Inherent genome instability underlies trisomy 21-associated myeloid malignancies

Constitutional trisomy 21 (T21) is a state of aneuploidy associated with high incidence of childhood acute myeloid leukemia (AML). T21-associated AML is preceded by transient abnormal myelopoiesis (TAM), which is triggered by truncating mutations in GATA1 generating a short GATA1 isoform (GATA1s). T21-associated AML emerges due to secondary mutations in hematopoietic clones bearing GATA1s. Since aneuploidy generally impairs cellular fitness, the paradoxically elevated risk of myeloid malignancy in T21 is not fully understood. We hypothesized that individuals with T21 bear inherent genome instability in hematopoietic lineages that promotes leukemogenic mutations driving the genesis of TAM and AML. We found that individuals with T21 show increased chromosomal copy number variations (CNVs) compared to euploid individuals, suggesting that genome instability could be underlying predisposition to TAM and AML. Acquisition of GATA1s enforces myeloid skewing and maintenance of the hematopoietic progenitor state independently of T21; however, GATA1s in T21 hematopoietic progenitor cells (HPCs) further augments genome instability. Increased dosage of the chromosome 21 (chr21) gene DYRK1A impairs homology-directed DNA repair as a mechanism of elevated mutagenesis. These results posit a model wherein inherent genome instability in T21 drives myeloid malignancy in concert with GATA1s mutations.

Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma

PURPOSE

Patients with relapsed or refractory T-cell acute lymphoblastic leukemia (T-ALL) or lymphoblastic lymphoma (T-LBL) have limited therapeutic options. Clinical use of genomic profiling provides an opportunity to identify targetable alterations to inform therapy.

EXPERIMENTAL DESIGN

We describe a cohort of 14 pediatric patients with relapsed or refractory T-ALL enrolled on the Leukemia Precision-based Therapy (LEAP) Consortium trial (NCT02670525) and a patient with T-LBL, discovering alterations in platelet-derived growth factor receptor-α (PDGFRA) in 3 of these patients. We identified a novel mutation in PDGFRA, p.D842N, and used an integrated structural modeling and molecular biology approach to characterize mutations at D842 to guide therapeutic targeting. We conducted a preclinical study of avapritinib in a mouse patient-derived xenograft (PDX) model of FIP1L1-PDGFRA and PDGFRA p.D842N leukemia.

RESULTS

Two patients with T-ALL in the LEAP cohort (14%) had targetable genomic alterations affecting PDGFRA, a FIP1-like 1 protein/PDGFRA (FIP1L1-PDGFRA) fusion and a novel mutation in PDGFRA, p.D842N. The D842N mutation resulted in PDGFRA activation and sensitivity to tested PDGFRA inhibitors. In a T-ALL PDX model, avapritinib treatment led to decreased leukemia burden, significantly prolonged survival, and even cured a subset of mice. Avapritinib treatment was well tolerated and yielded clinical benefit in a patient with refractory T-ALL.

CONCLUSIONS

Refractory T-ALL has not been fully characterized. Alterations in PDGFRA or other targetable kinases may inform therapy for patients with refractory T-ALL who otherwise have limited treatment options. Clinical genomic profiling, in real time, is needed for fully informed therapeutic decision making.

Transcriptional Antagonism by CDK8 Inhibition Improves Therapeutic Efficacy of MEK Inhibitors

Aberrant RAS/MAPK signaling is a common driver of oncogenesis that can be therapeutically targeted with clinically approved MEK inhibitors. Disease progression on single-agent MEK inhibitors is common, however, and combination therapies are typically required to achieve significant clinical benefit in advanced cancers. Here we focused on identifying MEK inhibitor-based combination therapies in neuroblastoma with mutations that activate the RAS/MAPK signaling pathway, which are rare at diagnosis but frequent in relapsed neuroblastoma. A genome-scale CRISPR-Cas9 functional genomic screen was deployed to identify genes that when knocked out sensitize RAS-mutant neuroblastoma to MEK inhibition. Loss of either CCNC or CDK8, two members of the mediator kinase module, sensitized neuroblastoma to MEK inhibition. Furthermore, small-molecule kinase inhibitors of CDK8 improved response to MEK inhibitors in vitro and in vivo in RAS-mutant neuroblastoma and other adult solid tumors. Transcriptional profiling revealed that loss of CDK8 or CCNC antagonized the transcriptional signature induced by MEK inhibition. When combined, loss of CDK8 or CCNC prevented the compensatory upregulation of progrowth gene expression induced by MEK inhibition. These findings propose a new therapeutic combination for RAS-mutant neuroblastoma and may have clinical relevance for other RAS-driven malignancies.

