A tough NUT carcinoma to crack

Abstract

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.

Keywords: NUT carcinoma; fusion gene; molecular analysis.

Figure 1.

Computed tomography (CT) scan reveals a voluminous neoformation in the hilum and the left side of the mediastinum infiltrating heart and great vessels.

Figure 2.

Morphological features of the neoplasia. a. Hematoxylin and eosin (H&E) stain shows a poorly differentiated cancer consisting of small to medium-size cells, round and oval nuclei, prominent nucleoli, admixed an inflammatory infiltrate (original magnification 20x). b. Papanicolaou smear shows small clusters or isolated atypical cells of intermediate size, alongside abundant neutrophils and lymphocytes (original magnification 20x).

Figure 3.

Immunohistochemical (IHC) analysis: neoplastic cells were negative for cytokeratin AE1/AE3 (a), positive for EMA (b), showed a typical “speckled” nuclear positivity for NUT1 (clone C52B1) (c), and a high proliferation index (MIB-1 80%, d) (original magnification 20x).

Figure 4.

Array-CGH results, focusing on the unbalanced regions in proximity of NUTM1 and BRD4. On the left side, NUTM1 (red circle) is about 700 kb upstream of the 15q14 deletion (a part of it is shown by a red rectangle); on the right side, BRD4 (red circle) is about 8 kb downstream of the 19p13.12 deletion (red rectangle). Part of the 19p13.3p13.12 duplication is indicated by a blue rectangle.