Array comparative genomic hybridization of thymic epithelial tumors identifies loss of CDKN2A as a prognostic factor and BCL2 family members as targets for therapy

Background: Thymic epithelial tumors (TETs) are rare and the genomic aberrations relevant to TET biology are unknown. The goal of this study was to identify recurrent genomic aberrations in TETs. Materials and Methods: From a series of 132 TET resected patients we selected 59 formalin fixed paraffin embedded (FFPE) samples with more than 80% of cancer cells in order to perform high-resolution array-CGH. We used ULS labeling kit (Agilent) and 105A array (Agilent) for 20 and 180K array (Agilent) for 39 samples. For the immunohistochemistry we used a tissue micro-array built from FFPE samples of the 132 patients. The viability assay MTS (Promega) was used to evaluate cytotoxicity of Gx15–070 and ABT-263 (Selleck Chemicals) in T1889, TY82 and T1682 TET cell lines. Results: Chromosome arm level copy number (CN) aberrations were considered those chromosome arms with more than 80% of their length affected by either CN gain or loss. Rare non-recurrent chromosome arm-level CN aberrations were observed in type A thymomas, whereas types B3 and thymic carcinomas shared frequent gains of chromosomes 1q, 5 and 7, as well as losses of chromosomes 6 and 13q. In addition, thymic carcinomas presented frequent losses of chromosomes 16p and 17q. We applied the GISTIC algorithm to the whole set of CN aberrations in order to distinguish aberrations driving the cancer phenotype from the background level of random CN aberrations. 72 CN gain and 54 CN loss peaks were identified (q<0.25). Only two peaks were associated with a significant (p<0.05) poor disease related survival and time to progression. These two peaks represented one CN gain (log2 ratio > 0.3) containing BCL2 locus and one high-level CN loss (log2 ratio < −0.7) containing CDKN2A/B loci. None of the samples with CDKN2A CN loss (5/59) expressed the related proteins p16INK4 and p14ARF. Patients with CDKN2A-negative immunohistochemistry results (85/119) had a poorer disease related survival (LogRank p=0.041). TET cell lines did not have CDKN2A CN loss or BCL2 CN gain, none of them expressed CDKN2A proteins and T1682 and TY82 expressed BCL2. All TET cell lines expressed multiple BCL2 anti-apoptotic family members including MCL1, and were resistant to ABT-263, a BCL2, BCL-XL and BCL-W inhibitor, but sensitive to Gx15–070, a pan BCL2 anti-apoptotic family member (IC50: range 35.8–99.6 nM). Conclusion: Our data indicate that TET histotypes differ by distribution of chromosome arm level CN aberrations. Loss of CDKN2A is prognostic in TETs, whereas Bcl-2 family members may be valuable targets for treatment of this disease.