Abstract 3866: Spatial multi-omics analysis targeting protein and RNA biomarkers on a single FFPE tissue section using an integrated staining workflow

Abstract

Abstract Biomarker detection approaches capable of rapid identification, quantification, and spatial mapping of many cellular sub-types of the tumor environment in FFPE tissue sections are becoming increasingly valuable for investigating the highly complex biology of tumors and their respective microenvironments. Multiplexed immunofluorescence (mIF) enables simultaneous identification of multiple protein targets within their spatial context in FFPE tissues, thereby facilitating more in-depth analysis including cellular phenotyping. In parallel, spatial transcriptomic analysis can provide additional insights into cellular function. Multi-omics analyses combining protein and nucleic acid biomarkers on a single tissue section can provide a deeper understanding of the complex cellular interactions in the context of the tumor. In this study, we demonstrate the versatility of Ultivue InSituPlex technology (ISP) through an integrated workflow for co-detection of protein and RNA on a single tissue section. FFPE tumor tissue samples were processed for protein and/or RNA detection on a single slide with an integrated workflow using ISP. Briefly, slides were stained for both protein and RNA targets using a Leica Biosystems BOND RX autostainer. Post-staining, the slides were imaged on ZEISS Axioscan.Z1 in five different fluorescent channels and evaluated using IndicaLabs HALO analysis software. In parallel, control serial sections were stained to perform comparative analyses. Here we report an efficient and streamlined integrated workflow for co-detection of protein and RNA on a single section, powered by ISP technology. The protein and RNA targets were detected both sequentially (over different imaging rounds) with increased multiplexing capabilities, as well as concurrently (in the same imaging round) for a higher throughput solution, thereby demonstrating the flexibility of the workflow. Comparative analyses between the different workflows confirmed minimal effect on staining performance of individual biomarkers (both protein and RNA). The gentle treatment of FFPE tissue sections through ISP technology preserves tissue integrity, and morphology enabling efficient detection of protein and RNA targets on a single section. The integrated workflows presented here demonstrate compatibility of the individual steps in the assay towards co-detection of protein and RNA targets with efficient sensitivity in terms of staining performance for individual biomarkers. Citation Format: Gourab Chatterjee, Grace E. Vezeau, Milena D. Lazova, Michael Sismour, Mael Manesse. Spatial multi-omics analysis targeting protein and RNA biomarkers on a single FFPE tissue section using an integrated staining workflow [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 3866.