Abstract 216: Profiling single cell and spatial transcriptomes in FFPE archived tissues

Abstract

Abstract Single cell and single nuclei RNA sequencing (scRNA-seq and snRNA-seq) have helped to identify cell type and subtypes that are present in complex tissues in both healthy samples and disease states. So far, scRNA-seq and snRNA-seq can only be performed in fresh tissues, or fresh frozen tissues. Most archived tissues are formalin-fixed, and paraffin-embedded (FFPE), making them inaccessible to the modern technology for characterization. Recently, 10x Genomics release a new reagent enabling single-cell fixed RNA characterization from fixed samples. The initial release is for fresh samples being fixed and then profiled later. However, FFPE archived tissues are not supported yet. We showed here two protocols to dissociate single cells and single nuclei from a 10-year-old FFPE human gastric tumor. We then profile them with 10x Genomics’ fixed RNA profiling kit. We further compare the data with the 10x Genomics’ Visium data obtained from the same tissues to understand the performance of these two protocols. In summary, we show that such technology will help to further characterize archived tissues that already have pathology annotation as well as clinical data and help biomarkers identification. Citation Format: Jasmine Ying-Jiun Chen, Quynh Le, Chris Kang, Roy Tam, Brian Tai, Kelly Lo, Nasim Rahmatpour, Perry Wasdin. Profiling single cell and spatial transcriptomes in FFPE archived tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 216.