDS/AML. CUX1 mutations and CUX1 deletions are associated with a poor prognosis, and are known to co-occur with adverse risk TP53 mutations and a complex cytogenetic background. Thus, there is a need for novel human models of MDS/AML to isolate the effect of CUX1 alterations. To address the need for high-fidelity models of MDS/AML with high-risk genetic changes, we transfected human inducible pluripotent stem cells (hiPSCs) with CUX1 targeting gRNA and CRISPR/Cas9 ribonucleotide-protein (RNP) complexes to generate isogenic hiPSC lines bearing CUX1+/- and CUX1-/- genotypes alongside parent hiPSCs and sham transfection lines with a CUX1+/+ background. These derivative cell lines underwent rigorous validation by karyotypic G-banding analysis, sequencing, immunoblotting, trilineage germ layer differentiation, and analysis of hiPSC transcriptional and immunophenotypic markers. We hypothesized that the loss of one or both alleles of CUX1 would result in transcriptional changes similar to CUX1 mutated and -7/del7q MDS/AML. This model can be further leveraged to identify potential treatment targets. We obtained bulk RNA sequencing of undifferentiated hiPSCs and hiPSC-derived hematopoietic stem and progenitor cells (i-HSPCs) of each genotype (CUX1+/+, CUX1+/-, and CUX1-/-). We identified several differentially expressed genes and novel long non-coding RNAs in hiPSCs with Cas9-mediated CUX1 deletions, including downregulation of distinct subsets of genes in CUX1-/- and CUX1+/- hiPSCs. Bulk RNA sequencing of CUX1-/- and CUX1+/- i-HSPCs identified an association between reduced expression of thioredoxin-interacting protein (TXNIP), a known regulator of autophagy. This study supports the use of hiPSC-based CRISPR/Cas9 gene editing as a novel platform to identify gene-specific alterations in genotypically and cytogenetically complex myeloid neoplasms. Joseph Michael Cannova, Kaina A. Millan, Yuqing Xue, Aubrianna S. Ramsland, Zara Khosravi, Adesewa Ogunsusi, Matthew Jotte, Megan McNerney, Michael Drazer. Application of human inducible pluripotent stem cells (hiPSCs) with CRISPR/Cas9-mediated deletion of CUX1 as a model for high-risk myeloid neoplasms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6500.

ABSTRACT:Long-term maintenance of somatic stem cells relies on precise regulation of self-renewal and differentiation. Understanding the molecular framework for these homeostatic processes is essential for improved cellular therapies and treatment of myeloid neoplasms. CUX1 is a widely expressed, dosage-sensitive transcription factor crucial for development and frequently deleted in myeloid neoplasia in the context of -7/(del7q). Here, using novel mouse models and single-cell approaches, we report that dynamic and distinct CUX1 levels are integral to hematopoietic stem cell (HSC) activity. Knockdown of CUX1 reverses HSC differentiation and strikingly reendows progenitors with stem cell function, accompanied by restoration of the HSC transcriptome and DNA accessibility landscape. CUX1 mediates these activities, in part, via suppressing endogenous retroelements (EREs) and the ensuing interferon-stimulated gene expression program. Both EREs and the interferon response are upregulated in CUX1-deficient acute myeloid leukemia, suggesting a conserved role of CUX1 in regulating these elements. These data establish an unexpected entwinement between stem cell-intrinsic innate immune activation and the transcriptional programs of stem cell identity. Furthermore, we reveal the profound effects of transcription factor levels in cell fate.

