NUT carcinoma of the upper respiratory tract: Two case reports and literature review

Abstract

NUT carcinoma is a rare and highly aggressive malignancy characterized by the rearrangement of the NUTM1 gene. It typically arises in midline structures, including the respiratory tract. Due to its rarity and poor prognosis, early diagnosis and effective treatment remain challenging. This report presents two cases of NUT carcinoma occurring in the respiratory tract, additionally, a review of the literature is provided to enhance understanding of this disease. Both patients were young females, one tumor was located in the larynx and the other in the left main bronchus. Endoscopic forceps biopsy samples revealed tumor growth beneath the superficial mucosal epithelium, arranged in sheets, cords, or nests with extensive necrosis. The tumor cells were uniform in size, with eosinophilic cytoplasm, ill-defined borders, and round or oval nuclei showing hyperchromasia and a high nuclear-to-cytoplasmic ratio. One case showed focal areas with squamous differentiation. Immunohistochemically, tumor cells were positive for P40, P63, and NUT, and fluorescence in situ hybridization detected NUT gene rearrangement, confirming the diagnosis of NUT carcinoma. One patient experienced rapid disease progression despite receiving chemotherapy and died within five months. Another patient declined further treatment after diagnosis. NUT carcinoma is a rare and aggressive malignancy of the respiratory tract with a poor prognosis. Early diagnosis through molecular testing is crucial for appropriate management. However, diagnosis is often delayed until advanced stages, contributing to low survival rates. Increased awareness of this tumor among clinicians and pathologists may facilitate earlier detection and potentially improve patient outcomes.

1. Introduction

NUT carcinoma is a rare and highly aggressive malignancy that predominantly occurs in the thorax, head, and neck regions. It is defined by the presence of NUTM1 gene rearrangements, most frequently forming a BRD4::NUTM1 fusion. ¹ Despite its rarity, NUT carcinoma carries a dismal prognosis, with a median overall survival of less than one year. ² Herein, we report two cases of NUT carcinoma involving the respiratory tract and provides a review of the current literature.

2. Case presentation

2.1. Case 1

A female in her early teens presented to the 920th Hospital of Joint Logistics Support Force of PLA in June 2023 with a one-month history of wheezing. Her symptoms had worsened over the preceding two weeks and were accompanied by hoarseness. Physical examination revealed stridor and signs of respiratory distress. Contrast-enhanced neck CT demonstrated significant, irregular thickening of the laryngopharyngeal wall, most pronounced in the region of the left vocal cord. The lumen at the narrowest point measured approximately 6 mm in the anteroposterior diameter and 3.5 mm transversely. The lesion exhibited mild contrast enhancement after contrast administration. These imaging findings were consistent with a laryngopharyngeal mass causing severe pharyngeal stenosis (Figure 1(A)). After admission, the lesion identified via laryngoscopy, and the swollen tissue was biopsied with forceps for pathological examination. Histological evaluation revealed a tumor situated in the submucosa, beneath the squamous epithelium and interspersed among mucous glands. It exhibited a growth pattern of solid sheets, cords, and nests, accompanied by extensive necrosis (Figure 1(B)). The tumor cells were uniform in size, with eosinophilic cytoplasm, indistinct cell boundaries, round or oval nuclei, hyperchromatic nuclei demonstrating a high nuclear-to-cytoplasmic ratio. Focal squamous differentiation was noted (Figure 1(C) and (D)). Immunohistochemical staining showed the tumor cell were positively stained with CK5/6, CK14, P40 (Figure 1(E)), P63, CKpan, CK8/18 and NUT (Figure 1(F)), while negative with CD56, CD99, chromogranin (CgA), Desmin, INSM1, MyoD1, Myogenin, Syn, CD20, CD3, S-100, SOX10. Fluorescence in situ hybridization (FISH) using a break-apart probe confirmed the presence of NUT gene rearrangement (Figure 1(G)). Based on the combined histomorphological, immunohistochemical, and molecular findings, a diagnosis of NUT carcinoma was established. The patient was subsequently started on chemotherapy. Despite aggressive treatment, her disease progressed rapidly, and she succumbed to the disease within five months of diagnosis.

Figure 1.

Case1 (A) CT scans of the neck in sagittal and axial planes. (B–D) The small blue round tumor cells exhibit invasive growth, with focal areas showing squamous cell differentiation. HE staining at ×40, ×200, and ×400 magnification respectively. (E) The carcinoma is positive for P40, (F) positive for NUT (immunohistochemical staining, magnification ×200). (G) NUT gene breakage positive (fluorescence in situ hybridization, magnification ×1000).

