oligonucleotides

2022-10-14 | Cancer-Specific Sequences in the Diagnosis and Treatment of NUT Carcinoma

NUT carcinoma (NC) is a solid tumor caused by the rearrangement of NUTM1 that usually develops in midline structures, such as the thorax. No standard treatment has been established despite high lethality. Thus, we investigated whether targeting the junction region of NUTM1 fusion breakpoints could serve as a potential treatment option for NC.We designed and evaluated a series of small interfering RNAs (siRNAs) targeting the junction region of BRD4-NUTM1 fusion (B4N), the most common form of NUTM1 fusion. Droplet digital polymerase chain reaction using the blood of patients was also tested to evaluate the treatment responses by the junction sequence of the B4N fusion transcripts.As expected, the majority of NC fusion types were B4N (12 of 18, 67%). B4N fusion-specific siRNA treatment on NC cells showed specific inhibitory effects on the B4N fusion transcript and fusion protein without affecting the endogenous expression of the parent genes, resulting in decreased relative cell growth and attenuation of tumor size. In addition, the fusion transcript levels in platelet-rich-plasma samples of the NC patients with systemic metastasis showed a negative correlation with therapeutic effect, suggesting its potential as a measure of treatment responsiveness.This study suggests that tumor-specific sequences could be used to treat patients with fusion genes as part of precision medicine for a rare but deadly disease.

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2022-01-06 | miR-766-5p Targets Super-Enhancers by Downregulating CBP and BRD4.

Super-enhancers (SE) are clusters of transcription enhancers that drive gene expression. SEs are typically characterized by high levels of acetylation of histone H3 lysine 27 (H3K27ac), which is catalyzed by the histone lysine acetyltransferase CREB binding protein (CBP). Cancer cells frequently acquire tumor-specific SEs at key oncogenes, such as MYC, which induce several hallmarks of cancer. BRD4 is recruited to SEs and consequently functions as an epigenetic reader to promote transcription of SE-marked genes in cancer cells. miRNAs can be potent candidates for nucleic acid therapeutics for cancer. We previously identified miR-766-5p as a miRNA that downregulated MYC expression and inhibited cancer cell growth in vitro. In this study, we show that miR-766-5p directly targets CBP and BRD4. Concurrent suppression of CBP and BRD4 cooperatively downregulated MYC expression in cancer cells but not in normal cells. Chromatin immunoprecipitation analysis revealed that miR-766-5p reduced levels of H3K27ac at MYC SEs via CBP suppression. Moreover, miR-766-5p suppressed expression of a BRD4-NUT fusion protein that drives NUT midline carcinoma. In vivo administration of miR-766-5p suppressed tumor growth in two xenograft models. Collectively, these data suggest that targeting SEs using miR-766-5p-based therapeutics may serve as an effective strategy for the treatment of MYC-driven cancers. SIGNIFICANCE: This study demonstrates that miR-766-5p targets CBP and BRD4, which can mitigate the protumorigenic consequences of SEs and oncogenic fusion proteins.

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2019-06-25 | Analysis of DNA methylation and microRNA expression in NUT (nuclear protein in testis) midline carcinoma of the sinonasal tract: a clinicopathological, immunohistochemical and molecular genetic study.

The aim of this study was a detailed clinicopathological investigation of sinonasal NUT midline carcinoma (NMC), including analysis of DNA methylation and microRNA (miRNA) expression. Three (5%) cases of NMC were detected among 56 sinonasal carcinomas using immunohistochemical screening and confirmed by fluorescence in situ hybridization. The series comprised 2 males and 1 female, aged 46, 60, and 65 years. Two tumors arose in the nasal cavity and one in the maxillary sinus. The neoplasms were staged pT1, pT3, and pT4a (all cN0M0). All patients were treated by radical resection with adjuvant radiotherapy. Two patients died 3 and 8 months after operation, but one patient (pT1 stage; R0 resection) experienced no evidence of disease at 108 months. Microscopically, all tumors consisted of infiltrating nests of polygonal cells with vesicular nuclei, prominent nucleoli and basophilic cytoplasm. Abrupt keratinization was present in only one case. Immunohistochemically, there was a diffuse expression of cytokeratin (CK) cocktail, CK7, p40, p63, and SMARCB1/INI1. All NMCs tested negative for EBV and HPV infection. Two NMCs showed methylation of RASSF1 gene. All other genes (APC, ATM, BRCA1, BRCA2, CADM1, CASP8, CD44, CDH13, CDKN1B, CDKN2A, CDKN2B, CHFR, DAPK1, ESR1, FHIT, GSTP1, HIC1, KLLN, MLH1a, MLH1b, RARB, TIMP3, and VHL) were unmethylated. All NMCs showed upregulation of miR-9 and downregulation of miR-99a and miR-145 and two cases featured also upregulation of miR-21, miR-143, and miR-484. In summary, we described three cases of sinonasal NMCs with novel findings on DNA methylation and miRNA expression, which might be important for new therapeutic strategies in the future.

