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Riess JW, Rahman S, Kian W, Edgerly C, Heilmann AM, Madison R, Ramkissoon SH, Klaitman SS, Chung JH, Trabucco SE, Jin DX, Alexander BM, Klempner SJ, Albacker LA, Frampton GM, Roisman LC, Miller VA, Ross JS, Schrock AB, Gregg JP, Peled N, Sokol ES, Ali SM. Genomic profiling of solid tumors harboring BRD4-NUT and response to immune checkpoint inhibitors. Transl Oncol 2021; 14:101184. [PMID: 34333275 PMCID: PMC8340305 DOI: 10.1016/j.tranon.2021.101184] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 07/20/2021] [Accepted: 07/20/2021] [Indexed: 12/28/2022] Open
Abstract
NUT carcinoma is a rare but aggressive solid tumor that can be diagnosed by presence of the BRD4-NUT fusion. This series presents 31 cases of solid tumors that harbor BRD4-NUT but often carry other diagnoses such NSCLC—NOS and NSCLC-SCC. Despite lack of PD-L1 expression and a low tumor mutational burden, two index cases responded to either nivolumab or atezolizumab+chemotherapy with partial response or better with 4–5 month duration of response. The unexpected response to checkpoint inhibitors could be explained by a very high affinity of the fusion peptide at the junction of BRD4 and NUT to the MHC complex as recently suggested for an exceptional response to an immune checkpoint inhibitor in a fusion bearing low TMB, low PD-L1 expression head and neck carcinoma.
Background The translocation t(15:19) produces the oncogenic BRD4-NUT fusion which is pathognomonic for NUT carcinoma (NC), which is a rare, but extremely aggressive solid tumor. Comprehensive genomic profiling (CGP) by hybrid-capture based next generation sequencing of 186+ genes of a cohort of advanced cancer cases with a variety of initial diagnoses harboring BRD4-NUT may shed further insight into the biology of these tumors and possible options for targeted treatment. Case presentation Thirty-one solid tumor cases harboring a BRD4-NUT translocation are described, with only 16% initially diagnosed as NC and the remainder carrying other diagnoses, most commonly NSCLC—NOS (22%) and lung squamous cell carcinoma (NSCLC-SCC) (16%). The cohort was all microsatellite stable and harbored a low Tumor Mutational Burden (TMB, mean 1.7 mut/mb, range 0–4). In two index cases, patients treated with immune checkpoint inhibitors (ICPI) had unexpected partial or better responses of varying duration. Notably, four cases – including the two index cases - were negative for PD-L1 expression. Neo-antigen prediction for BRD4-NUT and then affinity modeling of the peptide-MHC (pMHC) complex for an assessable index case predicted very high affinity binding, both on a ranked (99.9%) and absolute (33 nM) basis. Conclusions CGP identifies BRD4-NUT fusions in advanced solid tumors which carry a broad range of initial diagnoses and which should be re-diagnosed as NC per guidelines. A hypothesized mechanism underlying responses to ICPI in the low TMB, PD-L1 negative index cases is the predicted high affinity of the BRD4-NUT fusion peptide to MHC complexes. Further study of pMHC affinity and response to immune checkpoint inhibitors in patients with NC harboring BRD4-NUT is needed to validate this therapeutic hypothesis.
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Affiliation(s)
- Jonathan W Riess
- UC Davis Comprehensive Cancer Center, Sacramento, CA, United States
| | | | - Waleed Kian
- Legacy Heritage Oncology Center/Larry Norton Cancer Institute, Soroka Medical Center, Ben-Gurion University, Beer Sheva, Israel
| | | | | | | | | | - Shai Shlomi Klaitman
- Legacy Heritage Oncology Center/Larry Norton Cancer Institute, Soroka Medical Center, Ben-Gurion University, Beer Sheva, Israel
| | - Jon H Chung
- Foundation Medicine, Cambridge, MA, United States
| | | | - Dexter X Jin
- Foundation Medicine, Cambridge, MA, United States
| | | | | | | | | | - Laila C Roisman
- Legacy Heritage Oncology Center/Larry Norton Cancer Institute, Soroka Medical Center, Ben-Gurion University, Beer Sheva, Israel
| | | | - Jeffrey S Ross
- Foundation Medicine, Cambridge, MA, United States; SUNY Upstate Medical University
| | | | - Jeffrey P Gregg
- UC Davis Comprehensive Cancer Center, Sacramento, CA, United States; Foundation Medicine, Cambridge, MA, United States
| | - Nir Peled
- Legacy Heritage Oncology Center/Larry Norton Cancer Institute, Soroka Medical Center, Ben-Gurion University, Beer Sheva, Israel
| | | | - Siraj M Ali
- Foundation Medicine, Cambridge, MA, United States.
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