Abstract LB034: Evaluation of a novel single-cell RNA sequencing methodology for use in clinical trial settings

Abstract

Abstract Bulk RNA sequencing (RNA-seq) is regularly employed for transcriptional profiling but provides only a snapshot of the average population. Particularly when studying disease, understanding differences in diverse cells is essential thus single-cell resolution is a necessity due to significant cellular heterogeneity. High-throughput droplet- and microfluidic-based approaches for performing single-cell RNA-seq (scRNA-seq) are invaluable techniques for uncovering changes in cells such as differential gene expression and epigenetic states in cancer research. A challenge for scRNA-seq, however, is sample preparation as typically tissues must be processed immediately after collection. We and others have reported alternative approaches to stabilize samples prior to analysis such as cryopreservation of cells and tissues and methanol-based fixation of cells. However, the inclusion of these approaches is still limited in many settings due to the challenging logistics involved in sample collection. To further broaden the ability of researchers to deploy scRNA-seq, we report our experiences from testing a pre-commercial workflow developed by 10x Genomics to resolve these sample management limitations. The use of paraformaldehyde (PFA) to fix samples at the collection site allows samples to be transported to remote laboratories for downstream processing without sacrificing integrity or data quality. This advance has enabled new possibilities for sample accessibility, throughput, and batched analysis in basic and translational research settings. Furthermore, this approach also allows for analysis of transcriptome-wide gene expression at high sensitivity with simultaneous cellular readouts. Here we report a case study comparing the PFA method to standard approaches, and highlight advantages and potential applications previously not possible with reported sample preparation strategies. Citation Format: David Corney, Yang Han, Yu Qiu, Yongjun Fan, Michael Stephens, Andrea O'Hara, Laure Turner, Christopher Mozdzierz, Haythem Latif, Ginger Zhou. Evaluation of a novel single-cell RNA sequencing methodology for use in clinical trial settings [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 LB034.