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2018-03-08 | miR-3140 suppresses tumor cell growth by targeting BRD4 via its coding sequence and downregulates the BRD4-NUT fusion oncoprotein

Bromodomain Containing 4 (BRD4) mediates transcriptional elongation of the oncogene MYC by binding to acetylated histones. BRD4 has been shown to play a critical role in tumorigenesis in several cancers, and the BRD4-NUT fusion gene is a driver of NUT midline carcinoma (NMC), a rare but highly lethal cancer. microRNAs (miRNAs) are endogenous small non-coding RNAs that suppress target gene expression by binding to complementary mRNA sequences. Here, we show that miR-3140, which was identified as a novel tumor suppressive miRNA by function-based screening of a library containing 1090 miRNA mimics, directly suppressed BRD4 by binding to its coding sequence (CDS). miR-3140 concurrently downregulated BRD3 by bind to its CDS as well as CDK2 and EGFR by binding to their 3' untranslated regions. miR-3140 inhibited tumor cell growth in vitro in various cancer cell lines, including EGFR tyrosine kinase inhibitor-resistant cells. Interestingly, we found that miR-3140 downregulated the BRD4-NUT fusion protein and suppressed in vitro tumor cell growth in a NMC cell line, Ty-82 cells. Furthermore, administration of miR-3140 suppressed in vivo tumor growth in a xenograft mouse model. Our results suggest that miR-3140 is a candidate for the development of miRNA-based cancer therapeutics.

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2007-10-15 | BRD–NUT oncoproteins: a family of closely related nuclear proteins that block epithelial differentiation and maintain the growth of carcinoma cells

An unusual group of carcinomas, here termed nuclear protein in testis (NUT) midline carcinomas (NMC), are characterized by translocations that involve NUT, a novel gene on chromosome 15. In about 2/3rds of cases, NUT is fused to BRD4 on chromosome 19. Using a candidate gene approach, we identified two NMCs harboring novel rearrangements that result in the fusion of NUT to BRD3 on chromosome 9. The BRD3–NUT fusion gene encodes a protein composed of two tandem chromatin-binding bromodomains, an extra-terminal domain, a bipartite nuclear localization sequence, and almost the entirety of NUT that is highly homologous to BRD4–NUT. The function of NUT is unknown, but here we show that NUT contains nuclear localization and export sequences that promote nuclear-cytoplasmic shuttling via a leptomycin-sensitive pathway. In contrast, BRD3–NUT and BRD4–NUT are strictly nuclear, implying that the BRD moiety retains NUT in the nucleus via interactions with chromatin. Consistent with this idea, FRAP studies show that BRD4, BRD4–NUT and BRD3–NUT have significantly slower rates of lateral nuclear diffusion than that of NUT. To investigate the functional role of BRD–NUT fusion proteins in NMCs, we investigated the effects of siRNA-induced BRD3–NUT and BRD4–NUT withdrawal. Silencing of these proteins in NMC cell lines resulted in squamous differentiation and cell cycle arrest. Together, these data suggest that BRD–NUT fusion proteins contribute to carcinogenesis by associating with chromatin and interfering with epithelial differentiation.

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small molecules

2026-05-01 | Molecular reclassification of tracheoesophageal squamous cell carcinoma to BRD4–NUTM1–rearranged NUT midline carcinoma with early osseous metastases: A rare case highlighting the importance of molecular profiling

Nuclear protein in testis (NUT) carcinoma is a rare and highly aggressive malignancy characterized by rearrangement of the NUT midline carcinoma family member 1 (NUTM1) gene, most commonly involving a bromodomain-containing protein 4 (BRD4)–NUTM1 fusion, and is frequently underdiagnosed due to its histologic resemblance to poorly differentiated squamous cell carcinoma. We report a 41-year-old male who presented with cough and respiratory distress requiring airway stabilization and tracheobronchial stenting. Initial biopsy suggested poorly differentiated nonkeratinizing squamous cell carcinoma in the tracheoesophageal groove, and the patient received platinum-based chemotherapy followed by definitive chemoradiation, achieving a partial locoregional metabolic response. However, within 2 months, he developed early skeletal metastases confirmed on positron emission tomography/computed tomography and magnetic resonance imaging. Comprehensive molecular profiling subsequently identified a BRD4–NUTM1 fusion, leading to molecular reclassification as NUT carcinoma. The tumor demonstrated low Programmed Death-Ligand 1 (PD-L1) expression, low tumor mutational burden, and microsatellite stability. The patient was enrolled in a clinical trial evaluating bromodomain and extra-terminal domain inhibitors/BRD4 degraders. This case highlights the aggressive clinical course, diagnostic challenges, and the critical role of molecular profiling in accurately identifying NUT carcinoma and guiding targeted therapeutic strategies.

