In total, 10 genes (STAMBP, TIMP4, TMEM14C, CANX, SUV420H1, HSP90B1, PDIA3, MTHFD2, BCAT1, and SLC22A15) were regulated by miR-99a-3p in HNSCC cells and were closely involved in HNSCC molecular pathogenesis. Here, BCAT1 is linked to head and neck squamous cell carcinoma.