Light Microscopy-Based Techniques to Identify TFEB-Altered Renal Cell Carcinoma

TFEB‑altered renal cell carcinomas are rare neoplasms, frequently mimicking other tumors. Although FISH remains the diagnostic gold standard, its limited availability has prompted the evaluation of light microscopy‑based ancillary markers. This study compares the performance of immunohistochemistry and RNA‑ISH in detecting TFEB‑altered renal cell carcinomas and distinguishing them from other renal neoplasms. Sixteen FISH/molecularly confirmed TFEB‑altered renal cell carcinomas (12 rearranged, 4 amplified) were analyzed by immunohistochemistry for TFEB (3 different clones), cathepsin K (clone 3F9), and GPNMB, and RNA‑ISH for TRIM63 and TFEB. Forty-eight clear cell renal cell carcinomas, 48 papillary renal cell carcinomas, 72 chromophobe renal cell carcinomas, 48 oncocytomas, 5 TFE3‑rearranged renal cell carcinomas, and 4 FLCN/mTOR-mutated renal cell neoplasms served as controls. Staining patterns and diagnostic performance were assessed and compared. TFEB immunohistochemistry demonstrated variable sensitivity, with the Bethyl assay showing the greatest reliability. Cathepsin K (clone 3F9) and GPNMB displayed high sensitivity but lacked specificity, labeling 40% and 50% of TFE3‑rearranged tumors, respectively, and subsets of common renal neoplasms. Similarly, TRIM63 RNA‑ISH was strongly positive in all TFEB‑altered renal cell carcinomas but also in TFE3‑rearranged neoplasms. Instead, TFEB RNA‑ISH demonstrated exclusive expression in all TFEB‑altered renal cell carcinomas, with stronger signals in rearranged tumors, whereas it was negative in all control cases, including TFE3‑rearranged neoplasms. TFEB RNA‑ISH emerged as the most accurate light microscopy‑based method for detecting TFEB‑altered renal cell carcinomas, reliably distinguishing them from TFE3‑rearranged and other renal tumors, potentially representing a practical and cost‑effective alternative to FISH, particularly when molecular diagnostics are lacking.