Abstract The small intestine digests and absorbs nutrients, a role made possible by specialized secretory and absorptive cells that constantly replenish from the intestinal stem cell niche. Disruption in intestinal epithelium homeostasis has been linked to pathologies including inflammatory bowel disease (IBD) and cancer. However, the processes regulating differentiation in healthy and disease setting are incompletely understood. CUX1 is a highly conserved homeodomain-containing transcription factor that is expressed in small intestinal crypts and has been previously shown to be essential in mice and Drosophila. CUX1 is upregulated upon inflammatory stress conditions, including intestinal damage and in IBD. In addition, CUX1 is predicted to be protective against IBD from genome-wide association studies. The aim of the current work is to determine the mechanistic role of CUX1 in secretory intestinal cells differentiation and epithelial homeostasis. To this end, we have generated transgenic mouse models that modulate CUX1 levels in an inducible manner. Mice with near-null CUX1 levels exhibit rapid weight loss requiring euthanasia while mice with ~50% residual CUX1 halt normal weight gain. Histologic examination of tissues from mice with CUX1 knock-down reveals a lack of mature secretory cells, including goblet and Paneth cells, the latter playing a supportive role to intestinal stem cells. Moreover, mouse intestinal tissues from our knock-down models demonstrated decreased proliferation with increased apoptosis. In transcriptome profiling, we observed downregulation of proliferation, intestinal stem cell, and digestive system developmental gene signatures and decreased levels of key secretory cell regulators, pointing towards a role for CUX1 in stem cell maintenance and differentiation. Indeed, reducing CUX1 levels decreased β-catenin protein levels, while Wnt/β-catenin signaling is required for the organization of the crypt-villus axis. Finally, CUX1 knock-down compromises the ability to form budding organoids, demonstrating the cell intrinsic role for CUX1 in stem cell differentiation. In ongoing studies, we are identifying CUX1 genome-wide binding targets and the epigenetic impact of CUX1 in intestinal epithelium cells. Our findings indicate that CUX1 is a critical regulator of intestinal epithelium homeostasis that has a role in differentiation and potential role in injury-induced de-differentiation in healthy as well as IBD patients. We propose that CUX1 regulates stem cell maintenance and crypt composition by regulating Wnt/β-catenin signaling and inducing fetal-like transcriptomic repair program shown to be coopted by colon cancers. Resolving an intricate network of transcriptional regulation of differentiation in the intestinal crypt holds the potential to successfully target inflammation-related damage in human intestines. Citation Format: Katarzyna Zawieracz, Ningfei An, Megan McNerney. CUX1 transcriptionally regulates intestinal epithelial homeostasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5636.

Abstract Monosomy 7 (-7) or del(7q) are recurrent in high-risk myeloid neoplasms, including up to 50% of myeloid neoplasms arising after prior exposure to chemotherapy and/or radiation. Although putative chromosome 7 tumor suppressor genes have been identified, the effects of combinatorial 7q gene loss remain unclear. A barrier to understanding the pathogenesis of -7/del(7q) is the challenge of modeling aneuploidy in animal models. To address this knowledge gap, we established an in vivo model of del(7q) clonal hematopoiesis and drug resistance using multiplex CRISPR-Cas9 to simultaneously target four 7q genes (Cux1, Ezh2, Kmt2c, and Kmt2e) in murine hematopoietic stem cells. After chemotherapy exposure, we observe significant myeloid expansion of clones edited for both Cux1 and Ezh2. Compared to the transcriptomes of control or single gene edited cells, Cux1;Ezh2-deficient cells fail to induce DNA damage response pathways after genotoxic stress. Cux1;Ezh2-deficient cells also display reduced deposition of γH2AX after DNA damage, as well as persistent, unrepaired DNA breaks, indicating perturbations to DNA damage recognition and repair. Collectively, our data support the concept of 7q as a contiguous gene syndrome region, in which combined loss of multiple genes drives drug resistance and disease development. This work reveals a genetic interaction between CUX1 and EZH2, and sheds light on how -7/del(7q) contributes to the development and inherent drug resistance characteristic of high-risk myeloid disease. Further, our CRISPR-based approach may serve as a framework for interrogating other recurrent aneuploid events in cancer. Citation Format: Matthew R. Jotte, Angela Stoddart, Tanner C. Martinez, Yuqing Xue, Molly K. Imgruet, Megan E. McNerney. Combined loss of the chromosome 7 genes CUX1 and EZH2 promotes chemotherapy resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5598.

CUX1 is a homeodomain-containing transcription factor that is essential for the development and differentiation of multiple tissues. CUX1 is recurrently mutated or deleted in cancer, particularly in myeloid malignancies. However, the mechanism by which CUX1 regulates gene expression and differentiation remains poorly understood, creating a barrier to understanding the tumor -suppressive functions of CUX1. Here, we demonstrate that CUX1 directs the BAF chromatin remodeling complex to DNA to increase chromatin accessibility in hematopoietic cells. CUX1 preferentially regulates lineage -specific enhancers, and CUX1 target genes are predictive of cell fate in vivo. These data indicate that CUX1 regulates hematopoietic lineage commitment and homeostasis via pioneer factor activity, and CUX1 deficiency disrupts these processes in stem and progenitor cells, facilitating transformation.