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2026-04-29 | IRS4 is a PI3K-activating cancer dependency up-regulated through DNA rearrangements or epigenetic mechanisms in multiple solid tumors.

Cancer therapeutics frequently fail in clinical trials because of poor therapeutic index (efficacy-to-toxicity ratio). We systematically identified targets likely to have a good therapeutic index, revealing insulin receptor substrate 4 (IRS4) as a dependency in IRS4-expressing cancers. Pan-cancer analysis of pediatric-enriched cancers revealed IRS4 expression consistent with dependency in 68% of choroid plexus, 37% of malignant rhabdoid, 31% of NUT midline, and 5% of osteosarcomas, while in adult cancers, it was expressed in 8% of uterine leiomyosarcomas and 1 to 2% of lung squamous, stomach, and breast carcinomas. IRS4 expression in adult tumors was associated with enhancer hijacking rearrangements, including recurrent GATA3-IRS4 and ANKRD30A-IRS4 in breast cancer, while rhabdoid and NUT midline cancers expressed IRS4 epigenetically. IRS4 fueled cancer dependency through PI3K-Akt activation, and domain analysis revealed the PH and PTB domains, which have a predicted drug pocket, to be dispensable, suggesting degradation-based modalities. These data reveal IRS4 as a target in IRS4-expressing cancers and suggest inhibitory approaches.

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2026-01-28 | NUTM1-rearranged sarcoma arising in the descending colon presenting as a submucosal mass: a case report

Abstract Purpose NUT midline carcinoma family number 1 ( NUTM1) -rearranged sarcoma is extremely rare and characterized by NUTM1 gene rearrangement with variable morphological features. The gastrointestinal tract is one of the most common sites. These sarcomas showing similar histopathological findings have yielded poor clinical outcomes. Case presentation A healthy 52-year-old Japanese man presented with a solitary, localized submucosal mass, 3 cm in size, in the descending colon. Microscopically, the sarcoma comprised sheet-like proliferation of plump epithelioid/rhabdoid cells, fibrosarcoma-like spindle cells showing an intersecting fascicular pattern, and neoplastic cell nests in hyalinized stroma. Immunohistochemistry (IHC) revealed that sarcoma cells were diffusely positive for NUT. Fluorescence in situ hybridization (FISH) confirmed NUTM1 gene rearrangement. Recurrences in the retroperitoneum at 9 and 21 months after initial surgery were surgically excised. The histopathological features and the results of IHC and FISH for the sarcoma coincided with those of previously reported NUTM1 -rearranged sarcoma occurring in the colon. The sarcoma recurred three times within a short time after the initial surgery. Therefore, the behavioral aggressiveness and site in which the sarcoma arose were also consistent with those of NUTM1 -rearranged sarcoma in the colon. Of note, these recurrent sarcomas comprised only a plump epithelioid/rhabdoid cell component. Conclusion We reported here an unusual sarcoma with unexpected poor outcomes. Our case may provide additional useful information regarding this extremely rare sarcoma of colonic submucosal origin.

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2026-01-28 | NUT carcinoma of the cheek managed with chemotherapy and surgical resection.

NUT(Nuclear Protein in Testes) carcinoma is a rare and aggressive malignancy characterised by rearrangements of the NUTM1 gene, primarily affecting midline structures in children and adults. We report a middle childhood male who presented with a left cheek swelling initially noticed 2 months earlier, surgically resected 1 month ago and recurred over the past week. Histopathology revealed a poorly differentiated neoplasm, with immunohistochemistry showing diffuse CK5/6, P63, P40 expression, intact SMARCA4, P16 negativity and speckled NUT nuclear staining confirming NUT carcinoma. Imaging demonstrated local extension with small-volume nodal metastases. He was treated with nine cycles of VDC-IE(vincristine, doxorubicin, and cyclophosphamide alternating with ifosfamide and etoposide) chemotherapy given at 3-week intervals, complicated by transient iron deficiency anaemia, followed by surgical excision with neck dissection and fibular flap reconstruction. Post-treatment positron emission tomography scan showed no metabolically active disease. Maintenance therapy with the histone deacetylase inhibitor vorinostat was initiated. This case highlights the importance of early recognition, multimodal therapy and emerging targeted treatment in improving outcomes for NUT carcinoma.

