RNA-protein Co-detection using spatial analysis to profile tumor-infiltrated immune cells

Abstract

Abstract Interrogating complex tumor microenvironment requires a multi-omics approach. Detecting target immune cell markers using immunohistochemistry/Immunofluorescence (IHC/IF) and visualizing cytokine expression with in situ hybridization (ISH) can provide comprehensive information about the activation states of immune cells. Here, we demonstrate a newly developed integrated ISH and IHC/IF workflow compatible with manual and automated platforms with improved RNA-protein co-detection. We demonstrate the use of our RNA-Protein Co-detection assay in combination with the automated and manual RNAscope Multiplex Fluorescent assay as well as the automated RNAscope Chromogenic Duplex assay to detect T cell markers, macrophage markers and checkpoint markers in the tumor microenvironment by using a microarray with different tumor samples. We identified CD4+ helper T cells, CD8+ cytotoxic T cells and determined their activation states by visualizing IFNG, GZMB and IL-2 expression. We were also able to identify macrophages detected by CD68 protein expression and differentiate the M1 and M2 subtypes by using M2-specific marker, CD163. We could also delineate tumor-stroma border in the samples by using the Pan-CK probe which distinctly marks the tumor cells and visualize expression of immunoregulatory receptors PD-L1 and CTLA4 in the tumor. This assay is enables for multiplexing by combining with our fluorescent assays or enables target detection while retaining morphological context when combined with our chromogenic assays. Overall, the new RNAscope-ISH-IHC/IF co-detection workflow and reagents enable simultaneous visualization of RNA and protein targets by enhancing the compatibility of antibodies with minimal optimization.