Novel BRD4–NUT fusion isoforms increase the pathogenic complexity in NUT midline carcinoma

• Published in: Oncogene Vol. 32; no. 39; pp. 4664 - 4674
• Main Authors: Thompson-Wicking, K, Francis, R W, Stirnweiss, A, Ferrari, E, Welch, M D, Baker, E, Murch, A R, Gout, A M, Carter, K W, Charles, A K, Phillips, M B, Kees, U R, Beesley, A H
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 26.09.2013; Nature Publishing Group
• Subjects: 631/208/212/2019; 692/420/755; 692/699/67; Adolescent; Antineoplastic Combined Chemotherapy Protocols - therapeutic use; Apoptosis; Base Sequence; Cancer; Carcinoma; Carcinoma - drug therapy; Carcinoma - genetics; Carcinoma - pathology; Care and treatment; Cell Biology; Cell Differentiation; Cell fusion; Cell Line, Tumor - metabolism; Cell Line, Tumor - ultrastructure; Cell signaling; Cell Size; Cellular biology; Child; Chromosomes, Human, Pair 15 - genetics; Chromosomes, Human, Pair 15 - ultrastructure; Chromosomes, Human, Pair 19 - genetics; Chromosomes, Human, Pair 19 - ultrastructure; Drug Resistance, Neoplasm; Ectopic expression; Epithelial tumors; Exons; Exons - genetics; Fatal Outcome; Female; Gene expression; Gene mutations; Genetic aspects; Genetic diversity; Human Genetics; Humans; In Situ Hybridization, Fluorescence; Internal Medicine; Isoforms; Karyotypes; Lung Neoplasms - drug therapy; Lung Neoplasms - genetics; Lung Neoplasms - pathology; Medicine; Medicine & Public Health; Molecular Sequence Data; Neoplastic processes; Nuclear Proteins - antagonists & inhibitors; Nuclear Proteins - genetics; Nuclear Proteins - physiology; Nucleotide sequence; Observations; Oncogene Proteins, Fusion - antagonists & inhibitors; Oncogene Proteins, Fusion - genetics; Oncogene Proteins, Fusion - physiology; Oncology; original-article; Polyproline; Protein Isoforms - genetics; Protein Isoforms - physiology; Protein Structure, Secondary; Proteins; Ribonucleic acid; RNA; RNA Interference; RNA, Small Interfering - pharmacology; Sequence Alignment; Sequence Homology, Nucleic Acid; siRNA; Therapeutic targets; Thymus Neoplasms - genetics; Thymus Neoplasms - pathology; Transcription; Transcriptomes; Translocation, Genetic; Young Adult; NUT; carcinoma; NMC; RNA-Seq; transcriptome; BRD4
• ISSN: 0950-9232; 1476-5594
• DOI: 10.1038/onc.2012.487

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.