P739: THE EPI-GENOMIC LANDSCAPE OF MONOSOMY 7 IN ADULT MDS/AML

Abstract

Background: Monosomy 7 is one of the most frequent aneuploidies in myeloid malignancies often occurring in the context of high-risk Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML) and associated to poor prognosis. Despite several studies have focused on the pathogenetic role of genes mapping at chromosome 7q, its molecular landscape remains undetermined. Aims: The aim of this study was to characterize biological features of adult MDS/AML with isolated monosomy 7 by investigating the epi-genomic landscape. Methods: Epi-genomic characterization included karyotype, Fluorescent In Situ Hybridization (FISH), Single Nucleotide Polymorphism Array (SNPa), Targeted Genomic Sequencing, RNA sequencing and multiplex Enhanced Reduced Representation Bisulfite Sequencing (mERRBS). This comprehensive approach was used in analyzing a cohort of three adult MDS/AML cases with isolated monosomy 7 against a cohort of three non-neoplastic cytopenias and against dic(1;7)(q10;p10) cases previously characterized by our group (Leukemia, 2019). Results: Karyotype identified the presence of isolated monosomy 7 in all cases, interphase-FISH showed clonality as accounting for 65-85% of the total bone marrow population. Targeted sequencing showed multiple variants affecting myeloid genes (mean 5.3 events; from 2 to 9 per case) but did not identify a common mutational marker. Gene expression profile (FDR<0.1, log2FC>I1I) provided us with a specific signature differentiating monosomy 7 from both controls [632 differentially expressed genes (DEGs): 405 up and 227 down] and dic(1;7) [1.706 DEGs: 832 up and 874 down]. In keeping with monosomy, a strong gene dosage effect at chromosome 7 genes emerged. Functional pathways analysis specifically identified the presence of active stemness programs in monosomy 7, through deregulation of mTOR pathway, Rho-GTPases and hematopoietic stem cell markers. Deregulation of genes involved in apoptosis escape, included in TP53 and heat-shock proteins signaling, supported the undifferentiated phenotype. Interestingly, PTCH1 tumor suppressor downregulation was a differential feature of monosomy 7 with respect to the other groups and it was validated in an independent cohort of MDS/AML with isolated monosomy 7. Global methylation further delineated specific boundaries between monosomy 7 and dic(1;7) cases showing a methylation gradient that defined monosomy 7 as the most hypermethylated group. Private localization of differentially methylated regions in monosomy 7 emerged at intergenic enhancers, enriched for homeo-domain transcription factors binding sites, and at CTCF binding sites linked to promoters. A subset of hypermethylated enhancers in monosomy 7 was in accordance with repression of their respective target genes, almost totally located on chromosome 7 (ARPC1A, CCZ1, IKZF1, PMS2, RBAK, RBM33, RHEB, RNF216P1, ZNF12 and ZNF853). Their downregulation was related not only to the chromosome loss but also to the effect of enhancer hypermethylation in the retained chromosome, supporting a combined cytogenetic and epigenetic mechanism in determining biallelic deregulation. Among these deregulated genes, IKZF1 and its target genes accounted for > 6% of the whole typical expression profile. Summary/Conclusion: In conclusion our results first identified a specific signature of DNA methylation and an active epi-genomic program reminiscent of stem cells in MDS/AML with monosomy 7, providing new insights to the knowledge of biological targets in this aggressive aberration.