Abstract 3392: Rapid, scalable isolation of human tumor nuclei for single cell genomics

Abstract

Abstract Sample preparation remains a significant roadblock to the implementation and scaling of single cell technologies in clinical and translational research. Time consuming, custom dissociation protocols performed on fresh tissue by experts are often utilized to obtain high quality single cell data. However, these complex protocols result in low sample throughput and high variability driven by logistical challenges and user variability. Additionally, many samples that are of interest for clinical and translational studies arrive in research labs snap frozen, leaving nuclei extraction as the only viable path to generate single cell/nuclei data. To overcome these challenges, we present a scalable, easy to use, spin column-based nuclei isolation platform that generates single nuclei that are ready for input into downstream 10x Genomics single cell assays in under an hour. We processed eight unique human tumors in parallel (skin melanoma, breast, ovary, prostate, lung, kidney, colorectal, and pancreas). Starting from snap frozen tissue, we were able to generate single nuclei suspensions for all samples, in parallel, within 90 minutes. The resulting single nuclei were run through the 10x Genomics Single Cell Gene Expression, Single Cell Immune Profiling, and Single Cell ATAC workflows. Single cell gene expression data retained high data complexity across all tumor types tested. Expected cell type clusters, including tissue-specific tumor cells, surrounding/infiltrating immune cells and stromal cells were easily identified and profiled via gene expression analysis. Even fragile cell types often missing in single-cell data (e.g. mature adipocytes) were preserved and profiled in this experiment. Additionally, epigenetic changes as measured by Single Cell ATAC profiling were consistent with both general and tissue-specific epigenetics of each cancer type analyzed. In summary, this platform streamlines sample preparation for single cell studies from snap frozen tissue, enabling these samples to be used much more routinely and unlock biobanked sample cohorts. The findings presented here demonstrate that this fast and easy to use nuclei isolation system provides a consistent platform for generating high quality single nuclei data at scale for clinical, translational and basic research studies alike. Citation Format: Michael Gibbons, Alaina Puleo, Jill Herschleb, Sarah Taylor. Rapid, scalable isolation of human tumor nuclei for single cell genomics [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 3392.