Molecular Characterization of NUT Carcinoma: A Report from the NUT Carcinoma Registry.

Abstract

NUT carcinoma (NC) is an underdiagnosed, poorly differentiated squamous cell cancer with a median survival of 6.7 months. Defined by NUTM1 fusions, NC enhances oncogene transcription, including MYC. We investigated the ability of standard next-generation sequencing (NGS) to identify NUTM1 fusions and describe additional molecular features of NC. This study included 116 patients with NC whose tumors underwent broad-panel NGS (>80 genes) of DNA, ctDNA, and/or RNA fusion sequencing between 2013 and 2024. NGS reports and medical records were manually reviewed. Of 116 patients (median age, 38; 40.5% female), 84.5% had DNA, 12.1% had ctDNA, and 51.7% had RNA fusion testing. In a subset of 100 patients with DNA/ctDNA testing, 92.9% (n = 79/85) had <10 pack-years/never-smoking history, and 58.8% (n = 47/80) had a BRD4::NUTM1 fusion. The median tumor mutational burden was 1.0 mut/Mb (range 0.0-16.0; n = 71 known), and 19.7% (n = 13/66) had PD-L1 expression ≥1%. DNA, ctDNA, RNA fusion, NUT IHC, and NUTM1 FISH detected NC fusions in 21.6%, 21.4%, 83.9%, 100.0%, and 91.9% of tests, respectively. Co-occurring pathogenic mutations included oncogenes PIK3CA, RET, and FGFR3 and tumor suppressors ATM and BRCA1 (n = 1 each). Secondary genes altered in >5% of NCs included LDL receptor-related protein 1B (LRP1B; 10.4%), histone-lysine N-methyltransferase 2D (KMT2D; 8.0%), and FAT atypical cadherin 1 (FAT1; 5.5%); common pathways with mutated genes were epigenetic (57.0%), cell cycle (26.0%), and DNA repair (24.0%). Standard DNA NGS detects less than a quarter of NCs; RNA-based fusion testing, or NUT IHC/NUTM1 FISH, should be routine for suspected NC. NCs are enriched in co-occurring epigenetic, cell cycle, and DNA repair alterations, warranting further evaluation.