2.2. Case 2

A female patient in her early twenties presented to the 920th Hospital of the Joint Logistics Support Force of the PLA in November 2024 with a three-week history of cough and shortness of breath. She reported decreased endurance and sleep disturbances but no significant weight loss. Physical examination revealed bilateral supraclavicular lymphadenopathy, the lymph nodes were firm, fixed, non-tender, and measured approximately the size of a broad bean. Chest CT demonstrated a heterogeneously enhancing soft-tissue mass in the left hilar region with ill-defined margins. The left upper lobe bronchus appeared truncated, and the left lower lobe bronchus was partially compressed. Patchy opacities were noted in the left lung with partial atelectasis of the left lower lobe. Additionally, small patchy opacities were present in the posterior basal segment of the right lower lobe. Mediastinal lymphadenopathy was evident, with the largest node measuring 42 × 34 mm. Flexible bronchoscopy revealed an exophytic, mucosa-covered mass causing extrinsic compression and stenosis of the mid-portion of the left main bronchus (Figure 2(A)). A biopsy was obtained for histopathological examination. Microscopic examination showed the tumor was located in the submucosa and consisted of infiltrative sheets of small, blue, round cells associated with necrosis. The cytomorphology was similar to that described in the first case, but no squamous differentiation was identified (Figure 2(B)–(D)). Immunohistochemically, the tumor cell were positively stained with P40, P63, TTF-1 (Figure 2(E)) CD99 and NUT (Figure 2(F)), but negative for Pan-CK, WT-1, CD56, CgA, CK5/6, CK7, INSM1, LCA, NapsinA, P40, P63, Syn, TTF-1, BCOR, CD20, CD3, CyclinD1, Desmin, Fli-1, HMB45, Mpo, MyoD1, Myogenin, NKX2.2 and EMA, The Ki67 proliferation index was approximately 60%. FISH using a break apart probe confirmed rearrangement of the NUT gene (Figure 2(G)). After the diagnosis was established, the patient and her family were informed of the disease and its prognosis. Given the advanced stage of her illness, the patient declined further treatment and opted for discharge against medical advice.

Figure 2.

Case2 (A) Bronchoscopy, a grayish-white mass is observed obstructing the bronchus. (B–D) The small blue round tumor cells exhibit invasive growth. HE staining magnification at ×40, ×200, and ×400 respectively. (E) The carcinoma is positive for TTF-1, (F) positive for NUT (immunohistochemical staining, magnification ×200). (G) NUT gene breakage positive (fluorescence in situ hybridization, magnification ×1000).

3. Discussion

NUT carcinomas are poorly differentiated malignant neoplasms that show significant morphologic overlap with other undifferentiated or poorly differentiated tumors. As such, diagnosis requires a careful and deliberate approach, with strong consideration given to the use of NUT immunohistochemistry. Although the cytologic features are not specific, certain findings on H&E can serve as helpful clues, including abrupt keratinization, dyscohesive growth, marked nuclear atypia, small round blue cell morphology, and areas of necrosis. ³ Abrupt keratinization is a characteristic feature of NUT carcinoma compared to other undifferentiated cancers, ¹ observed in the first case but absent in the second case, possibly due to the limited sampling of small biopsy specimens. The tumor cells typically have round to oval nuclei with a variable chromatin pattern and inconspicuous cytoplasm, often appearing as “naked nuclei” on histologic sections. In some cases, abrupt keratinization may be present and is occasionally accompanied by small but distinct nucleoli. Therefore, the tumor is almost indistinguishable from small round cell tumors in terms of organizational morphology, and NUT carcinoma should be considered for differential diagnosis of small round cell tumors, especially those originating from midline structures and the head and neck region.

Because of their rarity and variable morphology, NUT carcinomas are often misdiagnosed as other poorly differentiated or undifferentiated malignancies, such as poorly differentiated squamous cell carcinoma, small cell carcinoma, Ewing sarcoma, or other round blue cell tumors. Immunohistochemistry plays a critical role in narrowing the differential diagnosis, but findings can be nonspecific. For example, NUT carcinomas often express p63, P40 and cytokeratins, which can mimic squamous differentiation. ⁴ The previous study found that CD34 was expressed in some cases, ⁵ this may indicate the primitive or undifferentiated nature of many tumor cells, further suggesting that the tumor is highly invasive. Definitive diagnosis requires demonstration of NUT protein expression by immunohistochemistry or confirmation of NUT gene rearrangement by molecular methods such as FISH or next-generation sequencing. ⁵ Both patients in this report exhibited a diagnostic immunohistochemical profile (positive for P63, P40, and NUT), which was further confirmed by the detection of NUT gene rearrangement via FISH. These findings are consistent with established literature.