SIGNIFICANCE

Transcriptional adaptation to MEK inhibition is mediated by CDK8 and can be blocked by the addition of CDK8 inhibitors to improve response to MEK inhibitors in RAS-mutant neuroblastoma, a clinically challenging disease.

Abstract PR003: Lineage plasticity dictates responsiveness to anti-GD2 therapy in neuroblastoma

Epigenetic dysregulation is frequently observed in the disease pathology of pediatric cancers, including neuroblastoma, the most common extracranial solid tumor in pediatric patients. Neuroblastoma tumors co-opt developmentally linked adrenergic or mesenchymal super-enhancer landscapes that rewire their transcriptional programs. Here, we describe that the lineage commitment to a mesenchymal epigenetic state is an important mechanism of resistance to anti-GD2 therapy through loss of GD2 antigen, a ganglioside glycolipid expressed on the cell surface. Low GD2 expression was significantly correlated with the mesenchymal state in a large panel of neuroblastoma cell lines and a forced adrenergic-to-mesenchymal transition conferred downregulation of GD2 and resistance to anti-GD2 antibody. Mechanistically, low-GD2 expressing cell lines demonstrated significantly reduced expression of the ganglioside synthesis enzyme ST8SIA1 (GD3 synthase), resulting in a bottlenecking of GD2 synthesis. Genome-wide CRISPR/Cas9 screening to identify regulators of GD2 in neuroblastoma revealed that the ablation of the polycomb repressive complex 2 (PRC2) significantly upregulates GD2 expression in GD2-low cells. Pharmacologic inhibition of EZH2 resulted in epigenetic rewiring of mesenchymal neuroblastoma cells into an adrenergic-like state, re-expressed ST8SIA1, and restored surface expression of GD2 and sensitivity to anti-GD2 antibody. These data identify developmental lineage as a key determinant of sensitivity to anti-GD2 based immunotherapies and credential PRC2 inhibitors for clinical testing in combination with anti-GD2 antibody to enhance outcomes for children with neuroblastoma.

Citation Format: Nathaniel W. Mabe, Min Huang, Daniel A. Schaefer, Guillermo N. Dalton, Giulia Digiovanni, Gabriela Alexe, Anna C. Geraghty, Delan Khalid, Marius M. Mader, Michal Sheffer, Miles H. Linde, Nghi Ly, Maria Caterina Rotiroti, Benjamin A. H. Smith, Marius Wernig, Carolyn R. Bertozzi, Michelle Monje, Constantine Mitsiades, Ravindra Majeti, Ansuman T. Satpathy, Kimberly Stegmaier, Robbie G. Majzner. Lineage plasticity dictates responsiveness to anti-GD2 therapy in neuroblastoma. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr PR003.

Transition to a mesenchymal state in neuroblastoma confers resistance to anti-GD2 antibody via reduced expression of ST8SIA1

Immunotherapy with anti-GD2 antibodies has advanced the treatment of children with high-risk neuroblastoma, but nearly half of patients relapse, and little is known about mechanisms of resistance to anti-GD2 therapy. Here, we show that reduced GD2 expression was significantly correlated with the mesenchymal cell state in neuroblastoma and that a forced adrenergic-to-mesenchymal transition (AMT) conferred downregulation of GD2 and resistance to anti-GD2 antibody. Mechanistically, low-GD2-expressing cell lines demonstrated significantly reduced expression of the ganglioside synthesis enzyme ST8SIA1 (GD3 synthase), resulting in a bottlenecking of GD2 synthesis. Pharmacologic inhibition of EZH2 resulted in epigenetic rewiring of mesenchymal neuroblastoma cells and re-expression of ST8SIA1, restoring surface expression of GD2 and sensitivity to anti-GD2 antibody. These data identify developmental lineage as a key determinant of sensitivity to anti-GD2 based immunotherapies and credential EZH2 inhibitors for clinical testing in combination with anti-GD2 antibody to enhance outcomes for children with neuroblastoma.

