Less than 25% of patients diagnosed with acute myeloid leukemia (AML) survive longer than 5 years. Current treatment regimen are based on non-specifically acting cytotoxic drugs that cause severe side effects. More effective and more specific, targeted therapies are thus needed. Progress, however, has long been hampered by a lack of understanding of the molecular vulnerabilities of the disease. We here propose to identify and study synthetic lethal interactions with mutations in nucleophosmin 1 (NPM1) in AML. Up to 35% of AML patients bear mutations in NPM1 leading to a localization of this nucleolar protein to the cytoplasm and a characteristic change in gene expression pattern. Moreover, NPM1 mutations appear to be driver events and stable over multiple courses of therapy and relapse. Identifying cellular pathways or proteins that are essential in an NPM1 mutated background but not in NPM1 wild type cells may thus not only contribute to a better understanding of NPM1 biology but also yield entry points for the development of drugs that selectively kill NPM1 mutated AML cells. We will take an integrated chemical biology approach to first identify small molecules that selectively kill NPM1 mutated over NPM1 wild type cells and then elucidate their mode of action to gain insight into the underlying biology. This project thus uniquely builds on the longstanding experience of the host laboratory and institute in chemical screening, the elucidation of the mode of action of small molecules and in hematological malignancies. The proposal is designed to complement the experienced researchers current knowledge in chemical synthesis, assay development, solid tumor biology and small animal imaging techniques to become a well-rounded chemical biologist with a disease focus on solid and liquid cancers. The hosting institution will gain from the researcher´s chemical expertise and find opportunities to expand its network of international collaborations.

Aging is a complex biological process that manifests across diverse anatomical scales, from molecules and cells to organs and organisms. Despite the significance of age-associated diseases in affecting quality of life and mortality, our understanding of how cellular-level changes result in tissue-specific loss of function remains incomplete. Several limitations persist: the inability of animal models to fully mirror human physiology, the restricted scope of longitudinal human studies to easily accessible organs, and a prevalent cell-centric focus that overlooks the broader microanatomical context. Additionally, the challenge of uncoupling aging from pathology is exacerbated by the absence of baselines defining healthy aging, hindering the accurate interpretation of alterations. To address these challenges, the proposed project leverages large-scale human tissue imaging datasets and machine learning techniques. Specifically, Aim 1 employs unsupervised learning to systemically quantify and categorize microanatomical structures across 40 human tissues. In a parallel stream, Aim 2 aims to detect and characterize the manifestation of age-associated pathologies in tissue, pinpointing the molecular changes associated with them, across spatial scales. Aim 3 integrates the insights from previous aims, seeking to identify how they contribute to the process of aging and onset of age-associated diseases. Ultimately, this will unearth early predictors of pathology, providing a transformative approach to disease detection and management. This project will not only offer a novel, comprehensive view of human tissue complexity in the context of aging but also challenge the traditional notion that age-associated pathology is merely an aggregation of cellular dysfunctions. By quantifying the interconnected aspects of tissue architecture changes with age, and the manifestation of pathology, we aim to redefine our understanding of the onset of age-associated diseases.

Epigenetics research has revealed that in the cell’s nucleus all kinds of biomolecules–DNA, RNAs, proteins, protein posttranslational modifications–are highly compartmentalized to occupy distinct chromatin territories and genomic loci, thereby contributing to gene regulation and cell identity. In contrast, small molecules and cellular metabolites are generally considered to passively enter the nucleus from the cytoplasm and to lack distinct subnuclear localization. The CHROMABOLISM proposal challenges this assumption based on preliminary data generated in my laboratory. I hypothesize that chromatin-bound enzymes of central metabolism and subnuclear metabolite gradients contribute to gene regulation and cellular identity. To address this hypothesis, we will first systematically profile chromatin-bound metabolic enzymes, chart nuclear metabolomes across representative leukemia cell lines, and develop tools to measure local metabolite concentrations at distinct genomic loci. In a second step, we will then develop and apply technology to perturb these nuclear metabolite patterns by forcing the export of metabolic enzymes for the nucleus, aberrantly recruiting these enzymes to selected genomic loci, and perturbing metabolite patterns by addition and depletion of metabolites. In all these conditions we will measure the impact of nuclear metabolism on chromatin structure and gene expression. Based on the data obtained, we will model for the effects of cellular metabolites on cancer cell identity and proliferation. In line with the recent discovery of oncometabolites and the clinical use of antimetabolites, we expect to predict chromatin-bound metabolic enzymes that can be exploited as druggable targets in oncology. In a final aim we will validate these targets in leukemia and develop chemical probes against them. Successful completion of this project has the potential to transform our understanding of nuclear metabolism in control of gene expression and cellular identity.