Abstract 782: Multiomic single cell sequencing identified regulatory elements in prostate cells

Abstract

Abstract Introduction: Despite significant progress, the genetic role of regulatory elements in gene expression is still poorly understood in prostate cells. Recent development in single cell sequencing by combining ATAC-seq and RNA-seq has made it possible to determine genome-wide linkages between chromatin accessibilities and gene expression. Methods: To test the feasibility of using single cell multiome sequencing in dissecting regulatory linkages between chromatin accessibilities and gene expressions, we applied 10X Genomics Chromium Single Cell Multiome ATAC + Gene Expression platform to simultaneously encapsulate Tn5 transposase tagged nuclei from two prostate cell lines. We applied down-sampling linkage analysis to determine highly reproducible genome-wide associations between ATAC-seq peaks and RNA-seq gene expressions. To investigate the chromatin accessibilities related to human transcription factor binding sites, we scanned the JASPAR motif collection with genome-wide Tn5 insertion analysis. Results: This study encapsulated 3,096 multiome RWPE-1 nuclei cultured in serum-free condition, 6,978 and 8,487 multiome LNCaP nuclei treated with methanol (LNCaP-M) or dihydrotestosterone (DHT, LNCaP-D). Our analysis captured 210,990, 264,802, and 278,154 ATAC-seq peaks from RWPE-1, LNCaP-M, and LNCaP-D by macs2 narrow peak model (FDR q<0.01), which included over 90% peaks identified by bulk ATAC-seq datasets. Through downsampling linkage analysis, we identified 1,595, 2,507, and 4,183 linkage associations between ATAC-seq and RNA-seq from the above three experiments, respectively. Scatter plots showed that the correlation coefficient of the linkage association was negatively associated with the distance between ATAC-seq and RNA-seq signals. By comparing to bulk ChIP-seq data from RWPE-1 cells, we confirmed that the single cell ATAC-seq peaks in linkages were co-localized at histone modified regions, including H3K4me1 (25.7%), H3K27ac (14.3%), and H3K4me3 (4.9%). JASPAR database (634 motifs) search found that the Tn5 footprints surrounding AR, NR3C1, and NR3C2 motifs in LNCaP-D showed significantly higher enrichment than that of the LNCaP-M group, indicating increased androgen receptor DNA binding following DHT treatment. Interestingly, in RWPE-1 cells harboring TP53 p.P72R polymorphism (rs1042522), we found differential Tn5 footprints surrounding TP53 binding motif between its ATAC-seq subclusters at whole genome scale. Conclusion: Our preliminary data in prostate cell lines outlined a regulatory landscape of single-cell resolution. Multiomic single cell sequencing will help locate regulatory elements and target genes. Citation Format: Yijun Tian, Alex Soupir, Liang Wang. Multiomic single cell sequencing identified regulatory elements in prostate cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 782.