While molecular confirmation of NUTM1 rearrangement by FISH or sequencing can be useful, it is not always necessary for diagnosis^6. In most cases, immunohistochemistry using the C52B1 clone is both highly sensitive and specific for NUT carcinoma and can serve as a standalone diagnostic tool when results are unequivocally positive in the appropriate morphologic and clinical context. ⁷ FISH or other molecular testing may be reserved for cases with equivocal IHC staining or when clinical suspicion remains high despite negative or weak IHC results. Since the NUT antibody used in our laboratory was a different clone (not C52B1) and the morphological features were atypical, we proceeded with FISH for confirmation. This case underscores that in diagnostic practice, atypical histology necessitates a comprehensive approach integrating immunohistochemistry and molecular testing.

In the differential diagnosis, undifferentiated carcinoma should be considered firstly. It may have histological features identical to those of NUT carcinoma, making differentiation challenging. ⁸ The tumor cells of undifferentiated carcinoma are medium to large, round to oval elements. They exhibit pleomorphic and hyperchromatic nuclei with inconspicuous to prominent nucleoli, along with variable amounts of eosinophilic cytoplasm and a high nuclear-to-cytoplasmic ratio. These features are accompanied by a marked increase in mitotic activity (often with atypical forms), as well as tumor necrosis and apoptosis. A definitive diagnosis of undifferentiated carcinoma can be established only after excluding all more specific tumor types—such as NUT carcinoma, esthesioneuroblastoma, and neuroendocrine carcinoma—through immunohistochemistry, based on morphology consistent with undifferentiated carcinoma. When tumors occur in the upper respiratory tract, differentiation between NUT carcinoma and small cell neuroendocrine carcinoma is also required. Compared to small cell carcinoma, NUT carcinoma cells are larger, have abundant cytoplasm, and loose nucleoli, lacking the distinct fine nuclear chromatin characteristic of small cell carcinoma. Additionally, both tumors can present with widespread chromatin compression forming “compression artifacts.” Immunohistochemistry can aid in differentiating between the two. Although the prognosis for small cell carcinoma is also poor, patients can benefit from combination therapy with etoposide and platinum-based drugs. ⁹ Since patients with NUT carcinoma tend to be younger. It is important to differentiate them from Ewing’s sarcoma, rhabdomyosarcoma, lymphohematopoietic system tumors, synovial sarcoma, and other small blue round cell tumors. These tumors can be distinguished by their specific immunohistochemistry and molecular characteristics. Ewing sarcoma characteristically expresses CD99 (diffuse membranous positivity) and NKX2.2 (nuclear positivity); the diagnosis of rhabdomyosarcoma relies on the nuclear positivity of MyoD1 and myogenin; hematolymphoid tumors commonly express LCA (CD45) and require further immunophenotyping for subclassification; synovial sarcoma typically shows at least focal positivity for epithelial markers (CK/EMA), often accompanied by nuclear positivity for TLE1 and SS18, and harbors the SS18-SSX fusion gene.

The prognosis of NUT carcinoma is poor, with most patients surviving less than one year despite aggressive treatment. ² The median survival time of NUT carcinoma patients was less than one year, and the five-year survival rate was 7.09%.^10,11 Of the two patients reported here, one succumbed to disease progression after five months of treatment, while the other discontinued therapy. Presently, there is no definitive and effective treatment for this tumor, although complete surgical resection is effective in improving the survival rate. According to a retrospective study, patients with complete tumor resection had a significantly longer survival time. Most NUT carcinoma were poorly responsive to cytotoxic chemotherapy. ¹² However, targeted therapies, such as BET inhibitors, are under investigation and may offer hope for improved outcomes in the future. ¹³ BET inhibitors target the bromodomain of BRD4, disrupting the oncogenic activity of the BRD4-NUT fusion protein. ¹⁴ Early-phase clinical trials have shown promise, ¹⁵ but further research is needed to establish their efficacy and safety.

4. Conclusion

NUT carcinoma is a rare and aggressive malignancy of the respiratory tract with a poor prognosis. Early diagnosis through molecular testing is crucial for appropriate management, including timely treatment decisions and therapeutic strategies. However, the tumor is usually diagnosed at an advanced stage, which contributes to lower survival rates due to delayed intervention. Therefore, raising awareness of the disease could help clinicians and pathologists make early diagnoses that could potentially extend patients’ lives. Further research into targeted therapies, such as BET inhibitors, is needed to improve survival outcomes for patients with this devastating disease.