Small-molecule-mediated targeting of oncogenic condensates

The spatial organization of human cells is essential for their function. A key principle of this organization is the formation of biomolecular condensates. Biomolecular condensates are membrane-less, liquid-like compartments that act as biochemical workshops where proteins and nucleic acids are concentrated to regulate processes such as gene expression and signal transduction. In many cancers like some aggressive leukemias, this organizational system is disrupted, as cancer- driving proteins can hijack the formation of biomolecular condensates to induce the formation of abnormal condensates that promote oncogenic programs. The SMOC project investigates NUP98-fusion-driven leukemia, a blood cancer of children that is characterized by therapy resistance and poor prognosis. It is driven by fusion oncoproteins containing intrinsically disordered regions (IDRs). These flexible protein segments act as molecular adhesives, assembling abnormal condensates in the nucleus of cancer cells. These pathological droplets misdirect the transcriptional machinery to incorrect genomic sites, triggering uncontrolled growth. Because these NUP98 fusion oncoproteins lack a stable structure, they have long been considered undruggable. Our preliminary work revealed an unexpected opportunity: we identified four drug candidates that act as condensate localizers. Instead of destroying the NUP98 oncoprotein, they alter the physical properties of the condensates and displace the cancer driving proteins from their active sites. The SMOC project now aims to uncover the molecular mechanisms behind this displacement. To achieve this, we combine a broad range of cutting-edge methods. Super-resolution microscopy (STED) and fluorescence lifetime imaging (FLIM-FRET) allow us to study the internal dynamics and material properties of the cancer-associated droplets in living cells. Using proximity labelling coupled to Mass Spectrometry (BioID), we map the molecular neighbourhood of NUP98 fusion oncoproteins to determine which interaction partners are lost when the oncoprotein condensates are perturbed. The project will also focus on the functional analysis of the epigenomic landscape. With sensitive sequencing approaches such as SLAM-seq, we measure how quickly oncogenic gene production stops once onco-condensates are disrupted. CUT&Tag profiling reveals how chromatin marks change when the cancer-driving fusion oncoprotein is displaced, helping us understand how normal gene regulation is restored. A crucial part of the project is testing therapeutic selectivity. We examine whether the treatment specifically targets oncogenic condensates while sparing other biomolecular condensates that essential for cellular functions, such as nucleoli or P-bodies. By clarifying how spatial organization in the nucleus can be therapeutically manipulated, this project may open the door to a new cancer treatments that target aberrant biomolecular condensates in leukemia.