Unleashing Cell-Intrinsic Inflammation as a Strategy to Kill AML Blasts

Leukemic blasts are immune cells gone awry. We hypothesized that dysregulation of inflammatory pathways contributes to the maintenance of their leukemic state and can be exploited as cell-intrinsic, self-directed immunotherapy. To this end, we applied genome-wide screens to discover genetic vulnerabilities in acute myeloid leukemia (AML) cells implicated in inflammatory pathways. We identified the immune modulator IRF2BP2 as a selective AML dependency. We validated AML cell dependency on IRF2BP2 with genetic and protein degradation approaches in vitro and genetically in vivo. Chromatin and global gene-expression studies demonstrated that IRF2BP2 represses IL1β/TNFα signaling via NFκB, and IRF2BP2 perturbation results in an acute inflammatory state leading to AML cell death. These findings elucidate a hitherto unexplored AML dependency, reveal cell-intrinsic inflammatory signaling as a mechanism priming leukemic blasts for regulated cell death, and establish IRF2BP2-mediated transcriptional repression as a mechanism for blast survival.

SIGNIFICANCE

This study exploits inflammatory programs inherent to AML blasts to identify genetic vulnerabilities in this disease. In doing so, we determined that AML cells are dependent on the transcriptional repressive activity of IRF2BP2 for their survival, revealing cell-intrinsic inflammation as a mechanism priming leukemic blasts for regulated cell death. See related commentary by Puissant and Medyouf, p. 1617. This article is highlighted in the In This Issue feature, p. 1599.

Abstract P5-01-02: Single cell RNA transcriptomics reveals tumor promoting mammary cell subpopulation upon replication stress in BRCA1 mutant breast cancer mouse model

Women with BRCA1 (B1) mutation have an exceptionally high risk of developing breast cancer. The only effective preventive strategy currently offered to these women is the life altering prophylactic mastectomy. In light of limited treatment options available, it is critical that new therapeutic and preventive strategies be identified. Design of such strategies requires an understanding of early events in the breast cells that drive tumorigenesis. B1 heterozygous mouse models can help us identify these early changes in mammary tissue as the cells become tumor cells. However, despite the well-established association between B1 heterozygosity and cancer predisposition in humans, there are currently no such B1 mouse models that faithfully recapitulate this high risk of tumor formation. B1 heterozygous mice are not tumor-prone. This makes it difficult to use these models to study the role of B1 heterozygosity and to identify early tumor promoting changes in the breast tissue. We have now established a mouse model that induces mammary tumors in B1 heterozygous (Brca1wt/flx,Trp53flx/flx,K14cre) mice upon replication stress (RS), thus giving us a tool to study early tumor promoting changes in B1 heterozygous breast tissue. Our approach is based on our published work that reveals haploinsufficiency for RS suppression in B1 heterozygous cells. Given the importance of RS development in tumorigenesis, this effect would be a logical contributor to B1 mutant cancer development. Indeed, increasing RS in B1 heterozygous mice resulted in accelerated mammary tumorigenesis. RS in this mouse model was delivered by injecting DNA-adduct forming 4-nitroquinoline-1-oxide via mammary intraductal injection over a course of 7 weeks. RS served as an efficient and abnormally rapid driver of tumor formation (30 days post completion of injection regimen) in B1 heterozygous, but not B1 wild type mice. B1 heterozygous mice formed mammary adenocarcinoma and ductal carcinoma in-situ. Immunofluorescence based tissue section analysis and transcriptomic analysis reveals that adenocarcinomas formed in B1 heterozygous mice carry a basal epithelial phenotype like those found in human breast cancer. Such an accelerated tumor model system could prove to be invaluable in understanding the earliest events in B1 mutant breast cancer.Furthermore, our scRNAseq-based analysis has revealed early changes that occur in the breast tissue as different cell types (luminal and basal) respond to RS, and have identified new cell populations that emerge exclusively in B1 heterozygous mammary tissue undergoing RS. For this analysis, cells were collected from naïve mammary tissue, tissue collected midway through injections, and post-tumor tissue. This analysis identified a unique population of trans-differentiated cells expressing prognostic markers that have correlation to poor outcome in human breast cancer. This RS-induced mammary cell population in B1 heterozygous tissue also expresses both luminal progenitor and basal epithelial markers. Interestingly, this population was enriched for proliferation markers like Top2a, Ube2c, mKi67, and Ccnb2. Given that such proliferation markers are a hallmark of cancer stem cells, we suspect that this transdifferentiated population, which is primarily enriched in B1 heterozygous mammary tissue undergoing RS, marks some of the early cancer promoting changes in the breast tissue.Altogether, our integrative approach reveals that B1 heterozygosity in combination with RS leads to accumulation and proliferation of a specific mammary cell population that contributes to breast tumorigenesis. Identification of such early drivers is critical for the design of effective preventive and therapeutic strategies for women with B1 mutation.

