Characterization of Nut Gene Translocation in Midline Carcinoma

NUT-rearranged carcinomas are a family of related cancers involving chromosomal translocation and fusion of NUT to another gene, most commonly BRD4. BRD4-NUT carcinomas account for 2/3 of the cases and NUT-variants carcinomas constitute the remaining. Most of these highly lethal and therapy resistant carcinomas arise along the midline region, mainly in the upper respiratory tract. The NUT-variant carcinoma under study, which arose within the mid-abdomen in a 2 year old boy, is characterized by a translocation between chromosomes 1 and 15, t(1;15). The plasma membrane localization of the NUT-variant protein is unusual, as all other known NUT-fusion proteins localize to the nucleus. Identification of the variant partner to NUT may provide insight into the oncogenic function of NUT fusion proteins. Based on precedent, it is predicted that NUT is the 3' partner in this NUT-variant. Thus, the promoter is typically donated by the 5' fusion partner. PTPRU is hypothesized to be the 5' partner because it is one of the closest genes to the breakpoint in chromosome 1p35.3, and because it is the only membrane protein encoded within the breakpoint region. RT-PCR, Western Blotting, FISH & RACE techniques were performed to determine and characterize the variant fusion partner to NUT. Western Blotting revealed that the 215kDa NUT-variant protein is 35kDa smaller than BRD4-NUT, and 50kDa larger than NUT. FISH and RT-PCR suggest that neither BRD4 nor PTPRU are involved in this case. The NUT-variant is most probably a fusion protein, but the partner to NUT still needs to be characterized by additional RACE.