Combining the Best of Both Worlds: Immune Profiling the Tumor Microenvironment with RNA and Protein

Cancer immunotherapy has benefitted many cancer patients across multiple malignancies, but there remains a need to develop predictive cancer biomarkers to identify patients who are most likely to benefit from various immunotherapeutic strategies. While many biomarker analysis technologies are available, most do not provide spatial and cell type-specific information critical for assessing the specific immune cell types with lineage and functional information in the evolving microenvironment of each tumor. Furthermore, multiplexing capabilities are highly desirable in order to obtain comprehensive single cell-level co-expression information and to maximize the use of limited biopsied sample material.

In this study, we demonstrate the development of an improved fluorescence multiplex in situ hybridization (ISH) method to detect three RNA biomarkers simultaneously in FFPE and fresh frozen tissues on the Leica BOND RX automated slide staining system. The presented method detects RNA biomarkers in a highly specific and sensitive manner, overcoming the inherent challenge of auto-fluorescence in FFPE tissues.