Citation Format: Shailja Pathania, Joshua Rivera, Delan Khalid, Monica Manne, Stevenson Tran, Kemmie Kibaja, Carman MC Li, Joan Brugge. Single cell RNA transcriptomics reveals tumor promoting mammary cell subpopulation upon replication stress in BRCA1 mutant breast cancer mouse model [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-01-02.

Abstract B36: Tracking the path of breast tumorigenesis in BRCA1 mutant breast cancer

Women with mutations in breast cancer (BrCa) gene BRCA1 are highly predisposed to BrCa. In these families, cancer develops almost exclusively in females and often at very young ages. The molecular pathogenic steps, especially the earliest ones that drive the transition of normal mammary epithelial cells (BRCA1mut/+) to tumor cells, are largely unknown. Mouse model-based studies have not successfully addressed this question, in part because, unlike women with BRCA1 (B1) mutations, B1 heterozygous mice do not form mammary tumors any faster than the wild-type (wt) mice. A mouse model that can biologically mimic what is happening in the mammary tissue of B1 mutation carriers would be an invaluable tool to study B1 mutant BrCa. Furthermore, most of the efforts to study breast tumor-associated gene changes have been based on GWAS studies or RNA-seq based analysis of the breast tumor samples. Such studies have shown that the transcriptional network is altered in the breast tumors compared to wild-type tissue. However, whether those changes are tumor initiating, i.e., “driver” changes, or are “passenger” mutations/changes is still not clear. Given the role of B1 in suppressing replication stress (RS), a tumor-promoting event, and the increased RS observed in B1 heterozygous cells, we have established an RS-driven B1 BrCa mouse model to study the early genetic changes that drive B1 mutant cancer. We find that intraductal injections of 4-nitroquinoline-1-oxide (4NQO1, a replication stress-inducing agent) leads to breast adenocarcinoma in B1flx/wt;Trp53flx/flx,K14Cre mice on average 84 days post injections unlike B1 wt mice that do not make tumors. This is the first RS-induced BrCa model that can successfully recapitulate B1 mutant BrCa. The fast timeline of tumor formation provides significant advantage for studying tumor formation, progression, and response to therapy. Furthermore, single-cell RNA sequencing analysis of the breast adenocarcinoma and tissue collected early during injections in these mice has revealed presence of a highly proliferative “transdifferentiated population” that shares properties of both luminal and basal cells (e.g., K8+K18+) and also exists in the hyperplastic tissue. No such population was found in control PBS injected mammary fat pad of B1flx/wt;Trp53flx/flx,K14Cre mice, indicating that this population might be dependent on RS. We also find that this population is enriched very early during mammary tumorigenesis and some of the top hits include cancer stem cell markers. We have also confirmed the presence of this population by immune histochemistry-based experiments. Finally, our study provides evidence for a BrCa mouse model where basal-like tumor formation is driven by RS. We also found evidence for an early precancerous transdifferentiated population that is enriched upon RS and have identified early markers that can potentially drive breast tumorigenesis in B1 mutant BrCa. Identification of such candidate genes is critical in the design of future preventive and/or therapeutic strategies.

Citation Format: Joshua Rivera, Delan Khalid, Stevenson Tran, Kemmie Kibaja, Shailja Pathania. Tracking the path of breast tumorigenesis in BRCA1 mutant breast cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr B36.