Abstract 5370: Massively parallel barcoding enables high-throughput single-cell RNA sequencing from formalin-fixed paraffin-embedded tissues for immuno-oncology research

Abstract Formalin-fixed paraffin-embedded (FFPE) tissue samples provide a reliable and long-term storage solution for valuable tumor specimens, enabling future analyses. However, the chemical processes involved can compromise cellular integrity, hindering certain downstream applications such as single-cell RNA sequencing (scRNA-seq). Although recent advancements have enabled scRNA-seq analysis of archival FFPE samples, these techniques are often constrained by limited throughput and reduced sensitivity. Scale Bio provides a solution for profiling single cells/nuclei from FFPE samples at an unprecedented throughput with the flexibility for sample multiplexing by leveraging the power of combinatorial indexing. The probes targeted to the interested regions are hybridized to mRNA inside cells/nuclei extracted from FFPE sample, then released and captured by barcoded beads confined in the individual compartment. The library is finally amplified from the beads, containing the cell barcode and target sequence. The workflow is streamlined to be completed in 2 days from cells/nuclei extraction to sequencing library for ∼1.2M single cells/nuclei. Here we provide an early demonstration of the Scale Bio QuantumScale FFPE scRNA kit in immuno-oncology . We isolated nuclei from 12 bio-banked breast cancer FFPE tumor samples and profiled the transcriptional levels of 1000 clinically actionable genes. QuantumScale FFPE scRNA provides unprecedented insights into the cellular transcriptome at massive scale to analyze the biology of the tumor, microenvironment, and immune response in a single assay. We observed robust cell recovery, with good sensitivity across all samples profiled. Citation Format: Fan Zhang, Herbert Gong, Emmanuel Jimenez, Nate Chapin, Bryce Alves, Sanika Vinayak Khare, Bob James. Massively parallel barcoding enables high-throughput single-cell RNA sequencing from formalin-fixed paraffin-embedded tissues for immuno-oncology 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 5370.