29. When amplification meets gene fusion: Molecular characterization of PPP1CB-ALK fusion and amplification in pediatric HGG

      Anaplastic lymphoma kinase (ALK) is a well-known proto-oncogene. Different mechanisms leading to constitutively activated ALK protein have been reported, such as chromosomal rearrangements creating ligand-independent ALK chimeric protein and gene amplification resulting in overexpression of ALK. However, ALK rearrangement and amplification rarely co-exist in the same tumor. Here we report a high-grade glioma with PPP1CB-ALK fusion and amplification of the fusion gene. PPP1CB-ALK, which juxtaposed exon5 of PPP1CB with exon20 of ALK, and fusion gene amplification were identified by CHOP Comprehensive Solid Tumor Panel and confirmed by qPCR and FISH. Immunohistochemistry stain confirmed the overexpression of ALK protein. Taking advantage of the amplification only involving fused genes, we narrowed the breakpoints in both genes to a ∼700bp region and identified the genomic sequence of the fusion encompassing parts of PPP1CB intron5 and ALK intron19 along with a 7-bp linker in between. Multiple qPCR studies showed that four genes close to PPP1CB were amplified along with the fusion gene and the remaining genes between PPP1CB and ALK were copy neutral, suggesting that the PPP1CB-ALK fusion resulted from an inverted insertion of 5′PPP1CB into ALK, with subsequent episomal amplification. Compared to the few PPP1CB-ALK positive brain tumors reported, this patient, who died 2-days after birth, had a much poorer outcome, probably due to the synergistic effect of ALK rearrangement and amplification. Molecular characterization of the fusion suggested a possible fusion formation mechanism and provided genomic evidence supporting the therapeutic value of ALK inhibitors.
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