83 Spatially resolved transcriptomic and proteomic investigation of breast cancer and its immune microenvironment

Background The tumor microenvironment (TME) is composed of highly heterogeneous extracellular structures and cell types such as endothelial cells, immune fibroblasts that dynamically influence communicate with each other. constant interaction between a its plays critical role in cancer development progression can significantly affect tumor’s response to therapy capacity for multi-drug resistance. High resolution analyses gene protein expression spatial context provide deeper insights into the interactions cells surrounding within TME, where better understanding underlying biology improve treatment efficacy patient outcomes. Here, we demonstrated ability perform streamlined multi-omic by utilizing 10X Genomics Visium Spatial Gene Expression Solution FFPE multiplex enablement. This technique simultaneously assesses elucidate immunological profile different breast samples conjunction standard pathological methods. Methods Serial (5 µm) sections human were placed on (GEX) slides. GEX slides incorporate ~5,000 molecularly barcoded, spatially encoded capture spots onto which tissue are placed, stained, imaged. Following incubation whole transcriptome, probe-based RNA panel an immuno-oncology oligo-tagged antibody panel, developed Abcam conjugated antibodies, tissues permeabilized representative probes captured. Paired libraries generated section then sequenced Illumina NovaSeq at depth ~50,000 reads per spot. Resulting from both aligned overlaid H&E-stained images, enabling analysis mRNA expression. Additional data visualizations performed Loupe Browser v4.1 desktop software. Conclusions transcriptomics technology complements examination combining histological assessment throughput deep biological insight highly-multiplexed detection RNA-seq. Taken together, our work provides spatially-resolved, multi-analyte view microenvironment, greater cellular behavior around tumors help drive discovery new biomarkers therapeutic targets.