Abstract LB-264: Whole genome sequencing of an adrenocortical carcinoma reveals a pathogenic context and exposes therapeutic options
Authors: Michael J. Demeure, Kathleen Schwartz, Winnie Liang, Christophe Legendre, Waibhav Tembe, David Craig, John Carpten, Kimberly J. Bussey
Journal: Cancer Research (2011)

Abstract Adrenocortical carcinoma (ACC) is an aggressive endocrine malignancy with a 5-year survival rate of 20–30%. There are few treatment options for patients in part because the rarity of the tumor makes its study difficult. Previous work in our lab and by others has highlighted the importance of IGF2-IGF1R signaling, beta-catenin signaling, dysregulation of p53, and the G2/M transition in ACC pathogenesis. In order to advance knowledge of ACC biology and facilitate drug target discovery, we performed whole genome sequencing on an ACC tumor and matched peripheral blood. An ACC sample was obtained during surgery on a 51 year old female who had locally recurrent disease that progressed despite chemotherapy. DNA extracted from both tumor and blood was processed independently, and libraries were paired-end sequenced on the Illumina HiSeq 2000 platform. Sequencing data was aligned to the reference genome, build hg18. Variations were predicted in the tumor and blood separately using two different SNP calling algorithms: samtools and SolSNP. After SNP prediction, results were combined to identify variations called by both algorithms, submitted to PolyPhen2 to assess predicted functional consequence, and filtered to yield those SNPs most likely to represent deleterious, non-synonymous changes in coding regions of the genome in the tumor specifically, as well as those shared by the tumor and blood (i.e. constitutional changes).Our preliminary analysis identified a total of 1,724,133 single nucleotide changes in peripheral blood and 2,820,476 in the tumor prior to filtering. The transition to transversion ratio was 2.2 for blood and 2.0 for tumor. We did not observe mutations in known tumor suppressor or oncogenes. There were no coding mutations observed in any of the genes in the canonical pathways for IGF2 or beta-catenin signaling; p53 was wild-type. Inspection of constitutional changes indicates that the patient harbors a constitutive putative mutation in E2F2. In mice, knock-outs of E2F transcription factors result in developmental problems within the adrenal cortex. In our preliminary analysis, we identified a network that may possibly explain the aberrant p53 function that characterizes ACC. The tumor harbors a predicted mutation in SETD8. SETD8 encodes Set8, a lysine methyltransferase that has been implicated in gene silencing via histone 4 methylation, and is a negative regulator of p53 through methylation of p53 at lysine 382. Loss of p53 activity leads to increased activity of c-myc and SP1, both of which drive the expression of E2F2. Further work is required to characterize whether and how the mutations in SETD8 and E2F2 alter protein function and play a role in ACC pathogenesis. Finally, putative mutations in genes involved homologous repair such as ATM, FANCM, and BRCA2 suggests DNA cross-linking agents like mitomycin C may be useful in treating this patient's cancer. Data analysis is ongoing. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-264. doi:10.1158/1538-7445.AM2011-LB-264