Mp65-10 Single-Cell Assay for Transposase-Accessible Chromatin Sequencing Demonstrates Accessibility Overlying Gene Promoter Regions for Previously Established Basal Cell Markers

You have accessJournal of UrologyBladder Cancer: Basic Research & Pathophysiology III (MP65)1 May 2024MP65-10 SINGLE-CELL ASSAY FOR TRANSPOSASE-ACCESSIBLE CHROMATIN SEQUENCING DEMONSTRATES ACCESSIBILITY OVERLYING GENE PROMOTER REGIONS FOR PREVIOUSLY ESTABLISHED BASAL CELL MARKERS Jillian Egan, Jihyun Lee, Sabrina Camp, Amanda Garza, Jihye Park, Eliezer Van Allen, and Filipe L. F. Carvalho Jillian EganJillian Egan , Jihyun LeeJihyun Lee , Sabrina CampSabrina Camp , Amanda GarzaAmanda Garza , Jihye ParkJihye Park , Eliezer Van AllenEliezer Van Allen , and Filipe L. F. CarvalhoFilipe L. F. Carvalho View All Author Informationhttps://doi.org/10.1097/01.JU.0001008756.24343.22.10AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Cisplatin-based chemotherapy followed by radical cystectomy is the standard-of-care for patients with localized muscle-invasive bladder cancer (MIBC). Neoadjuvant chemotherapy has demonstrated a 5-year overall survival benefit of 5-10%. However, the benefit is largely restricted to those patients who experienced a complete response. Several molecular signatures defining subtypes with the potential to predict response and survival have been proposed. Our goal is to dissect single-cell chromatin accessible regions in genes that define MIBC molecular subtypes in tumors that progressed over neoadjuvant cisplatin-based chemotherapy. METHODS: We performed single-cell Multiome Assay for Transposase-Accessible Chromatic (ATAC) and gene expression sequencing (simultaneous identification of gene expression and open chromatin regions within the same) in tumors that had a complete response and those that had no response or progress over neoadjuvant cisplatin based chemotherapy. Single cell suspensions were prepared following the 10x Genomics protocol. A total of 15 samples were sequenced, CellRanger ARC was used for sequence alignment, MACS2 used for peak calling and downstream chromatin accessibility analysis performed in Seurat. RESULTS: Non-responder samples were subset to the urothelial/tumor compartment. Differentially accessible peaks and differential gene activity were determined. We found increased accessibility, indicating open chromatin regions, in the promoters of several basal (CD44, KRT6A, KRT5) and basal-squamous (EGFR, STAT3, HIF1A) cell makers (Figure 1). Moreover, open chromatin and accessible promoters regions were associated with a significant RNA expression in the same tumor cells suggesting active transcription of basal-squamous genes. CONCLUSIONS: Single-cell ATAC sequencing has the ability to identify areas in the genome associated with open chromatin in MIBC treated with cisplatin chemotherapy. We found increased accessibility of the promoters of CD44, KRT6A, EGFR, STAT3 and HIF1A – genes associated with basal and basal-squamous molecular subtypes – in cisplatin non-responders. This demonstrates the ability to identify areas of open chromatin using single-cell ATAC sequencing and future studies will better define the role of chromatin remodeling and downstream implications with respect to response to cisplatin-based chemotherapy in patients with MIBC. Source of Funding: None © 2024 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 211Issue 5SMay 2024Page: e1080 Advertisement Copyright & Permissions© 2024 by American Urological Association Education and Research, Inc.Metrics Author Information Jillian Egan More articles by this author Jihyun Lee More articles by this author Sabrina Camp More articles by this author Amanda Garza More articles by this author Jihye Park More articles by this author Eliezer Van Allen More articles by this author Filipe L. F. Carvalho More articles by this author Expand All Advertisement PDF downloadLoading ...