Small RNA Sequencing for Squamous Cell Carcinoma Research

Abstract

Small noncoding RNAs are important transcriptional regulators implicated in several aspects of cell biology. Recent studies have demonstrated that qualitative and quantitative information on these molecules may be clinically useful for the cancer community. Next-Generation Sequencing is quickly becoming the technology of choice to study their role since a single equipment run may provide thorough information on small RNA populations. Expression levels, mutational status, and the opportunity to identify novel molecules are among the resources of most sequencing platforms. However, challenges include sample processing and an appropriate data analysis pipeline. This chapter describes the workflow for small RNA sequencing analysis, discussing sample preparation, small RNA alignment for quantification, differential expression analysis, and novel small RNA molecule identification. We are currently studying small noncoding RNAs in head and neck squamous cell carcinoma (HNSCC). Arising from epithelial cells in the lining of the upper aerodigestive tract and strongly associated with tobacco and alcohol consumption, HNSCC is among the leading cancers by incidence worldwide. Information on the relevance of small RNA molecules for this cancer type is still scarce but may become useful for diagnostic and prognostic purposes when comprehensive datasets become available.