Condensates in Leukemias

St. Jude Children'S Research Hospital, Memphis TN

Investigators

Abstract

PROJECT SUMMARY - PROJECT 2 Acute leukemias are the most common pediatric malignancy and are broadly defined by their cell lineage into acute lymphoblastic leukemia (ALL) or acute myeloid leukemia (AML). Regardless of lineage, pediatric leukemias are commonly defined by fusion oncoproteins (FOs) that involve transcription factors, epigenetic regulators and tyrosine kinases, many of which are associated with chemotherapy failure and disease relapse. A deeper understanding of the molecular mechanisms that drive aberrant transcriptional activity in FO-driven leukemias has the potential to nominate new therapeutic options for these high-risk leukemias. Our previous efforts focused on NUP98 FOs, a subtype of high-risk pediatric AML, demonstrated that these FOs form biomolecular condensates mediated by intrinsically disordered regions (IDRs) within NUP98 and associations between non-IDR regions and DNA. Further we showed that disrupting this process abrogates hematopoietic cell transformation. While these studies established a causal link between IDRs and other structural features, condensate formation and the potential for hematopoietic cell transformation, the broader importance of FO- mediated condensate formation in cellular transformation, and its relevance to therapeutic targeting across the landscape of pediatric leukemia FOs, is poorly understood. Importantly, our preliminary analyses using a machine learning model trained on physicochemical features of known condensate forming proteins predict that 73% of ALL FOs and 86% of AML FOs will form condensates in cells. These collective preliminary data provide the scientific premise to dissect the mechanistic links between condensate formation and transcriptional deregulation in pediatric acute leukemias. We hypothesize that condensate formation driven by folded domains and IDRs in FOs and associated partner proteins is a central feature of acute leukemia FOs that leads to deregulated transcriptional networks and potential therapeutic vulnerabilities. We will test our hypothesis with the following specific aims using a combination of genetic tools, biochemical strategies and functional genomics. Aim 1 will dissect the impact of FO structural features on transforming potential and chromatin landscapes. Aim 2 will establish the contributions of FO interacting proteins to cellular transformation and condensate formation. Aim 3 will decipher the direct impact of FO IDRs on target gene expression. Not only will the proposed studies elucidate the mechanistic underpinnings of altered transcriptional activity resulting from condensate formation, but they will also nominate potential therapeutic vulnerabilities for pediatric leukemias.