Shebl, B. | Search bioRxiv

bioRxiv2025

Specific degrader for fusion oncokinase kills tumors and is augmented by bimodal degrader-siRNA

Oncogenic fusions of two native proteins are challenging to block without disturbing the parental proteins. A mRNA delivered peptide degrader, selectively eliminates the oncogenic fusions DNAJB1::PRKACA and ATP1B1::PRKACA in fibrolamellar carcinoma (FLC), cholangiocarcinoma and intraductal pancreatic neoplasm, without effect on native PRKACA. Specific degradation reflected structural properties of the fusion proteins. The degrader was lethal to FLC tumor cells in a preclinical model, with no effect on non-FLC cells. To enhance efficacy and speed, we modified the mRNA to simultaneously encode the degrader and an siRNA against the fusion transcript, reducing new protein synthesis which accelerated degradation of DNAJB1::PRKACA, offering a wide therapeutic index for mutation-driven disease.

cancer biology↗

bioRxiv2024

The influence of downstream structured elements within mRNA on the dynamics of intersubunit rotation in ribosomes

Proper codon/anti-codon pairing within the ribosome necessitates linearity of the transcript. Any structures formed within a messenger RNA (mRNA) must be unwound before the respective codon is interpreted. Linearity, however, is not always the norm; some intricate structures within mRNA are able to exert unique ribosome/mRNA interactions to regulate translation. Intrinsic kinetic and thermal stability in many of these structures are efficient in slowing translation causing pausing of the ribosome. Altered translation kinetics arising from atypical interactions have been shown to affect intersubunit rotation. Here, we employ single-molecule Forster Resonance Energy Transfer (smFRET), to observe changes in intersubunit rotation of the ribosome as it approaches downstream structured nucleic acid. The emergence of the hyper-rotated state is critically dependent on the distance between downstream structure and the ribosome suggesting interactions with the helicase center are allosterically coupled to intersubunit rotation. Further, molecular dynamics (MD) simulations were performed to determine ribosomal protein/mRNA interactions that may play a pivotal role in helicase activity and ultimately unwinding of downstream structure.

biophysics↗