Molecular characterization of NUT carcinoma: A report from the NUT carcinoma registry.
Authors: Luo Jia , Kim Justin J. , Walton Sara A. , Nguyen Tom , Paik Paul K. , Chaft Jamie E. , Hsu Robert , Piha-Paul Sarina A. , Janne Pasi A. , Sholl Lynette M. , DuBois Steven G. , Hanna Glenn J. , Shapiro Geoffrey Ira , French Christopher Alexander 
Published: June 2024

8553

Background: NUT carcinoma (NC) is an underdiagnosed, poorly differentiated squamous cell cancer with a median survival of 6.7 months. NC is defined and driven by NUTM1 fusions; NUT fusion oncoproteins enhance oncogene transcription, including that of MYC. The ability of standard NGS assays to identify NUTM1 fusions is unknown and other molecular features of NC are undefined. Methods: Patients (pts) with NC who consented to participate in a worldwide registry and whose tumors underwent standard of care (SOC) broad panel NGS (>80 genes) of DNA, ctDNA, and/or RNA sequencing were included. Primary NGS reports and medical records were manually reviewed. Results: A cohort of 95 pts had their NC tumors sent for SOC panel DNA (88.4%, n=84), ctDNA (15.5%, n=13), and/or RNA fusion (43.2%, n=41) testing; 97.9% (n=93) pts had sufficient sample for at least one test. The median age was 39 (range 8-77); 37.9% were female, 63.2% had a thoracic primary, and 58.5% had metastatic disease. There were 17 unique DNA, 4 ctDNA, and 16 RNA fusion assays; 55.9% (52/93) pts’ NUT fusions were detected by at least one of these tests. Fusions diagnostic of NUT carcinoma ( NUTM1 or a common NC fusion partner [ BRD4, NSD3,and BRD3]) were detected in 24.1% of DNA tests (18/80 [22.5%] DNA, 3/13 [23.1%] ctDNA, n=6 had both tests) and 82.1% (32/39) RNA tests. Only 43.5% (37/80) DNA, 38.5% (5/13) ctDNA, and 92.3% (36/39) RNA fusion assays tested for NUTM1 or all common partners; of these, NUT fusions were detected in 34.6% (18/52) DNA, 60.0% (3/5) ctDNA, and 88.9% (32/36) RNA tests. A subset of 83 pts with NC and panel DNA testing were examined; the median age was 39 (range 10-77), 37.3% were female, and 94.6% had a <10 py/never smoking history (n=74 known); 63.9% of pts had thoracic primaries; 54.7% of fusions were driven by BRD4::NUTM1 (n=64 known). The median tumor mutation burden (TMB) was 1.0 mt/Mb (range 0.0-16.0, n=54 known) and 23.3% of PD-L1 tumor proportion scores were ≥1% (range 0-70%, n=43 known). Tier 1/2 mutations included oncogenes PIK3CA, RET, and FGFR3 (each, n=1), and tumor suppressors TP53 (n=3) and BCOR (n=2). Altered genes in >5% of NCs with potential biological significance included KMT2D/MLL2(15.6%), SPEN(8.1%), ATM (7.2%), CHEK2 (6.4%), BRCA2 (6.0%), and APC (6.0%); common pathways with mutated genes were 62.7% epigenetic, 34.9% DNA repair, and 30.1% cell cycle. Of the NC pts with a CHEK2 alteration (n=5), all had a non-thoracic primary. As the most common second alteration, we evaluated the prognostic impact of MLL2 alteration and found no association with survival. Conclusions: Standard DNA NGS testing detects 24% of NUT carcinomas; only one DNA assay contained all three common NC gene fusion partners ( BRD4, NSD3,and BRD3). RNA-based fusion testing, or NUT IHC/ FISH should be routine in any suspected case of NC. NUT carcinomas are enriched in co-occurring epigenetic, DNA repair, and cell cycle alterations, which merit further evaluation for functional significance.