Molecular Interrogation and Functional Studies of Acute Leukemia

Abstract: Hematological malignancies are defined by their underlying genetic alterations, many of which are used to diagnose patients to classify them to different risk groups that dictate the therapy given. Recent advances in high-throughput sequencing have highlighted the presence of co-occurring genetic lesions and that they may form distinct genetic clones that evolve throughout disease progression. Acute leukemia is a group of diseases affecting either the lymphoid or myeloid lineage in hematopoiesis, resulting in acute lymphoblastic leukemia (ALL) or acute myeloid leukemia (AML). Certain genetic alterations are closely tied to specific leukemia types, while others are more promiscuous. In this thesis, we have used high-resolution genome-wide methods and murine models to study leukemia as a way to increase our knowledge how leukemia arises and best can be treated.In the first study (Article I) we characterized the genetic alterations in a case presenting with a rare myelodysplatic/myeloproliferative neoplasm, unclassifiable (MDS/MPN-U) that later progressed to AML. Through comprehensive analyses of the MDS/MPN-U and AML samples, we observed that all genetic lesions detected at AML diagnosis were present already at the MDS/MPN-U stage, likely in a similar clonal composition. Further, targeted drug analysis of the AML sample suggested clinically approved drugs from which the patient could benefit at a potential relapse.Genetic rearrangements of the epigenetic regulator KMT2A (KMT2A-R) often co-occur with activating mutations in genes involved in intracellular signaling. In the second study (Article II) we show that mutations in FLT3 and NRAS significantly accelerate KMT2A-R driven AML onset, even when present in a subclone as exemplified by the FLT3N676K mutation. The presence of an activating mutation affected the leukemias transcriptional profiles by further enhancing transcriptional programs previously associated with KMT2A-Rs. Genomic characterization of mouse leukemias unveiled de novo signaling mutations in several mice harboring only a KMT2A-R, emphasizing the importance of such mutations in KMT2A-R leukemogenesis. KMT2A-Rs occur in both ALL and AML but the molecular and/or biological mechanisms determining the lineage affiliation remain largely elusive for this disease. In the third study (Article III) we demonstrated the that FLT3N676K promote myeloid expansion of KMT2A-R leukemia in primary human cells. We further showed that established KMT2A-R ALL and AML cells displayed expression profiles closely linked to their respective lineage but that these cells still display a certain immunophenotypic plasticity.Previously, a large portion of pediatric B-cell precursor ALL (BCP-ALL) patients could not be classified to any of the established molecular subtypes. Chromosomal alterations are a hallmark of BCP-ALL and in the last study (Article IV) we employed high-throughput sequencing to define the fusion gene landscape of 195 pediatric BCP-ALL. Besides identifying several novel in-frame fusion genes, we also described two new oncogenic leukemia subtypes. These two subtypes were associated with distinct genetic lesions, including genetic rearrangements of the DUX4 gene and genetic alterations of ETV6 and IKZF1. Taken together, the work included in this thesis highlights the major impact that specific genetic alterations have on leukemogenesis, and how their autonomous and non-autonomous cooperation influence clonal evolution, disease phenotype, and molecular profiles of the leukemia.