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2025-10-16 | Exploring Target-Based Screening, Molecular Dynamics Simulation and Principal Component Analysis for Drug Repurposing in NUT Midline Carcinoma

Purpose: NMC, a particularly malignant and invasive cancer resulting from the fusion of the NUT and BRD4 genes, yields a fusion protein that influences cell growth and regulates transcription. The deregulation of this protein has been documented in numerous cancerous conditions. The BD1 domain of BRD4-containing proteins has been demonstrated to bind to acetylated lysine residues on histone proteins, thereby impacting gene expression and chromatin remodeling. Methods: The DrugRep database was used for target-based screening (TBS) of FDA-approved drugs. CurPocket, an integrated tool within DrugRep, was employed to automatically identify potential binding pockets, and docking was performed using AutoDock Vina 1.1.2. SwissADME tools were utilized to assess pharmacokinetics and drug-likeness attributes. Additionally, the GROMACS and Galaxy platforms were employed for MD simulations and principal component analysis, respectively. Results: The TBS technique was used to evaluate 100 drug candidates for human intestinal absorption and blood-brain barrier permeability using the Egan-Egg model. 84 met the filtration criteria, and the drug-likeness models narrowed the pool to 48. Toxicophoric parameters, including the PAINS and Brenk alerts, further refined the subset of potential drugs to 39. The lead-likeness criteria identified five drugs, which were evaluated based on binding free energy and hydrogen bond analysis. MD simulation and PCA led to more in-depth evaluations, ultimately leading to the selection of estrone as a potential repurposed drug for NMC. Conclusion: These results indicated that ataluren may be a suitable candidate for the development of a therapeutic drug to treat NMC. However, additional laboratory experiments are required to validate these preliminary findings.

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proteins

2025-03-24 | Primary cutaneous NUT adnexal carcinoma: morphologic, genetic and methylation analysis of seven new cases with comparison to extracutaneous NUT carcinoma and NUTM1-rearranged porocarcinoma.

NUT carcinoma is a rare malignant neoplasm characterised by recurrent NUTM1 rearrangements, initially reported in the midline. Recently, 10 cases of cutaneous NUT carcinoma with adnexal differentiation harbouring BRD3::NUTM1, NSD3::NUTM1, BRD4::NUTM1 or BRD3::NUTM2B fusions have been reported. Accordingly, 'NUT adnexal carcinoma' (NAC) has been introduced as a provisional tumour entity to the fifth edition of the WHO Classification of Skin Tumours. We report the histopathological, molecular genetic and epigenetic features of seven additional cases of NAC. The cohort consisted of four female and three male patients with a median age of 58 years. Follow-up was available for six cases, and documented diffuse metastatic spreading leading to death at 18 months after diagnosis for one case. Histopathological examination in all cases revealed dermal/subcutaneous neoplasms composed of poorly differentiated cells with large irregular vesicular nuclei and at least focally prominent nucleoli. All cases showed areas of duct/gland formation. Using immunohistochemistry, all tumours showed diffuse NUT expression with co-expression of SOX10 in five cases. P63 and P40 were diffusely positive in one case and confined to the periphery of the tumour nests in five cases. Molecular analysis showed BRD4::NUTM1 fusions (n = 3), BRD3::NUTM1 fusions (n = 3) and NSD3::NUTM1 (n = 1). Although being close to this latter group, methylation and transcriptional analysis revealed that NAC formed a unique cluster distinct from extracutaneous NUT carcinoma and NUTM1-rearranged porocarcinoma. Our results further support the existence of primary cutaneous NAC and suggest that it may represent an entity distinct from extracutaneous NUT carcinoma.

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2025-02-24 | A case report of NUT cancer in nasal sinus

Uclear protein in testis (NUT) carcinoma is a rare, aggressive, poorly differentiated squamous cell carcinoma caused by NUT gene rearrangement on chromosome 15. Because it occurs in the middle line structure of the head and neck and the chest, it is also known as midline cancer. These tumors favor midline and quasi-midline structures in the upper digestive tract and mediastinum and can affect patients of a wide age range, including children.

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2025-02-08 | Acetylation of histone H2B on lysine 120 regulates BRD4 binding to intergenic enhancers

BRD4 is a bromodomain-containing transcriptional co-regulator that plays important roles in driving transcription by binding to histone acetyl-lysines at enhancers and promoters while recruiting additional transcriptional cofactors. While the mechanisms by which BRD4 regulates transcription have been explored, the critical acetylations primarily responsible for targeting it to chromatin remain unclear. Through a machine learning approach, we determined that distinct sets of histone acetylations dominate the prediction of chromatin accessibility and BRD4 binding in distinct chromatin contexts (e.g. intergenic enhancers, gene body enhancers and promoters). Using human fibroblasts engineered to predominantly express specific histones with lysine-to-arginine mutations, we demonstrate that one such acetylation, H2BK120ac, is required to recruit BRD4 specifically to intergenic enhancers, while not affecting chromatin accessibility. Loss of H2BK120ac did not affect BRD4 binding to either promoters or gene body enhancers, demonstrating that the rules governing BRD4 recruitment to regulatory regions depends on the specific genomic context. Highlighting the importance of H2BK120ac in directing BRD4 recruitment, we found that expression of the H2BK120R mutant significantly reduces the phenotypes driven by BRD4-NUT, an oncogenic fusion protein that drives NUT midline carcinoma. This work demonstrates the critical nature that genomic context plays in BRD4 recruitment to distinct classes of regulatory elements, and suggests that intergenic and gene body enhancers represent classes of functional distinct elements.

