School of Medicine

Department of Pathology


The H&E sections show fragments of sinonasal mucosa with sheets of basaloid, monotonous and primitive appearing small- to medium-sized cells demonstrating round to oval nuclei with vesicular chromatin and prominent nucleoli. In some areas the infiltrate is arranged in a papillary architecture with mixed exophytic and inverted growth patterns, and foci of abrupt keratinization. There is brisk mitotic activity and coagulative tumor necrosis that is present through the vast majority of the tumor. Destructive bone invasion is also present.

By immunohistochemical staining, the tumor cells are positive for P63 (strong, diffuse), P16 (patchy), and NUT1 (diffuse, speckled), and negative for INSM1 and low-risk and high-risk human papillomavirus (HPV) subtypes by RNA in-situ hybridization. Tumor has wild type p53 staining. Given these morphologic features and immunophenotype, a diagnosis of NUT carcinoma (NC)is rendered.

NC an epithelial malignancy with a monotonous appearance, and genetically defined by a rearrangement of the Nuclear Protein in Testis (NUTM1) gene. Formerly known as NUT midline carcinoma, it is a poorly differentiated carcinoma arising from midline structures of the head and neck region. The pathogenesis involves the presence of chromosomal translocations and fusions of the NUTM1 gene with several fusion partners including BRD4, BRD3 and NSD3. NUT-fusion oncoproteins, most commonly BRD4-NUT, act as single drivers of NC that function by blocking differentiation and maintaining proliferation. The BRD4::NUTM1 fusion t(15;19)(q14;p13.1) is strongly associated with head and neck tumors.

NC is relatively rare with no sex or geographic predilection. It affects patients of all age groups with a median of 24 years. The etiology is unknown, and no associations with smoking, HPV, EBV, or other viral infections have been found. NC has an aggressive clinical course and is usually at an advanced stage at the time of diagnosis. These tumors generally show minimal response to radiation and conventional chemotherapy, while molecular targeted therapies with bromodomain inhibitors (BETi) and histone deacetylase inhibitors (HDACi) sometimes result in a growth arrest. Overall, the prognosis is poor and the median survival is less than one year.

Microscopically, the NC shows sheets of primitive-appearing, monotonous, small- to medium-sized cells with minimal granular, eosinophilic to amphophilic cytoplasm. The malignant cells have round to oval nuclei with variably prominent nucleoli. The mitotic rate is usually high and prominent tumor necrosis is present. Foci of abrupt squamous differentiation with keratin pearl formation is typically seen. Intratumoral acute inflammation with neutrophil infiltrates is observed in a subset of cases.

By immunohistochemistry, NC shows strong, diffuse, and speckled NUT1 nuclear positivity. They are typically positive for P63, P40, CK5/6, pancytokeratin, and EMA; while negative for CD99, NKX2.2, S100, synaptophysin, chromogranin, and INSM1. Demonstration of the NUTM1 rearrangement is required, which can be done by immunostaining or molecular techniques.

Differential diagnosis is with other poorly differentiated carcinomas of the head and neck, including basaloid squamous cell carcinoma, poorly differentiated neuroendocrine carcinoma, sinonasal undifferentiated carcinoma (SNUC), and adamantinoma-like Ewing sarcoma. Basaloid squamous cell carcinoma can show abrupt keratinization and p63 positivity, but it tends to be more pleomorphic rather than monotonous and is negative for NUT1. Poorly differentiated neuroendocrine carcinoma is a high-grade tumor with small cell or large cell morphology and expression of markers of neuroendocrine differentiation including synaptophysin, chromogranin, and INSM1, while negative for p63 and nuclear NUT1. SNUC shows higher grade nuclei with prominent pleomorphism. It is typically positive for pancytokeratins (AE1/AE3 and CAM5.2), and negative for p63 and NUT1. Some cases may have mutations of the IDH genes. Adamantinoma-like Ewing sarcoma predominantly involves the the head and neck region. Morphologically, it can also show abrupt keratinization and some p63 positivity, but these tumors are negative for NUT1 and positive for CD99 and NKX2.2. These tumors also have similar fusions as Ewing sarcoma (involving fusions of the FET family of genes to the ETS family of genes, FET-ETS), however, the relationship of these tumors to classic Ewing sarcoma is uncertain 

1. WHO Classification of Head and Neck Tumors (5th Edition), Online Version. International Agency for Research on Cancer. Available from:

2. McLean-Holden AC, Moore SA, Gagan J, French CA, Sher D, Truelson JM, Bishop JA. NUT Carcinoma in a Patient with Unusually Long Survival and False Negative FISH Results. Head Neck Pathol. 2021 Jun;15(2):698-703. doi: 10.1007/s12105-020-01220-5. Epub 2020 Sep 12. PMID: 32918711; PMCID: PMC8134642.

