Identifying molecular signatures associated with aging in myeloid malignancies

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Neelamraju, Yaseswini, Biochemistry and Molecular Genetics - School of Medicine, University of Virginia
Garrett-Bakelman, Francine, Department of Biochemistry and Molecular Genetics, University of Virginia

The average life span of individuals is increasing across the globe. Leukemia is one of the major causes of the global tumor burden among hematological malignancies with incidence rates positively correlated with age. The work presented in this dissertation is focused on one of the aggressive myeloid malignancies – acute myeloid leukemia (AML) and its antecedent disorder in approximately 25% of diagnosed cases - myelodysplastic neoplasms (MDS) both with a median age of diagnosis of 69 and 70 years respectively. Although these patients constitute the majority of the diagnosed cases, the treatment options are limited due to associated co-morbidities and a lack of understanding of the disease biology.
To address these gaps, we first utilized multi-omic data obtained at the time of diagnosis from patients over the age of 60(aAML) enrolled in a clinical trial to identify age-specific prognostic molecular signatures. To our knowledge, this is one of the largest cohorts of uniformly treated aAML patients that have been genomically profiled. Using genomic data, we identified a novel group of females prognostically similar to known good-risk NPM1 mutated AMLs (NPMc+). Together these formed a specific subgroup of AMLs (low-risk group) with better survival outcomes than the remaining of the cohort. Bulk RNA-sequencing analysis identified a pro-inflammatory state at the time of diagnosis with higher serum levels of Tumor necrosis factor alpha ( TNFα) and Interferon gamma (IFNγ) and higher transcript levels of Interleukin 1 beta (IL1β). These aAML patients also harbored gene signatures found in venetoclax-resistant patients and patients sensitive to MEK inhibitors and drugs that target mitochondrial metabolism. Furthermore, upregulation of heme synthesis is associated with longer overall survival times coupled with higher expression of the heme oxygenase that degrades excess heme suggesting iron overload in this patient subgroup. We hypothesize that this patient group may harbor the ability to overcome iron overload by triggering ferroptosis which is also shown to sensitize AML cells to chemotherapeutic agents in a previous study. Additional mechanistic and single-cell-based data are essential to validate and deduce further mechanisms. If proven, this will not only help understand the leukemic biology in the low-risk aAML group but also open avenues for identifying therapeutic targets in the remaining cohort with poor survival outcomes by studying the mechanisms or factors inhibiting these processes. In addition to genomics-based prognostication, we also aimed to identify DNA methylation sites predictive of overall survival in this patient cohort. However, the model was not successful in generalizing on unseen data and hence improvements are necessary to build a robust model. Lastly, the thesis also aims to investigate the role of TET2 ( Tet methylcytosine dioxygenase 2 ; one of the most commonly mutated genes in AML and its antecedent disorder, MDS) in contributing to the age-associated development of MDS in a zebrafish model. Loss of tet2 at 4 months of age in hematopoietic stem and progenitor cells (HSPCs) results in the development of a pre-MDS-like state by 15 months and MDS at 22 months. Loss of tet2 was associated with global hypermethylation in 4-month fish; however, tet2 loss resulted in a global hypomethylation at 15 months potentially resulting from the accumulation of mutations in genes such as WT1 or DNMT3A. Additionally, these changes in methylation were observed in the promoters of a subset of PRC2 targets. Further, tet2 loss at 4 months resulted in an upregulation of genes in the interferon response and mtorc1 signaling and a downregulation of genes in the heme metabolism pathways suggesting the requirement of tet2 in mediating these pathways. These changes remained stable during aging in the mutant fish suggesting that tet2 loss serves as an early event in dysregulation of these pathways. However, further single-cell-based assays are warranted to corroborate our findings and delineate mechanisms leading to MDS development and likely progression to AML. In conclusion, the work presented in this dissertation identifies genomic changes contributing to the disease biology in aged AML patients and those resulting in the development of MDS.

PHD (Doctor of Philosophy)
Acute myeloid leukemia, Myelodysplastic syndrome, Aging, Genomics, Machine learning
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