The RNA N6-methyladenosine (m6A) reader YTHDF1 is implicated in cancer etiology and progression. We discovered that radiotherapy (RT) increased YTHDF1 expression in dendritic cells (DCs) of PBMCs from patients with cancer, but not in other immune cells tested. Elevated YTHDF1 expression in DCs was associated with poor outcomes for patients receiving RT. We found that loss of Ythdf1 in DCs enhanced the antitumor effects of ionizing radiation (IR) by increasing the cross-priming capacity of DCs across multiple murine cancer models. Mechanistically, IR upregulated YTHDF1 expression in DCs through stimulator of IFN genes/type I IFN (STING/IFN-I) signaling. YTHDF1 in turn triggered STING degradation by increasing lysosomal cathepsins, thereby reducing IFN-I production. We created a YTHDF1 deletion/inhibition prototype DC vaccine that significantly improved the therapeutic effect of RT and radioimmunotherapy in a murine melanoma model. Our findings reveal a layer of regulation between YTHDF1/m6A and STING in response to IR, which opens new paths for the development of YTHDF1-targeting therapies.

Current therapies for high-grade TP53-mutated myeloid neoplasms (≥10% blasts) do not offer a meaningful survival benefit except allogeneic stem cell transplantation in the minority who achieve a complete response to first line therapy (CR1). To identify reliable pre-therapy predictors of complete response to first-line therapy (CR1) and outcomes, we assembled a cohort of 242 individuals with TP53-mutated myeloid neoplasms and ≥10% blasts with well-annotated clinical, molecular and pathology data. Key outcomes examined were CR1 & 24-month survival (OS24). In this elderly cohort (median age 68.2 years) with 74.0% receiving frontline non-intensive regimens (hypomethylating agents +/- venetoclax), the overall cohort CR1 rate was 25.6% (50/195). We additionally identified several pre-therapy factors predictive of inferior CR1 including male gender (P = 0.026), ≥2 autosomal monosomies (P < 0.001), −17/17p (P = 0.011), multi-hit TP53 allelic state (P < 0.001) and CUX1 co-alterations (P = 0.010). In univariable analysis of the entire cohort, inferior OS24 was predicated by ≥2 monosomies (P = 0.004), TP53 VAF > 25% (P = 0.002), TP53 splice junction mutations (P = 0.007) and antecedent treated myeloid neoplasm (P = 0.001). In addition, mutations/deletions in CUX1, U2AF1, EZH2, TET2, CBL, or KRAS (‘EPI6’ signature) predicted inferior OS24 (HR = 2.0 [1.5–2.8]; P < 0.0001). In a subgroup analysis of HMA +/-Ven treated individuals (N = 144), TP53 VAF and monosomies did not impact OS24. A risk score for HMA +/-Ven treated individuals incorporating three pre-therapy predictors including TP53 splice junction mutations, EPI6 and antecedent treated myeloid neoplasm stratified 3 prognostic distinct groups: intermediate, intermediate-poor, and poor with significantly different median (12.8, 6.0, 4.3 months) and 24-month (20.9%, 5.7%, 0.5%) survival (P < 0.0001). For the first time, in a seemingly monolithic high-risk cohort, our data identifies several baseline factors that predict response and 24-month survival.

Supplementary Figure 2 - PDF file 177K, Data showing survival and Hematologic Parameters of Nras heterozygous, hemizygous and homozygous mice

