Combining Intravital Microscopy and Transcriptomic Analysis to Study Head and Neck Squamous Cell Carcinoma

In recent years, multiphoton intravital microscopy has become a powerful tool that reveals cellular and molecular features of cancer initiation, progression, and metastasis in numerous cancer mouse models. In this chapter, we describe a method that combines intravital microscopy and RNA-seq to acquire molecular information on well-defined tumor lesions generated in a carcinogen model of tongue squamous cell carcinoma. Here, cancer lesions are first imaged longitudinally by intravital microscopy, and then precisely excised using a branding approach. The tumor epithelium is isolated, and the RNA is extracted and subjected to next-generation sequencing. This method enables the analysis of the transcriptome of tumor lesions with high precision during their progression.