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2012-11-05 | Novel BRD4–NUT fusion isoforms increase the pathogenic complexity in NUT midline carcinoma

Nuclear protein in testis (NUT)-midline carcinoma (NMC) is a rare, aggressive disease typically presenting with a single t(15;19) translocation that results in the generation of a bromodomain-containing protein 4 (BRD4)–NUT fusion. PER-624 is a cell line generated from an NMC patient with an unusually complex karyotype that gave no initial indication of the involvement of the NUT locus. Analysis of PER-624 next-generation transcriptome sequencing (RNA-Seq) using the algorithm FusionFinder identified a novel transcript in which Exon 15 of BRD4 was fused to Exon 2 of NUT, therefore differing from all published NMC fusion transcripts. The three additional exons contained in the PER-624 fusion encode a series of polyproline repeats, with one predicted to form a helix. In the NMC cell line PER-403, we identified the 'standard' NMC fusion and two novel isoforms. Knockdown by small interfering RNA in either cell line resulted in decreased proliferation, increased cell size and expression of cytokeratins consistent with epithelial differentiation. These data demonstrate that the novel BRD4–NUT fusion in PER-624 encodes a functional protein that is central to the oncogenic mechanism in these cells. Genomic PCR indicated that in both PER-624 and PER-403, the translocation fuses an intron of BRD4 to a region upstream of the NUT coding sequence. Thus, the generation of BRD4–NUT fusion transcripts through post-translocation RNA-splicing appears to be a common feature of these carcinomas that has not previously been appreciated, with the mechanism facilitating the expression of alternative isoforms of the fusion. Finally, ectopic expression of wild-type NUT, a protein normally restricted to the testis, could be demonstrated in PER-403, indicating additional pathways for aberrant cell signaling in NMC. This study contributes to our understanding of the genetic diversity of NMC, an important step towards finding therapeutic targets for a disease that is refractory to current treatments.

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antibodies

2026-02-27 | Assessing the Tumor Immune Microenvironment of Sinonasal Nut Carcinoma

Background: NUT carcinoma is a highly aggressive cancer defined by rearrangements of the NUT midline carcinoma family member 1 gene. Despite aggressive treatment, patients have a median survival of only seven months. Currently, there is no standard treatment for NUT carcinoma, highlighting the need for new experimental models and improved treatment strategies. In previous research, we established and characterized two novel sinonasal NUT carcinoma cell lines from a surgical specimen. To gain a deeper understanding of the disease, we conducted a multiplex immunofluorescence study on the surgical specimen from which these cell lines were derived. Materials and Methods: A formalin-fixed, paraffin-embedded surgical specimen from a 28-year-old man who was diagnosed with T4bN0M0 sinonasal NUT carcinoma was used in this study. The patient underwent two cycles of induction chemotherapy with docetaxel, cisplatin, and 5-fluorouracil at another institution, followed by surgical resection at the University of Texas MD Anderson Cancer Center. Opal 7-color multiplex immunofluorescence was performed on the surgical specimen, using antibodies for pan-cytokeratin (CK, clone 80), CD3, CD8, PD-L1, CD68, CD56/NCAM (an NK cell marker), and DAPI. Tissue identification, marker detection, and data extraction were conducted using QuPath (version 0.5.1). Tumor cells with low CK expression were categorized as 'CK low ' cells, and their proportion within the tumor was calculated as CK low / (CK low + CK + ) x 100. Results: Fifty-four percent of the tumor cells were classified as CK low , indicating heterogeneity within this tumor sample. CD8 + tumor-infiltrating lymphocytes were present at only 0.14%, suggesting that this specimen exhibits a less immunogenic 'cold' tumor profile. The percentage of PD-L1-positive tumor cells, which is associated with a better response to immunotherapy in various tumor types, was less than 0.2%. Furthermore, the percentage of CD68 + PD-L1 + macrophages, another indicator for response to certain types of immunotherapies, was found to be less than 5%. Conclusion: The sample of sinonasal NUT carcinoma that we analyzed exhibited heterogeneous cytokeratin expression and low immunogenic characteristics. Given that NUT carcinoma is primarily driven by a single fusion oncoprotein, it has a low tumor mutational burden, which may align with these findings. Since conventional treatments for NUT carcinoma, such as chemotherapy and radiation therapy, have shown very limited success, it is essential to develop strategies to address the tumor immune microenvironment and to incorporate immunotherapy and potential new targetable therapies effectively. We plan to create an advanced panel with additional markers and include more tumor samples to further investigate the biology of sinonasal NUT carcinoma in our future studies. Publication History Article published online: 27 February 2026 © 2026. Thieme. All rights reserved. Georg Thieme Verlag KG Oswald-Hesse-Straße 50, 70469 Stuttgart, Germany

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2025-05-28 | Efficacy profile of pembrolizumab for primary pulmonary NUT carcinoma: A systematic review and meta-analysis.

