Abstract 2377: Clonal evolution and mutational signatures in urothelial carcinoma revealed by paired exome analysis

• Published in: Cancer research (Chicago, Ill.) Ill.), 2016-07, Vol.76 (14_Supplement), p.2377-2377
• Main Authors: Nordentoft, Iver K., Lamy, Philippe, Birkenkamp-Demtröder, Karin, Borg Houlberg Thomsen, Mathilde, Vang, Søren, Villesen Fredsted, Palle, Hedegaard, Jakob, Borre, Michael, Bjerggaard Jensen, Jørgen, Høyer, Søren, Skou Pedersen, Jakob, Falck Ørntoft, Torben, Dyrskjøt Andersen, Lars
• Format: Article
• Language: English
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM2016-2377

Background: Bladder cancer (BC) is the 5th most common cancer in the western world. 75% of patients are diagnosed with a single or multifocal non-muscle invasive bladder tumor. About 70% of patients have disease recurrence, and 10-30% will eventually have disease progression. Synchronous and metachronous tumors are mono- or oligo clonal of origin, pointing towards a common ancestry (field disease). The field disease is acquiring molecular alterations over time that may fuel disease progression and metastasis. Detailed knowledge of tumor heterogeneity, clonality and mutational dynamic of early clonal mutations with disease driving potential are needed in order to determine the possible effect of targeted treatment. Methods: In this study we characterized genomic alterations in two to five metachronous tumors from 29 patients initially diagnosed with stage Ta disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ∼50x mean read depth), Ultra deep targeted sequencing (∼6,809x mean read depth) and whole transcriptome RNA-seq was performed for all samples. In addition multiregional WES was performed on 8 adjacent regions from a single tumor. Results: We observed more variation in the mutational spectrum of the tumors from PD patients compared to NPD patients (P = 0.0013). The frequency of APOBEC-related mutations was also higher in tumors from PD patients, and intra-patient shift in APOBEC classification was observed in only one NPD patient (1/14), while it was seen in 53% (8/15) of PD patients (P = 0.009). We also observed a higher proportion of clonal mutations in the ancestral branch compared to sample-specific branches (P = 0.002), based on analysis of phylogenetic trees of disease evolution and calculation of cancer cell fractions. Analysis of paired tumors revealed a high degree of intra-patient mutational heterogeneity, whereas multiregional sequencing of 8 regions from a single tumor biopsy showed little intra-tumor heterogeneity. A low number of subpopulations were present in the individual tumors (PyClone), and overall we found the presence of a subclone in all cancerous cells from all patient samples and the presence of one or two subclones characterizing individual sample. Finally, allele specific expression (ASE) in Ta tumors was found to be higher in tumors from PD patients compared to NPD patients (P = 1.18e-56), with tumor suppressor genes sh