Abstract 3749: Mapping the DNA accessibility landscape of BCP-ALL patients revealed principles of tumor evolution

Abstract

Abstract Pediatric B-Acute Lymphoblastic Leukemia (B-ALL) is the primary cause of death from hematological disease in children. Despite the enormous improvement of treatments based on innovative immunotherapy, applications of new approaches constitute a significant emergency in clinical practice. We have built the most extensive map of the accessibility landscape of 35 B-Cell Precursor ALL (BCP-ALL) to date. We integrated this map with a plethora of transcriptomic and epigenomics pan-cancer profiles to define the key determinant of BCP-ALL post-therapy relapse. We show that chromatin accessibility dynamics play a major regulatory role in BCP-ALL heterogeneity and sustain disease evolution. We have analyzed a large cohort of tissues from healthy donors (N=6) and BCP-ALL patients at time of Primary onset (N=11), Remission (N=7),or Relapse (N=9. We generated genome-wide accessibility profiles using the Assay for Transposase- Accessible Chromatin (ATAC-seq) at the coverage of 50-60 million reads of each sample. We observed that regulatory elements are strongly associated with epigenetic heterogeneity, but dominant elements have a higher chance of being shared across patients. By differential analysis of chromatin layout between healthy profiles and primary tissues, we identified 688 regulatory regions being deactivated and 758 activated during cancer early stages. Interestingly, novel activated sites recapitulate B-ALL characteristics interrogating the Disease Ontology database and gene ontology (Pval< 10-5). Relapsed patients are dominated by regulatory elements (N=~6000)originally represented at diagnosis that shrinks undertreatments and subsequently re-expand, driving the relapse. HiC maps, H3K27ac, and H3K4me1 ChIP-seq experiments integrated with chromatin maps obtained from ENCODE, GTEX, TCGA, and transcriptomic data generated by the TARGET project confirm that a large percentage of these elements are high fidelity active enhancers. The activity of these enhancers increases the risk of relapse significantly. Particularly, DCTD, MYB, and BCL2 genes are actively regulated by a set of plastic enhancer elements characterized with experimental and computational approaches. We gained insights into the role ofthe DCTD gene regulation using CRISPR-Cas9-mediated deletion of the DCTD-enhancer, leading to decreased level of DCTD gene mRNA of 40% accompanied by acell proliferation reduction of 30%. Next, we characterized the cistrome landscape of our patient cohort at accessible sites relative to the disease status. Foot printing analysis suggested ERG and EBF transcription factors (TFs) as a fundamental player in sustaining the activity of the most dynamical enhancers. In conclusion, chromatin accessibility shifts can be used to trace phenotypic changes throughout the journey of BCP-ALL patients and provide novel insights in targeting cancer phenotypical modulators. Citation Format: Giacomo Corleone, Cristina Sorino, Matteo Caforio, Stefano Di Giovenale, Francesca De Nicola, Valentina Bertaina, Angela Pitisci, Franco Locatelli, Maurizio Fanciulli, Valentina Folgiero. Mapping the DNA accessibility landscape of BCP-ALL patients revealed principles of tumor evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3749.