Mp15-15 Characterization of Bladder Carcinoma in Situ Using Single-Cell Dna Sequencing

You have accessJournal of UrologyBladder Cancer: Basic Research & Pathophysiology I (MP15)1 May 2024MP15-15 CHARACTERIZATION OF BLADDER CARCINOMA IN SITU USING SINGLE-CELL DNA SEQUENCING Benjamin I. Joffe, Clémentine Le Coz, Zejian Wang, John R. Christin, Caroline Laplaca, G. Joel DeCastro, Christopher B. Anderson, James M. McKiernan, Michael Shen, and Andrew T. Lenis Benjamin I. JoffeBenjamin I. Joffe , Clémentine Le CozClémentine Le Coz , Zejian WangZejian Wang , John R. ChristinJohn R. Christin , Caroline LaplacaCaroline Laplaca , G. Joel DeCastroG. Joel DeCastro , Christopher B. AndersonChristopher B. Anderson , James M. McKiernanJames M. McKiernan , Michael ShenMichael Shen , and Andrew T. LenisAndrew T. Lenis View All Author Informationhttps://doi.org/10.1097/01.JU.0001009500.87761.bf.15AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Bladder carcinoma in situ (CIS) is a specific form of non-muscle invasive bladder cancer that is histomorphologically and clinically distinct as a significant proportion will progress to muscle-invasive disease if left untreated. CIS is often resistant to standard therapies and the mechanisms that lead to progression have not been fully characterized. Sequencing and characterization of CIS remains elusive due to the low-volume, non-bulky nature of these tumors. Here, we present the first molecular characterization of CIS using single-cell DNA sequencing (scDNA-seq) to overcome these limitations. METHODS: An established bladder organoid (SCBO-23) from a patient with known CIS was utilized. SCBO-23 parental tumor was processed into single nuclei for library creation and barcoding using the Tapestri single-cell instrument and sequenced on a NovaSeqX. All data was processed using the Tapestri Pipeline software to generate single-cell genotypes and quantify clonal architecture of the tumor. Bulk DNA sequencing from the SCBO-23 organoid was available for comparison. Sequencing of additional patients with CIS is currently underway. RESULTS: Bulk sequencing of SCBO-23 organoid identified TP53 mutation Q167*. Using this mutation as a reference, three major clonal groups within the parental sample were identified: 627 cells (12%) of homozygous TP53 mutation, 1197 cells (23%) of heterozygous TP53 mutation, and 3378 cells (65%) of wild-type phenotype. Among the homozygous group, there were subclones with increased copy number variations (CNVs) in known oncogenes PIK3CA and KRAS and decreased CNVs in tumor-suppressor genes RB1 and KDM6A. There were no subclones with these CNVs in the wild-type group. Within the heterozygous group, there was a smaller proportion of subclones with these CNVs. CONCLUSIONS: Novel scDNA-seq identified three major clonal groups within the sample, with homozygous TP53 mutated clones likely representing CIS and heterozygous TP53 potentially being pre-malignant. The CIS clonal group had CNVs of known oncogenes and tumor-suppressor genes. These signatures may have an important role in understanding CIS progression and mechanisms of resistance. Additional samples are currently undergoing sequencing to further characterize this previously undescribed yet clinically highly relevant entity. Download PPT Source of Funding: Maple Place Foundation © 2024 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 211Issue 5SMay 2024Page: e235 Advertisement Copyright & Permissions© 2024 by American Urological Association Education and Research, Inc.Metrics Author Information Benjamin I. Joffe More articles by this author Clémentine Le Coz More articles by this author Zejian Wang More articles by this author John R. Christin More articles by this author Caroline Laplaca More articles by this author G. Joel DeCastro More articles by this author Christopher B. Anderson More articles by this author James M. McKiernan More articles by this author Michael Shen More articles by this author Andrew T. Lenis More articles by this author Expand All Advertisement PDF downloadLoading ...