DNA copy number variation profiling and transcription profiling by array of 93 human lung squamous cell carcinoma samples

The basaloïd carcinoma (pure) and the basaloïd variant of lung squamous cell carcinoma (SCC) have a dismal prognosis but their underlying specific molecular characteristics remain obscure. This experiment uses DNA copy number aberrations and mRNA expression pangenomic profiles of 93 SCC, including 42 basaloïd samples (24 pure, 18 mixed) to reveal that pure basaloid tumors display a specific mRNA expression profile, encoding factors controlling the cell cycle, transcription, chromatin and splicing, with prevalent expression in germline and stem cells, while genes related to squamous differentiation are underexpressed. The related study demonstrates, for the first time, that basaloïd SCC constitute a distinct histo-molecular entity, which justifies its histologic recognition and distinction from SCC NOS. Additionally, their characteristic molecular profile highlights their intrinsic resistance to cytotoxic chemotherapy and could serve as a guide for targeted therapies.