Abstract 314: Fixative eXchange (FX)-seq reveals single nucleus transcriptional landscapes of archived clinical cancer FFPE specimens

Abstract The wide availability of FFPE tissues stored in hospitals and biobanks could potentially be an invaluable resource to gain insights for improved medical treatment towards precision medicine by combining genomic and transcriptomic data with pathological annotations and medical records. Nevertheless, the majority of current single-cell sequencing methods depend on fresh or fresh-frozen samples to generate high-quality transcriptome data due to the limited reverse transcription (RT) yields in FFPE samples. Consequently, single-cell level transcriptomic studies of FFPE samples have been a longstanding challenge. Here, we present Fixative-eXchange (FX) -seq, a highly scalable snRNA-seq method for heavily paraformaldehyde (PFA) -fixed and/or FFPE samples. We successfully analyzed a total of nearly 320k nuclei from various samples, including PFA-fixed tissue, FFPE blocks, FFPE and hematoxylin and eosin (H Part 1 (Regular Abstracts) ; 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84 (6Suppl): Abstract nr 314.