3. Chau NG, Ma C, Danga K, Al-Sayegh H, Nardi V, Barrette R, Lathan CS, DuBois SG, Haddad RI, Shapiro GI, Sallan SE, Dhar A, Nelson JJ, French CA. An Anatomical Site and Genetic-Based Prognostic Model for Patients With Nuclear Protein in Testis (NUT) Midline Carcinoma: Analysis of 124 Patients. JNCI Cancer Spectr. 2019 Nov 6;4(2):pkz094. doi: 10.1093/jncics/pkz094. PMID: 32328562; PMCID: PMC7165803.

4. Edgar M, Caruso AM, Kim E, Foss RD. NUT Midline Carcinoma of the Nasal Cavity. Head Neck Pathol. 2017 Sep;11(3):389-392. doi: 10.1007/s12105-016-0763-0. Epub 2016 Oct 18. PMID: 27757815; PMCID: PMC5550387.

5. Bishop JA, French CA, Ali SZ. Cytopathologic features of NUT midline carcinoma: A series of 26 specimens from 13 patients. Cancer Cytopathol. 2016 Dec;124(12):901-908. doi: 10.1002/cncy.21761. Epub 2016 Jul 11. PMID: 27400194.

6. Sun H, McGuire MF, Zhang S, Brown RE. NUT Midline Carcinoma: Morphoproteomic Characterization with Genomic and Therapeutic Correlates. Ann Clin Lab Sci. 2015 Fall;45(6):692-701. PMID: 26663801.

7. Lauer UM, Hinterleitner M, Horger M, Ohnesorge PV, Zender L. NUT Carcinoma-An Underdiagnosed Malignancy. Front Oncol. 2022 Jul 26;12:914031. doi: 10.3389/fonc.2022.914031. PMID: 35957893; PMCID: PMC9360329.

8. Moreno V, Saluja K, Pina-Oviedo S. NUT Carcinoma: Clinicopathologic Features, Molecular Genetics and Epigenetics. Front Oncol. 2022 Mar 16;12:860830. doi: 10.3389/fonc.2022.860830. PMID: 35372003; PMCID: PMC8966081.

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Board type Review Questions:

1. A 30-year-old male patient presents with a three month history of nasal congestion, nasal bleeding and fatigue. Head and neck CT imaging shows a lesion causing opacification of the maxillary sinus and destructive invasion of the surrounding bones. A diagnosis of NUT carcinoma was made on a biopsy of the lesion. Besides the morphologic features, which of the below immunoprofiles helped with rendering this diagonosis?

A. CD99-/INSM1-/NKX2.2-/NUT1-/Pancytokeratin+/Synaptophysin-

B. CD99-/INSM1-/NKX2.2-/NUT1+/Pancytokeratin+/Synaptophysin-

C. CD99+/INSM1-/NKX2.2+/NUT1-/Pancytokeratin+/Synaptophysin-

D. CD99-/INSM1+/NKX2.2-/NUT1-/Pancytokeratin+/-/Synaptophysin+

B. CD99-/INSM1-/NKX2.2-/NUT1+/Pancytokeratin+/Synaptophysin-. NUT1 is a sensitive marker for NUT carcinoma, and it can be assessed by immunohistochemical staining or molecular techniques. The other choices listed are expected immunoprofiles for sinonasal undifferentiated carcinoma (A),  adamantinoma-like Ewing sarcoma (C), and  neuroendocrine carcinoma (D).

2. What is the most common genetic abnormality identified in NUT carcinoma?

A. FET-ETS fusion
B. IDH mutation
D. SMARCB1 gene deletion

C. NUT-BRD4. The most common genetic abnormality identified in NC is NUT-BRD4 fusion. FET-ETS fusion is seen in adamantinoma-like Ewing sarcoma; IDH mutations can be seen in SNUC; and SMARCB1 gene deletion is seen in SMARCB1 deficient carcinoma which is a poorly to undifferentiated sinonasal carcinoma defined by this deletion (not mentioned in discussion).