Identification and Functional Significance of Aberrant Long Non-coding RNAs in Acute Myeloid Leukemia : Biological and Prognostic Implications

Abstract: Acute myeloid leukemia (AML) is the most frequently diagnosed type of acute leukemia in adults. It commonly affects people aged 60 or older, as incidence increases with age, and it is characterized by the accumulation of immature hematopoietic progenitor cells in the bone marrow. Despite recent treatment advances and improvements for certain subtypes, as acute promyelocyte leukemia (APL), AML remains difficult to cure. While many patients reach remission after induction treatment, relapses are common and 5-year overall survival remains dismal. Long non-coding RNAs (lncRNAs) are involved in various regulatory cellular functions and, like coding genes, they are frequently dysregulated in cancer. In this thesis, the aim was to elucidate the functional implications of lncRNAs in the biology and treatment response of AML and normal hematopoiesis in order to improve understanding of AML pathology. In Paper I, whole-transcriptome sequencing identified the novel lncRNA MALNC. Clinical correlation analyses and CRISPR-knockout cell models were used to functionally explore its implications in AML. It was identified that enhanced MALNC expression is specifically associated with the AML-subtypes APL and AML with co-mutant NPM1/IDH2R140. Further, it was shown that MALNC is implicated in key factors of leukemogenesis, like differentiation and proliferation, and that MALNC expression associates with better overall survival in AML patients. Moreover, knockout of the MALNC gene sensitized AML cells to arsenic trioxide (ATO), all-trans retinoic acid (ATRA)-ATO combination and venetoclax treatment. In Paper II, three high-throughput functional CRISPR interference screens were performed to identify lncRNAs implicated in proliferation, differentiation or venetoclax response. Several novel lncRNAs were identified to potentially play a positive or negative role in these processes and furthermore were found to implicate AML prognosis. In Paper III, the lncRNA NEAT1 was studied in respect to its role in normal hematopoiesis and AML using CAGE- and RADICL-sequencing. It could be illustrated that NEAT1 expression positively correlates with cell maturity during normal hematopoiesis, in particular monocytes, and associates with core-binding factor AML inv(16) and t(8;21). Further, RADICL-sequencing identified that lncRNA NEAT1 binds to the genomic loci of key hematopoietic transcription factor RUNX2. In contrast to solid cancers, it was demonstrated, that higher NEAT1 expression correlated with better outcome in AML, independent of known risk factors. In summary, these studies have outlined the scope of functional implications of lncRNAs in normal and dysregulated hematopoiesis and have highlighted their potential roles as biomarkers for prognosis and drug sensitivity. These findings support the efforts to understand how lncRNAs could serve as novel biomarkers for personalized treatment.