8586 Background: Primary pulmonary NUT carcinoma is an exceedingly rare and aggressive malignancy characterized by chromosomal rearrangements involving the NUT gene. With limited therapeutic options and an extremely poor prognosis, treatment strategies have focused on identifying effective targeted and immunotherapeutic approaches. Pembrolizumab, an anti-PD-1 immune checkpoint inhibitor, has shown promise in various malignancies, particularly those with high tumor mutational burden or PD-L1 expression. However, despite its use, its efficacy in NUT carcinoma remains poorly understood due to the rarity of this disease and a paucity of robust clinical data. This systematic review and meta-analysis aim to explore the available evidence on the clinical data of pembrolizumab in treating primary pulmonary NUT carcinoma, focusing on progression-free survival (PFS), and overall survival (OS) by consolidating outcomes from case reports and case series. Methods: A systematic review and meta-analysis were conducted to evaluate the effectiveness of pembrolizumab in the treatment of primary pulmonary NUT carcinoma. A comprehensive search of PubMed, Embase, and Cochrane was performed for articles published between January 2014 and December 2024, using the keywords “pembrolizumab,” “Pulmonary NUT carcinoma,” and “NUT midline carcinoma.” Inclusion criteria included reports of patients treated with either pembrolizumab monotherapy or pembrolizumab in conjunction with other therapies for Primary Pulmonary NUT Carcinoma for any duration. Reports that did not mention PFS or OS were excluded. Results: A total of 39 reports involving 56 patients with primary pulmonary NUT carcinoma treated with pembrolizumab, either in conjunction with other therapies or monotherapy, were analyzed. The median overall survival (OS) was 7.3 months (95% CI: 5.2–8.8), and the median progression-free survival (PFS) was 4.6 months (95% CI: 3.1–5.7). Among three patients receiving pembrolizumab monotherapy as a second-line or later treatment, the median PFS was 2.9 months. Conclusions: Pembrolizumab has been explored as second-line or later therapy for primary pulmonary NUT carcinoma based on its success in treating NSCLC. Our analysis revealed a median progression-free survival of 4.6 months and a median overall survival of 7.3 months for patients with primary pulmonary NUT carcinoma receiving pembrolizumab, illustrating the continuing challenge of treating this rare malignancy. Importantly, there are no randomized controlled trials investigating pembrolizumab in this rare malignancy, highlighting a critical gap in evidence. Prospective clinical trials and further research into biomarkers predictive of treatment response are urgently needed to optimize therapeutic strategies and improve outcomes for patients with this aggressive disease.

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2024-12-23 | Consolidation immunotherapy following concurrent chemoradiotherapy in a patient with sinonasal NUT carcinoma: a case report.

Nuclear protein in testis (NUT) cancers, also known as midline cancers, tends to occur in organs near the midline, such as the nasal sinuses and mediastinum. NUT carcinoma is very rare and has a poor prognosis. We report the case of a 44-year-old female patient with sinonasal NUT carcinoma who presented with a soft tissue mass in the left frontal sinus, ethmoid sinus, and left nasal cavity on computed tomography; the tumor was poorly demarcated from the left rectus medialis. After discussion with a multidisciplinary team with expertise on head and neck tumors, the patient was considered inoperable, and definitive concurrent chemoradiotherapy (CCRT) was recommended. The patient underwent CCRT followed by three cycles of consolidation chemotherapy with albumin-bound paclitaxel and nedaplatin. Subsequently, the patient underwent 16 cycles of consolidation therapy with the programmed death-1 (PD-1) inhibitor tislelizumab. The immune-related adverse events included grade 2 hypothyroidism. After CCRT, consolidation chemotherapy, and consolidation immunotherapy, the patient achieved a favorable outcome. The patient survived for 31 months, and there were no signs of recurrence or metastasis during follow-up. At present, there is no clear consensus on the consolidation treatment plan after CCRT for sinonasal NUT cancer. We used consolidation immunotherapy for the first time and achieved good efficacy, providing an innovative and promising treatment plan for refractory sinonasal NUT cancer.

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2024-04-01 | Authors’ reply to Das et al.

