A tough NUT carcinoma to crack

We describe the case of a NUT carcinoma of the thorax in a 27-year-old male, non-smoker, presenting a voluminous neoformation in the hilum and the left side of the mediastinum infiltrating heart and great vessels. The biopsy revealed a poorly differentiated cancer with focal crush artifact consisting of undifferentiated small to medium-size cells, with minimal indistinct to clear cytoplasm, round or oval nuclei, nuclear molding and brisk mitotic activity. Suggestive morphological features often associated with NUT carcinoma, for example abrupt foci of keratinization, were not seen. Moreover, immunohistochemical (IHC) analysis showed negativity for epithelial markers, such as Cytokeratin AE1/AE3, CK7, CK-CAM5.2, CK5/6, p40 and TTF1; therefore, further immunohistochemical markers were evaluated, and the conclusive diagnosis was based on a diffuse speckled nuclear positivity for NUT1 (clone C52B1). Considering the unusual morphological and IHC findings, a comprehensive genome profiling, by FoundationOne®CDx Next Generation Sequencing (NGS), was performed on DNA from the transbronchial needle aspiration formalin-fixed and paraffin-embedded cell block. Neither NUTM1 gene fusions nor other pathogenic gene variants were detected. However, focal and segmental copy number variations (CNV) were seen in chromosome 19, in the middle of the BRD4 gene, the most common NUTM1 fusion partner. In addition, an array CGH (aCGH) analysis was performed: this analysis revealed different CNV, including a 2.7Mb deletion and a 14.4Mb duplication in chromosome regions were NUTM1 and BRD4 are respectively located. Finally, an RNA-based NGS confirmed the presence of a BDR4-NUTM1 fusion transcript, supporting IHC findings. IHC and molecular results all together are suggestive for a likely non-canonical BRD4-NUTM1 fusion. Our case showed unusual features both from a morphological and a molecular point of view: the diagnosis was driven by NUT1 positive immunohistochemistry, thus underlining the crucial role of this test.