Abstract 7131: Integrative single-cell transcriptomic and epigenomic immune profiling reveals parallel insights into cancer research

Abstract Introduction: Single-cell technologies have revolutionized immune profiling by enabling the detailed analysis of individual cells, uncovering cellular heterogeneity and complex regulatory mechanisms. Two common single-cell omics include single-cell RNA-sequencing (scRNA-seq) which profiles gene expression by capturing mRNA transcripts, and single-cell ATAC sequencing (scATAC-seq) which profiles gene regulation using hyperactive Tn5 transposase to assess chromatin accessibility. In this workflow, we demonstrate integrative analysis of both technologies that provides comprehensive view of a cell’s transcriptomic and epigenomic landscapes. Methods: Two independent scRNA-seq and scATAC-seq workflows were performed on peripheral blood mononuclear cells (PBMCs) and various cancer cell lines to provide accessible and convenient model system for various oncology applications. Libraries were prepared using Bio-Rad ddSEQ 3’ scRNA-seq and scATAC-seq Kits, which uses droplet-based ddSEQ technology for capturing cells with high sensitivity and recovery. Libraries were sequenced using Illumina NextSeq 2000. Data quality was assessed using the Omnition Analysis Software and Seurat was used for downstream tertiary analyses. Results: Here, we present an integrated analysis of scRNA-seq and scATAC-seq for comprehensive immune profiling of peripheral blood mononuclear cells (PBMCs) and various cancer cell lines. Our findings show consistent correlation of cell types and subtypes identified from each pair of samples. Furthermore, specific differentially expressed genes (DEGs) and differentially accessible regions (DARs) were found to be shared in corresponding cell types such as chromatin peak and increased gene expression of Epiregulin (EREG) in CD14+ monocytes. Conclusion: Bio-Rad ddSEQ 3’ scRNA-seq and scATAC-seq kits provide affordable and scalable method for profiling immune response from thousands of individual cells with increased sensitivity and accuracy. Combined analyses from these two approaches show strong potential for oncology applications. For example, the ability to identify novel immune cell subsets, discover tumor biomarkers, characterize tumor-infiltrating lymphocytes, and reveal regulatory elements driving immune responses in the tumor microenvironment can all be achieved. Citation Format: Errile Pusod, Patricia Schnepp, Srikanth Perike, Angelica Olcott, Elizabeth Dreskin. Integrative single-cell transcriptomic and epigenomic immune profiling reveals parallel insights into cancer research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7131.