Complex structural variations functionally inactivate the telomerase chaperone TCAB1 in osteosarcoma

Activation of the alternative lengthening of telomeres (ALT) pathway accounts for cellular immortalization in 75% of pediatric osteosarcoma. ALT does not rely on a single enzyme but instead, catalyzes telomere elongation via homologous recombination. There has been steady progress in defining the mechanisms that regulate the ALT pathway. However, the spectrum of genetic mutations that underlie activation of ALT remains unclear. Osteosarcomas, like many cancers, frequently harbor inactivating mutations in the tumor suppressor gene TP53. However, instead of single nucleotide variants that lead to expression of mutant TP53 protein, osteosarcoma tumors often acquire unique structural variants (SVs) within the first intron of the TP53 gene leading to complete gene inactivation. TP53 is located on chromosome 17p13.1 in a head-to-head orientation and partially overlapping with the gene WRAP53 (WD repeat containing antisense to TP53). WRAP53, also known as TCAB1, is an RNA chaperone that is an essential component of the telomerase holoenzyme. TCAB1 functions to facilitate trafficking of the telomerase RNA (hTR) within the nucleus to ensure assembly and localization of the telomerase enzyme to telomere ends to promote telomere elongation. Loss of TCAB1 function abolishes telomerase activity, driving progressive telomere attrition. Here, using whole-genome sequencing of osteosarcoma samples we identified SVs within the TP53 gene that not only compromise TP53, but also inactivate TCAB1. These TCAB1 SVs were prevalent in approximately 40% of ALT positive osteosarcoma tumors suggesting that functional inactivation of the telomerase holoenzyme is an early and previously unrecognized event contributing to the activation of the ALT pathway.