Aggressive leukemias can be driven by so-called fusion oncoproteins. Within cells, these proteins can accumulate in biomolecular condensates - dynamic, membrane-less structures in which different biomolecules interact to influence gene activity. Until now, however, little was known about which RNA molecules are involved in these "oncocondensates." "With the bicon-seq method we have developed, we can now systematically identify which RNAs are associated with biomolecular condensates. This makes a previously difficult-to-access layer of gene regulation measurable," explains Florian Grebien, senior author of the study and head of the Unit of Medical Biochemistry at the University of Veterinary Medicine Vienna.
A Central Research Focus: RNA as a Component of Oncocondensates
The current study focused on the fusion oncoprotein NUP98::KDM5A. This protein occurs in aggressive forms of AML and promotes the formation of condensates in leukemia cells that are required for the activation of leukemia-relevant genes.
The new bicon-seq analytical method provides quantitative information on the cellular solubility of RNA molecules. According to the researchers, changes in this parameter indicate whether an RNA is more strongly or more weakly associated with biomolecular condensates. "Importantly, this approach does not merely provide a snapshot. We can track how the RNA composition of condensates changes when key components are specifically disrupted or depleted," says Melanie Allram, first author of the study.
The lncRNA Gas5 Plays a Key Role in Leukemia Cell Proliferation
The analyses identified several long non-coding RNAs (lncRNAs) associated with NUP98::KDM5A oncocondensates. The lncRNA Gas5 was particularly notable: it was highly expressed in AML cells, co-localized with NUP98::KDM5A in condensates, and proved to be important for the proliferation of leukemia cells.
When Gas5 was specifically downregulated using CRISPRi - a method for targeted suppression of gene expression - the gene activity of AML cells changed substantially. Among the affected genes were those involved in differentiation and programmed cell death. "This shows that the Gas5 lncRNA is not only a component of these condensates, but can also influence their function," emphasizes Melanie Allram.
A New Method for Investigating the RNA Biology of Condensates
The study describes a new experimental approach for investigating biomolecular condensates. Florian Grebien explains: "bicon-seq enables us to quantitatively characterize the RNA composition of these structures under both normal and perturbed conditions. This opens up new opportunities to investigate the role of RNAs in regulating disease-relevant condensates."
The findings underscore the importance of non-coding RNAs for the function of fusion oncoproteins. Further studies by the Grebien Lab will now examine in greater detail how the interaction between Gas5 and the NUP98::KDM5A fusion protein affects gene activity and leukemia development.
