Abstract 3679: Paired tumor and normal whole genome and transcriptome sequencing of transitional cell carcinoma of the upper urinary tract
Authors: Irene Cherni, David W. Craig, Lori Phillips, Winnie S. Liang, Angela S. Baker, Tyler Izatt, Ahmet Kurdoglu, Alexis Christoforides, Shripad Sinari, Galen Hostetter, Michael J. Demeure, Daniel D. Von Hoff, John D. Carpten, Glen J. Weiss
Journal: Cancer Research (2012)

Abstract Background: Transitional cell carcinoma of the upper urinary tract (UUT) is a rare urothelial cancer, which most often affects males ages 50-70. Previous studies have shown some overlap with genetic alterations frequently observed in bladder cancer, however complete molecular characterization of UUT tumors is currently limited. A 20-year-old woman with treated acute lymphoblastic leukemia (ALL) in remission for ∼13 years, presented with present with numerous metastatic lesions involving bone, adrenal, retrocaval lymph node, and kidney. Biopsy confirmed a second primary carcinoma originating from the ureter or kidney. After two lines of systemic chemotherapy, the patient enrolled in a whole-genome (WGS) and whole transcriptome sequencing (WTS) pilot study. Methods: Tumor DNA and RNA was isolated from fresh-frozen tissue obtained by needle core biopsy of the right kidney tumor. Germline DNA was isolated from the patient's whole blood. Commercial benign ureter tissue was used for normal RNA comparison. Whole-genome paired-end library and transcriptome sequencing were done on Illumina's HiSeq 2000 platform. Burrows-Wheeler Transform algorithm was used in alignment to human reference genome (build 36). Several short nucleotide variants (SNVs) were selected for further validation with Sanger sequencing. Quantitative PCR with specific primers to either amplified or deleted genomic regions and ΔΔCt method were used to validate chromosomal copy number abnormalities. Results: WGS yielded 46X and 55X uniquely mappable reads for the tumor and normal samples, respectively. Seventy-one damaging somatic SNVs and a number of chromosomal aberrations were identified in regions of cancer relevant genes. Most notably, truncating mutations were found in p53 and KDM6A (oncogenic histone demethylase) genes as well as a damaging mutation in E2F8 transcription factor. KDM6A and E2F8 mutations were confirmed with bi-directional Sanger sequencing. A homozygous deletion encompassing the tumor suppressor p16 and a prominent focal 2MB high-level amplification at 7p11.2 that includes the EGFR oncogene were also detected. WTS produced ∼1006 reads for each sample. Expression analysis revealed loss-of-heterozygosity in p53 wild-type locus and a significant upregulation of EGFR. Additionally, a number of genes (MKI67, AURKA, TOP2A, BUB, FOXM, and PLK1) associated with cell cycle progression had &amp;gt;4-fold tumor overexpression. Genomic qPCR confirmed a 10-fold reduction in p16 while EGFR was amplified &amp;gt;40 times. Conclusion: Through WGS and WTS, a number of common oncogenic targets to be deregulated in this UUT, including p53 mutation, EGFR and MYC amplifications, and p16 deletion. These targets have previously been implicated in urothelial cancers, most notably in bladder. Given, negative KRAS mutation status, EGFR targeted therapy may be a reasonable treatment option for this patient. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3679. doi:1538-7445.AM2012-3679