e15092 Background: Philadelphia-negative myeloproliferative neoplasms (MPNs) are clonal hematopoietic malignancies. Nearly all MPNs are driven by somatic mutations in either: JAK2, CALR, or MPL. Although all three MPN driver mutations lead to constitutive activation of JAK/STAT signaling, JAK inhibitors are not curative and fail to alter disease progression and display unwanted side effects. Allogeneic stem cell transplantation remains the only curative therapy for MPNs, but is associated with substantial morbidity and mortality. Recently, glutaminolysis has been shown to play a critical role in cancer cell metabolism. During glutaminolysis, glutamine is metabolized through in a two-step reaction, the first of which involves the enzyme glutaminase (GLS) catalyzing the hydrolysis of glutamine to glutamate. Glutamate can then fuel for energy production into the TCA cycle, among several other possible metabolic fates. As many cancers have proven to be dependent on this pathway, targeting GLS has become an attractive therapeutic avenue. Because glutaminolysis has been understudied in MPNs, we sought to determine whether this pathway represents a novel, targetable vulnerability in MPNs. Methods: We evaluated the mRNA levels of GLS in peripheral blood mononuclear cells from 30 MPN patients and 5 healthy donors. We tested by qPCR for GLS and the protein levels of GLS by western blot in TF-1 cells, a human myeloid cell line, stably overexpressing either JAK2, MPL, or CALR mutated proteins. The latter also under treatment with the JAK inhibitor ruxolinitinib. We also evaluated the GLS enzyme activity through the use of a fluorimetric assay. Lastly, we tested the sensitivity of MPN cells to GLS inhibition with a GLS inhibitor, CB-839, which is currently in advanced phase clinical trials for other cancers including Myelodysplastic Syndromes. Results: GLS mRNA expression was increased in all MPN patients regardless of their driver mutation, where expression in JAK2V617F patients was higher in MF versus ET patients (p < 0.001). GLS protein expression and activity were increased in TF-1 cells expressing JAK2, MPL, and CALR mutations. We also found that GLS mRNA and protein expression was up-regulated in a JAK/STAT-dependent manner. Interestingly, despite increased expression of GLS across all MPN driver mutations, only JAK2 V617F cells demonstrated significant sensitivity to GLS inhibition with CB-839 in vitro and with preliminary data in vivo. We found that combination treatment with JAK inhibitor ruxolitinib further inhibited cell viability. Conclusions: GLS up-regulation is a common feature of all MPNs, and is JAK/STAT dependent. JAK2 V617F expressing cells show significant sensitivity to GLS inhibition. Combination treatment with ruxolitinib further enhances this effect. Treatment with CB-839 may thus represent a novel therapeutic avenue for JAK2 V617F+ MPNs.

-7/del(7q) is prevalent across subtypes of myeloid neoplasms. CUX1, located on 7q22, encodes a homeodomain-containing transcription factor, and, like -7/del(7q), CUX1 inactivating mutations independently carry a poor prognosis. As with loss of 7q, CUX1 mutations often occur early in disease pathogenesis. We reported that CUX1 deficiency causes myelodysplastic syndrome in mice but was insufficient to drive acute myeloid leukemia (AML). Given the known association between -7/del(7q) and RAS pathway mutations, we mined cancer genome databases and explicitly linked CUX1 mutations with oncogenic RAS mutations. To determine if activated RAS and CUX1 deficiency promote leukemogenesis, we generated mice bearing NrasG12D and CUX1-knockdown which developed AML, not seen in mice with either mutation alone. Oncogenic RAS imparts increased self-renewal on CUX1-deficient hematopoietic stem/progenitor cells (HSPCs). Reciprocally, CUX1 knockdown amplifies RAS signaling through reduction of negative regulators of RAS/PI3K signaling. Double mutant HSPCs were responsive to PIK3 or MEK inhibition. Similarly, low expression of CUX1 in primary AML samples correlates with sensitivity to the same inhibitors, suggesting a potential therapy for malignancies with CUX1 inactivation. This work demonstrates an unexpected convergence of an oncogene and tumor suppressor gene on the same pathway.