We thank Das et al.[1] for the invaluable insights on our molecular tumor board article, "NUT-midline carcinoma of the lung with rare BRD3–NUTM1 fusion."[2] Das et al.[1] highlighted the immunohistochemical (IHC) phenotypes of nuclear protein in testis (NUT) carcinoma. In our case presentation, IHC positivity of NUT confirmed the histopathologic diagnosis of NUT midline carcinoma of the lung. NUT expression is a hallmark of NUT carcinoma.[3,4] P40 is highly sensitive and specific for squamous cell carcinoma. However, its presence alone does not conclusively confirm squamous cell carcinoma (SCC), like other cancers, may also express P40. In the case described, the tumor cells were positive for both P40 and NUT. While P40 positivity might suggest squamous differentiation, the concomitant strong positivity for NUT is more indicative of NUT carcinoma over squamous cell carcinoma as the final diagnosis. Typically, NUT carcinomas usually occur in the midline structures of the body such as the head, neck, and mediastinum; however, they can also manifest in the non-midline areas. Recognition of NUT carcinoma in the non-midline areas is crucial for timely diagnosis and treatment. The authors' insight is quite compelling in emphasizing the distinctive features of the primary histomorphological examination to identify NUT carcinomas. They also highlighted how identification is more common when it occurs in the non-midline regions. The main histopathologic indications of NUT carcinoma are undifferentiated or poorly differentiated histology and atypical nuclear morphology. In addition, high mitotic index, diffuse growth pattern, elevated Ki-67 proliferation index, and absence of squamous differentiation markers (e.g. CK5/6, p63) in cases with squamous differentiation give strong attestation of NUT carcinoma.[3,5] Similarly, a conjecture of NUT carcinoma should be raised in non-midline regions when there are atypical clinical presentations, rapid tumor growth, characteristic histologic features, young age of onset, failure to respond to standard treatments, or evidence of metastasis. The confirmation of NUT carcinoma is reinforced by IHC staining and positivity for NUT protein, or next-generation sequencing (NGS). We strongly concur with the use of NGS, as it confirms the presence of NUT fusion and opens an avenue for the discovery of new therapeutic targets, deepening our understanding of the complex and aggressive biology exhibited by these tumors. However, NUT carcinoma poses a significant clinical challenge due to its status as an orphan disease, lacking established treatment protocols, and typically presenting a bleak prognosis. Das et al.[1] have provided a holistic overview of therapeutic options for these aggressive cancers. The available sparse information also indicates these tumors may be amenable to treatment with immune checkpoint inhibitors, warranting further investigation.[6] To summarize, an accurate diagnosis of NUT carcinoma requires a comprehensive evaluation by a multidisciplinary team, including pathologists who could employ clinicopathologic correlation for the advanced interpretation of the cases. NUT carcinoma remains a unique challenge in the landscape of solid cancers, with limited treatment options and a generally dismal outlook, making the search for effective therapies for the management of this rare and aggressive cancer more important than ever before. Financial support and sponsorship Nil. Conflicts of interest Kumar Prabhash is a member of the editorial board of Cancer Research, Statistics and Treatment. As such, he may have had access to information and/or participated in decisions that could be perceived as influencing the publication of this manuscript. However, he recused himself from the peer review, editorial, and decision-making process for this manuscript, to ensure that the content is objective and unbiased.

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2024-02-23 | A Rare Case of NUT Carcinoma of the Thyroid

Abstract NUT carcinoma is an aggressive, poorly differentiated squamous cell carcinoma, defined by rearrangement of the NUTM1 (Nuclear Protein in Testis) gene. Diagnosis is challenging due to histologic similarities with other poorly differentiated tumors requiring advanced diagnostic techniques. There is no established treatment, and prognosis remains extremely poor. A 27-year-old woman without known medical history presented with a rapidly enlarging neck mass and compressive symptoms. Chemotherapy for presumed squamous cell carcinoma with a component of anaplastic thyroid cancer based on pathology was initiated. Next-generation sequencing revealed thyroid NUT carcinoma with high PD-L1 expression, prompting PD-1 targeted therapy. The patient expired shortly afterwards from progressive disease. NUT carcinoma of thyroid origin is an extremely rare disease. This case brings awareness to the disease, highlights the importance of advanced diagnostic techniques and complexities in managing patients with NUT carcinoma.

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2025-11-01 | 274 Comprehensive spatial immune profiling of pediatric NUT carcinoma identifies novel prognostic signatures and B7-H3 as a target for CAR-T cell therapy

