👤 Alexander M Gout

Oncogenic fusions formed through chromosomal rearrangements are hallmarks of childhood cancer that define cancer subtype, predict outcome, persist through treatment, and can be ideal therapeutic targets. However, mechanistic understanding of the etiology of oncogenic fusions remains elusive. Here we report a comprehensive detection of 272 oncogenic fusion gene pairs by using tumor transcriptome sequencing data from 5190 childhood cancer patients. We identify diverse factors, including translation frame, protein domain, splicing, and gene length, that shape the formation of oncogenic fusions. Our mathematical modeling reveals a strong link between differential selection pressure and clinical outcome in CBFB-MYH11. We discover 4 oncogenic fusions, including RUNX1-RUNX1T1, TCF3-PBX1, CBFA2T3-GLIS2, and KMT2A-AFDN, with promoter-hijacking-like features that may offer alternative strategies for therapeutic targeting. We uncover extensive alternative splicing in oncogenic fusions including KMT2A-MLLT3, KMT2A-MLLT10, C11orf95-RELA, NUP98-NSD1, KMT2A-AFDN and ETV6-RUNX1. We discover neo splice sites in 18 oncogenic fusion gene pairs and demonstrate that such splice sites confer therapeutic vulnerability for etiology-based genome editing. Our study reveals general principles on the etiology of oncogenic fusions in childhood cancer and suggests profound clinical implications including etiology-based risk stratification and genome-editing-based therapeutics. Show less

Adenovirus penton base protein is involved in virus internalization. Searching for the cellular partners of this protein, we used dodecahedra, adenovirus subviral particles composed of 12 bases, for screening a human lung expression library. This screen yielded three ubiquitin-protein ligases, WWP1, WWP2, and AIP4, all of which belong to the HECT family and contain multiple WW domains. The xPPxY motif, known to interact with WW domains in partner proteins occurs twice in the N-terminal part of the base polypeptide chain. The recruitment of three ubiquitin-protein ligases was shown for two distinct virus serotypes, Ad2 and Ad3. The first N-terminal xPPxY motif in the base protein sequence is indispensable for the interaction. The association in vitro was shown by the protein overlay technique and in vivo by cotransfection followed by immunoprecipitation. The binding parameters studied by surface plasmon resonance confirmed the interaction of base protein with three ubiquitin-protein ligases. In case of WWP1 when the saturation of binding was achieved, the apparent dissociation constant of 65nM was calculated. This is the first demonstration of the interaction of nonenveloped viruses with ubiquitin-protein ligases of host cells. Show less