Monosomy 7 (−7) and del7q are the most common high-risk cytogenetic abnormalities and occur across the spectrum of myeloid disorders. -7/del(7q) also co-occur with other high-risk factors such as mutations or deletion of TP53. Standard, non-specific chemotherapy drugs are less effective in these high-risk patients, resulting in a median survival rate of approximately one year. To identify novel, targeted agents for these neoplasms, we sought “collateral lethal” genes, i.e. essential, druggable genes encoded on chromosome 7 that are haploinsufficient upon their loss of heterozygosity. To this end, we first identified essential genes located on chromosome 7. We mined genome-wide CRISPR/Cas9 screen data from 27 human acute myeloid leukemia (AML) cell lines within the DepMap database and identified 65 chromosome 7-encoded, candidate essential genes in AML. To determine those essential genes with known inhibitors, we intersected these 65 candidates with the Drug-Gene Interaction and canSAR.ai databases. We found that nicotinamide phosphoribosyltransferase ( NAMPT), the rate-limiting enzyme that catalyzes the first step of NAD + biosynthesis from nicotinamide, was one of four essential and druggable targets on chromosome 7. Notably, NAMPT was the only essential gene on chromosome 7 with a first-in-class orally bioavailable inhibitor, KPT 9274, currently in clinical trials (NCT04914845). Moreover, NAMPT DNA copy number, mRNA, and protein levels all negatively correlated with cell line sensitivity to NAMPT loss, implicating NAMPT as a collateral lethal candidate gene. We confirmed that isogenic human AML cell lines CRISPR-engineered to partially reduce NAMPT DNA copy led to reduced NAMPT protein levels, indicating NAMPT is a haploinsufficient gene. Cells with ~50% NAMPT levels were significantly more sensitive to the KPT 9274 treatment, and became less viable and more apoptotic, compared to control locus edited cells. To determine whether TP53 status could alter this vulnerability, we generated cell lines with both TP53 loss and 50% NAMPT loss. We found TP53 mutational status did not attenuate the observed effects of NAMPT inhibition on cell survival. Viability assays with primary patient AML samples confirmed that -7/del(7q) status imparts significantly elevated sensitivity to KPT 9274 treatment than samples with diploid chromosome 7 alleles. In summary, our findings reveal NAMPT heterozygosity as a therapeutic vulnerability in high-risk myeloid neoplasms that warrants clinical follow-up. Further, we provide a framework centered on data-mining for uncovering collateral lethal genes in other cancers with recurrent chromosomal arm level deletions.

Supplementary Figure 5 - PDF file 30K, Figure showing RAS expression in hematopoietic cancer cell lines and human pediatric AML samples

Supplementary Figure 4 - PDF file 64K, Data showing the molecular Analysis of AMLs from NrasG12D/+ Mice

Many transcription factors (TFs) function as tumor suppressor genes with heterozygous phenotypes, yet haploinsufficiency generally has an underappreciated role in neoplasia. This is no less true in myeloid cells, which are normally regulated by a delicately balanced and interconnected transcriptional network. Detailed understanding of TF dose in this circuitry sheds light on the leukemic transcriptome. In this review, we discuss the emerging features of haploinsufficient transcription factors (HITFs). We posit that: ( a) monoallelic and biallelic losses can have distinct cellular outcomes; ( b) the activity of a TF exists in a greater range than the traditional Mendelian genetic doses; and ( c) how a TF is deleted or mutated impacts the cellular phenotype. The net effect of a HITF is a myeloid differentiation block and increased intercellular heterogeneity in the course of myeloid neoplasia.

Monosomy 7 and del(7q) [-7/del(7q)] are recurrent in myeloid neoplasms and associated with chemoresistance. -7/del(7q) is identified in up to half of therapy-related myeloid neoplasms (t-MN), high-risk secondary malignancies arising after prior exposure to chemotherapy or radiation. -7/del(7q) is also detected in clonal hematopoiesis, suggesting chromosome 7 aberrations can be early events in disease etiology. Despite this prevalence, the pathogenesis of -7/del(7q) in leukemogenesis remains unclear. We previously reported that deficiency of the transcription factor CUX1, a 7q-encoded tumor suppressor gene, promotes hematopoietic stem and progenitor cell drug resistance and t-MN transformation. Herein, we determined the combined impact of CUX1 loss with additional 7q tumor suppressor genes. To this end, we established a CRISPR/Cas9-based murine model of del(7q) clonal hematopoiesis and drug resistance. After targeting four 7q genes simultaneously, combined deficiency of CUX1 and the histone methyltransferase EZH2 uniquely promoted clonal outgrowth under genotoxic pressure in vivo and in vitro. Mechanistically, clonal selection is due, in part, to decreased apoptosis after chemotherapy exposure. RNA-seq in the absence of genotoxic insult revealed that Cux1 and Ezh2 loss has an additive transcriptional impact that is enriched for -7/del(7q) patient-derived gene signatures. Overall, we reveal a previously unknown genetic interaction between the 7q genes CUX1 and EZH2, supporting the concept of 7q as a contiguous gene syndrome region . A refined understanding of the molecular pathways driving del(7q) pathogenesis and drug resistance will enable development of therapies designed to counter or prevent these high-risk malignancies. In addition, we report a tractable approach for interrogating the pathogenesis of aneuploid events more broadly in cancer.

Supplementary Figure 1 - PDF file 150K, Figure showing the generation and Functional Validation of a Conditional Mutant Nrasflox Allele