Background NUT carcinoma (NC) is a rare, aggressive cancer defined by NUTM1 gene rearrangements, often arising in midline structures such as the head, neck, and thorax. NC is associated with rapid progression, poor clinical outcomes, and resistance to standard treatments. Although the complexity of NC has been studied extensively, the disease remains incompletely understood. To address this critical scientific and clinical gap, we aimed to uncover key characteristics of immune and tumor cells within the tumor immune microenvironment (TIME) of NC, identifying prognostic factors and potential therapeutic targets to substantially improve patient outcomes.Methods We analyzed 14 NC tumor samples from children, adolescents, and young adults using classical immunohistochemistry, whole-genome DNA sequencing (WGS), RNA sequencing, and multiplexed tissue imaging. We employed MACSima imaging cyclic staining (MICS) to attain a detailed spatial profile of the TIME in NC. Our ultra-high content imaging pipeline 1 was optimized for formalin-fixed, paraffin-embedded (FFPE) samples, utilizing a custom immunophenotyping panel targeting 72 markers. This enabled deep profiling of cellular heterogeneity in tumor and immune cell populations, sub-phenotyping of immune cells, and mapping of cellular neighborhoods using sophisticated bioinformatic workflows to uncover interactions and niches in NC.Results Our comprehensive characterization of the immune landscape in NC revealed novel infiltration and interaction signatures. In particular, high proportions of intratumoral granulocytes, myeloid-derived suppressor cells (MDSCs), and M2-like macrophages could be associated with worse outcomes. Furthermore, we identified previously unreported immunologically ‘hot’ NC tumors that may benefit from immune checkpoint blockade and other immunotherapies. To uncover novel actionable targets in NC, we screened for the expression of immune checkpoint molecules and target antigens. B7-H3 emerged as particularly promising due to its uniform expression across all NC samples. We evaluated the therapeutic potential by utilizing B7-H3-targeted chimeric antigen receptor (CAR)-T cells, demonstrating specific elimination of NC both in vitro and in NC xenograft models.Conclusions This study provides the first large-scale, spatially resolved immunophenotyping of NC, offering a valuable framework for identifying and validating new diagnostic and therapeutic options. By comprehensively mapping the TIME in NC, we aim to advance precision immunotherapy approaches tailored to this challenging malignancy. Our findings highlight prognostic immune signatures and identify B7-H3 as a promising target for CAR-T cell therapy in NC, paving the way for novel, more effective treatments for patients with NC.Acknowledgements We thank the patients and families for their willingness to contribute to scientific research by participating in the study. We thank the NGS Core Facility, and the Omics IT and Data Management Core Facility (ODCF) of the German Cancer Research Center (DKFZ) for providing excellent WGS, RNA-seq, and data management services.Reference Scheuermann S, Kristmann B, Engelmann F, et al. Unveiling spatial complexity in solid tumor immune microenvironments through multiplexed imaging. Front Immunol. 2024;15:1383932. Published 2024 Mar 19. doi:10.3389/fimmu.2024.1383932Ethics Approval All patients or theri legal representatives gave their written informed consent for biobanking and the use of biomaterials and clinical data for scientific assessment, as approved by the ethics committee of the University Hospital Tübingen (ethics approval No. 879/2020B02).

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2025-03-05 | Sinonasal NUT Carcinoma: A Systematic Review With Pooled Analysis and Report of a Case of Extraordinary Survival.

NUT carcinoma (NC) is a rare and aggressive malignancy often occurring in the midline structures of the head and neck. In this study, we present a systematic review and pooled analysis on patients specifically with sinonasal NC (SNC), as well as report a case of a patient with extraordinary survival following presentation with an NC of the maxillary sinus. Among 3042 articles retrieved, 27 were included in the final analysis. Clinical outcomes were described for a patient presenting with SNC at a tertiary academic medical center. Predictors of survival were evaluated with Kaplan-Meier (KM) and Cox regression analyses. There were 45 patients with a relatively even gender distribution. The most common presenting symptoms were nasal obstruction (54%) and headache/facial pain (49%). Common primary sites of malignancy were the nasal cavity (50%), maxillary sinus (22%), and ethmoid sinus (16%). In terms of treatment, 31% underwent oncologic resection, 64% received radiation therapy, and 71% received chemotherapy. The overall cohort survival rate was 40% with an average survival of 12.4 months. The presence of nerve palsies (OR = 16.6, p < 0.001) was a substantial negative predictor for survival. Oncological resection with negative margins was associated with improved survival on KM analysis (p < 0.05). We also report a case of a 47-year-old female who presented with a left maxillary SNC with extra-sinus extension. She underwent a combined endoscopic/open oncologic resection with negative margins followed by chemoradiation. The patient remains alive 52 months after presentation. SNC remains an understudied clinical entity. Oncologic resection with negative margins is associated with improved survival. The presence of nerve palsies worsens overall survival. Further, large-scale studies are needed to determine optimal treatment protocols.

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2023-10-31 | P1.11-05 Application of the CRISPR/Cas9-based Gene Editing Technology for the Treatment of NUT Carcinoma

NUT carcinoma is a rare and highly aggressive form of cancer with a poor prognosis and limited treatment options. This cancer is characterized by the expression of the NUTM1 (NUT (nuclear protein in testis) family member 1) fusion protein, which is responsible for driving oncogenesis. Despite recent advances in the understanding of the molecular mechanisms underlying NUT carcinoma (NC), effective therapies for this disease are still lacking. In this study, we investigated the therapeutic potential of CRISPR/Cas9-mediated knockout of NUTM1.

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