<> "The repository administrator has not yet configured an RDF license."^^ . <> . . "Dissecting heterogeneity, clonal evolution, and epigenetic\r\nchanges in distinct and molecularly defined AML subsets\r\nby multi omics single-cell sequencing"^^ . "In acute myeloid leukemia (AML), initiation of tumorigenesis via multiple oncogenic\r\nmutations occurs throughout various stages of hematopoiesis that disrupt the\r\ncorresponding transcriptomic and epigenetic profiles. The cancer cells that emerge are\r\nreferred to as blasts and share biological features from these disease-specific alterations\r\nand patterns associated with differentiation and the tumor cell of origin. The resulting blasts\r\nshow a large inter- and intra-tumor heterogeneity within molecularly defined AML\r\nsubgroups that are highly relevant for risk stratification and personalized treatment\r\nstrategies. Sequencing methods that analyze the transcriptome (scRNA-seq) and epigenome\r\n(scATAC-seq) are ideally suited to resolve tumor cell heterogeneity as well as non-malignant\r\ncell types in the microenvironment. Additionally, scATAC-seq allows to map the binding of\r\ntranscription factors (TF) and infer cell-specific regulatory networks.\r\nHere, I dissected inter- and intra-tumor heterogeneity in patients with different genetic\r\naberrations representing major subgroups in AML, namely MLL fusions, IDH mutated, and\r\nFLT3-ITD rearranged AMLs. I established and adjusted the experimental and bioinformatic\r\nprocedures to generate reproducible and scalable data by scRNA/ATAC-seq of peripheral\r\nblood and bone marrow biopsies from AML patients. I could demonstrate that leukemic\r\ncells could be successfully distinguished from the microenvironment based on marker gene\r\nannotation from the human cell atlas and ploidy inference. Furthermore, I used the\r\nexperimental and data analysis framework to analyze specific molecular features of the\r\nthree AML subgroups.\r\nFirst, I characterized changes in the transcriptome and classified developmental stages of\r\nleukemic cells carrying MLL-EDC4 fusions along the hematopoietic stem cell to the myeloid\r\ntrajectory compared to other MLL fusions. Cell type prediction revealed extensive malignant\r\ncell diversity and a phenotype skewed towards stem- and progenitor-like populations in\r\nMLL-EDC4 leukemic cells. To further elucidate transcriptomic properties of MLL-EDC4 cells,\r\nTF activity was inferred. The results agreed with differential gene expression highlighting\r\nmany TFs that play a critical role in hematopoiesis, endothelial-to-hematopoietic transition,\r\nor leukemic stem cell activation. Second, I developed an approach to resolve the subclone-\r\nspecific response during FLT3 inhibition with midostaurin. Analysis from scRNA and scATAC\r\nV\r\nshowed different FLT3 activity/chromatin signatures within clusters of leukemic cells in the\r\nrelapse that could be explained by midostaurin resistance and the emergence of distinct\r\nsubclones as detected by scDNA-seq. Third, I characterized how the chromatin accessibility\r\nlandscape was influenced by IDH1 mutated cells treated ex vivo with targeted therapy\r\ncompared to IDH1 wild-type cells. Treatment with the IDH1 inhibitor revealed a partially\r\nreversible pattern of accessibility while other mutation-induced epigenetic modifications\r\ncould not be reverted.\r\nThe scRNA-seq data acquired for the three different AML subgroups were then exploited to\r\nperform a cell type prediction analysis. The relative abundance of different malignant cell\r\ntypes discovered varied amongst tumors, with some having just two identities and others\r\nhaving a wide range of malignant cells. MLL fusions, except for MLL-EDC4, generally\r\nconferred a more differentiated phenotype predominantly consisting of\r\nmonocytes/macrophage CD14-like and promonocyte-like cells. Both tumor entities\r\nharboring FLT3-ITDs or IDH1 mutations showed a more complex composition of cell types\r\nalong the myeloid differentiation trajectory than MLL fusions. The composition of cell types\r\nwas generally more skewed to early progenitors at the point of diagnosis when compared to\r\ntheir matching relapse sample. This indicates a partial differentiation of AML cells that\r\ntreatment might induce.\r\nIn summary, this thesis provides novel insights into the tumorigenesis process in AML by\r\nusing a systematic and functional analysis approach of the transcriptome and open\r\nchromatin in single cells for three major genetically defined AML subgroups. A better\r\ncomprehension of cellular hierarchies, epigenetic effects, clonal evolution, and their impact\r\non gene regulation might help to understand disease progression, stratify patient risk, and\r\nhelp to improve the treatment of hematopoietic malignancies in the future."^^ . "2022" . . . . . . . "Linda Christina"^^ . "Schuster"^^ . "Linda Christina Schuster"^^ . . . . . . "Dissecting heterogeneity, clonal evolution, and epigenetic\r\nchanges in distinct and molecularly defined AML subsets\r\nby multi omics single-cell sequencing (PDF)"^^ . . . "Thesis_Schuster_final-1.pdf"^^ . . . "Dissecting heterogeneity, clonal evolution, and epigenetic\r\nchanges in distinct and molecularly defined AML subsets\r\nby multi omics single-cell sequencing (Other)"^^ . . . . . . "indexcodes.txt"^^ . . . "Dissecting heterogeneity, clonal evolution, and epigenetic\r\nchanges in distinct and molecularly defined AML subsets\r\nby multi omics single-cell sequencing (Other)"^^ . . . . . . "lightbox.jpg"^^ . . . "Dissecting heterogeneity, clonal evolution, and epigenetic\r\nchanges in distinct and molecularly defined AML subsets\r\nby multi omics single-cell sequencing (Other)"^^ . . . . . . "preview.jpg"^^ . . . "Dissecting heterogeneity, clonal evolution, and epigenetic\r\nchanges in distinct and molecularly defined AML subsets\r\nby multi omics single-cell sequencing (Other)"^^ . . . . . . "medium.jpg"^^ . . . "Dissecting heterogeneity, clonal evolution, and epigenetic\r\nchanges in distinct and molecularly defined AML subsets\r\nby multi omics single-cell sequencing (Other)"^^ . . . . . . "small.jpg"^^ . . "HTML Summary of #32274 \n\nDissecting heterogeneity, clonal evolution, and epigenetic \nchanges in distinct and molecularly defined AML subsets \nby multi omics single-cell sequencing\n\n" . "text/html" . . . "500 Naturwissenschaften und Mathematik"@de . "500 Natural sciences and mathematics"@en . . . "570 Biowissenschaften, Biologie"@de . "570 Life sciences"@en . .