1376 Whole transcriptome spatial profiling of the tumor microenvironment in FFPE, fresh frozen, and fixed frozen tissues

• DOI: 10.1136/jitc-2024-sitc2024.1376
• Publication Date: 2024-11-05T14:58:54Z
• Authors: Jun Chiang; Naishitha Anaparthy; Nancy Conejo; Monica Nagendran; David Sukovich; David Patterson; Lauren Gutgesell; Govinda Kamath; Augusto Tentori
• Keywords: Profiling (computer programming)

<h3>Background</h3> The tumor microenvironment (TME) is composed of highly heterogeneous cell types that dynamically interact with each other. To more precisely distinguish and characterize cellular diversity disease states within tissues, technologies single-cell resolution are required. Visium HD Spatial Gene Expression assay (Visium HD) a high-resolution spatial technology utilizes whole-transcriptome probe panel, resolving data at the scale intact tissue sections. This offers comprehensive understanding behavior in around tumors, potentially leading to new insights into progression therapeutic responses. <h3>Methods</h3> Human breast cancer lung sections preserved using three common methods: formalin-fixed, paraffin-embedded (FFPE), fresh frozen (FF), PFA-fixed, OCT-embedded (fixed or FxF), were spatially profiled assay. Tissues mounted on glass slides stained hematoxylin eosin (H&amp;E). Probe pairs hybridized target RNA ligated samples transferred spatially-barcoded CytAssist instrument. capture area consists approximately 12 million 2 µm x barcoded squares without gaps. Data was binned 8 for visualization analysis. <h3>Results</h3> In this study, we characterized profiles various tissues fixation methods. Our findings demonstrate capability resolve oncogenes immune cells multiple tissues. samples, successfully identified glandular myoepithelial clusters, which closely mimic distinct localization observed ductal regions by H&amp;E staining. Additionally, high expression levels biomarkers <i>SPP1</i>, <i>MYC</i> <i>MZB1</i> these samples. mapped <i>EPCAM</i> back epithelial tissue. <h3>Conclusions</h3> unravels heterogeneity maps TME FFPE, FF FxF human resolution. allows deeper analyses interactions discovery potential novel gene markers. enables innovative pathology clinical translational research, extending its capabilities wide range biological applications.