AKAP95 condensates regulate transcription and can be targeted in MLL-fusion driven oncogenesis (CLIP-Seq)

Oncogenic transcription represents a crucial event in MLL rearranged (MLLr) leukemia, yet the precise role of transcription co-activators in MLL-fusion protein-associated transcription and their contribution to leukemogenesis remain incompletely understood. Here, we demonstrate that AKAP95 is notably up-regulated in both MLLr patients and in MLL-AF9-transformed mouse bone marrow. AKAP95 proves essential for initiating mouse MLL-AF9 leukemia, exhibiting widespread DNA binding across the genome, particularly at gene promoters. Interaction with the translocated MLL1 fragment primarily occurs through phase separation mechanisms. AKAP95's RNA-binding properties, coupled with its phase separation behavior, govern its binding to pre-mRNA and concurrent transcriptional regulation. Importantly, we engineered a peptide to disrupt its phase separation, effectively attenuating AKAP95-mediated transcriptional co-activation and inhibiting the growth of MLLr cell lines. These findings illustrate a vivid example of an RNA-binding protein orchestrating transcription and tumorigenesis via phase separation, underscoring the potential for targeting oncogenic condensation mechanisms therapeutically. Overall design: Flag-mEGFP was knocked into the N-terminus of the AKAP95 locus in HeLa cells to tag the endogenous AKAP95. Lentiviruses pLKO.1-shAKAP95, pCDH-CMV-HA-JD-PI95-puro, and pCDH-CMV-HA-H32Q-PI95-puro were packaged in 293T cells with the envelope plasmids psPAX2 and pMD2.G. One million HeLa cells were transduced with 200 µL of concentrated virus by spin infection at 1000 × g for one and a half hours. Overexpression of wild-type AKAP95 and phase separation mutants was performed in HeLa cells to establish the significance of AKAP95's phase separation ability in promoting tumorigenesis. The binding targets of AKAP95 in pre-mRNA were determined by CLIP-seq.