Modeling and targeting of erythroleukemia by hematopoietic genome editing

Abstract

Acute erythroid leukemia (AEL) is characterized by distinct morphology, mutational spectrum, a lack of preclinical models and poor prognosis. Here, using multiplexed genome editing of mouse hematopoietic stem and progenitor cells and transplant assay, we developed preclinical models of AEL and non-erythroid acute leukemia and demonstrated the central role of mutational cooperativity in determining leukemia lineage. Different combination of mutations in Trp53, Bcor, Dnmt3a, Rb1 and Nfix resulted in the development of leukemia with erythroid phenotype, and were accompanied by the acquisition of alterations in signaling and transcription factor genes that recapitulate human AEL by cross-species genomic analysis. Clonal expansion during tumor evolution was driven by mutational co-occurrence, with clones harboring a higher number of founder and secondary lesions (e.g. mutations in signaling genes) showing greater evolutionary fitness. Mouse and human AEL exhibited deregulation of genes regulating erythroid development, notably Gata1, Klf1, and Nfe2, driven by the interaction of mutations of the epigenetic modifiers Dnmt3a and Tet2 that perturbed methylation and thus expression of lineage-specific transcription factors. The established mouse leukemias were used as platform for drug screening. Drug sensitivity was associated with the leukemia genotype, with the PARP inhibitor talazoparib and the demethylating agent decitabine efficacious in Trp53/Bcor mutant AEL, CDK7/9 inhibitors in Trp53/Bcor/Dnmt3a mutant AEL and gemcitabine and bromodomain inhibitors in NUP98-KDM5A leukemia. In conclusion, combinatorial genome editing has demonstrated the interplay of founding and secondary genetic alterations in phenotype and clonal evolution, epigenetic regulation of lineage-specific transcription factors and therapeutic tractability in erythroid leukemogenesis.

BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes

“…Among these six PRC1 subcomplexes, PRC1.1 is most frequently mutated across solid and hematologic cancers. PRC1.1 alterations most commonly involve BCOR and BCORL1 and these genes are reported to be mutated in 5-10% of patients with acute myeloid leukemia (AML) and are associated with poor clinical outcomes (5)(6)(7)(8)(9)(10)(11)(12). In chronic myeloid leukemia (CML), which is driven by the BCR-ABL fusion oncogene, BCOR mutations have been linked to advanced disease and clinical resistance to BCR-ABL-targeted inhibitors (10).…”

Benchmarking Single-Cell mRNA–Sequencing Technologies Uncovers Differences in Sensitivity and Reproducibility in Cell Types With Low RNA Content

“…The SS2 protocol, [6] which was updated recently by the release of the SS3 protocol, [4] and Takara Bio's SMART-Seq technology are the most widely used methods in the scientific community to generate in-depth characterization of the transcriptome at the single-cell level. The goal was to compare the performance between these homebrew protocols and commercial methods.…”

“…In particular, single-cell RNA-seq (scRNA-seq) can provide cell identification in heterogeneous cell types and pinpoint the regulators of cell function, such as in the mammalian brain, [3] or the presence of specific mutations in diseases like cancer. [4] There are 2 main technologies used for scRNA-seq: droplet and full-length sequencing.…”

DNA Methylation Malleability and Dysregulation in Cancer Progression: Understanding the Role of PARP1

“…AML and acute lymphoblastic leukemia (ALL) have been both reported to have genomic alternations of PARP1 and compromised DNA-damage-response gene pathways. AML carries RUNX1-RUNX1T1 (transcription factor involved in the differentiation of hematopoietic stem cells into adult blood cells) fusion genes with functional deficiency in TET2 and DNMT3A genes [219], while TET1 is highly sensitive to PARP1 inhibitors in ALL patients, as shown in different clinical studies [206]. By reversion of mutations in BRCA1/2 genes, breastand ovarian-cancer cells become resistant to PARP inhibitors [220][221][222].…”