Complex chromosomal rearrangements by single catastrophic pathogenesis in NUT midline carcinoma

Abstract

BackgroundNuclear protein in testis (NUT) midline carcinoma (NMC) is a rare aggressive malignancy often occurring in the tissues of midline anatomical structures. Except for the pathognomonic BRD3/4–NUT rearrangement, the comprehensive landscape of genomic alterations in NMCs has been unexplored.Patients and methodsWe investigated three NMC cases, including two newly diagnosed NMC patients in Seoul National University Hospital, and a previously reported cell line (Ty-82). Whole-genome and transcriptome sequencing were carried out for these cases, and findings were validated by multiplex fluorescence in situ hybridization and using individual fluorescence probes.ResultsHere, we present the first integrative analysis of whole-genome sequencing, transcriptome sequencing and cytogenetic characterization of NUT midline carcinomas. By whole-genome sequencing, we identified a remarkably similar pattern of highly complex genomic rearrangements (previously denominated as chromoplexy) involving the BRD3/4–NUT oncogenic rearrangements in two newly diagnosed NMC cases. Transcriptome sequencing revealed that these complex rearrangements were transcribed as very simple BRD3/4–NUT fusion transcripts. In Ty-82 cells, we also identified a complex genomic rearrangement involving the BRD4–NUT rearrangement underlying the simple t(15;19) karyotype. Careful inspections of rearrangement breakpoints indicated that these rearrangements were likely attributable to single catastrophic events. Although the NMC genomes had >3000 somatic point mutations, canonical oncogenes or tumor suppressor genes were rarely affected, indicating that they were largely passenger events. Mutational signature analysis showed predominant molecular clock-like signatures in all three cases (accounting for 54%−75% of all base substitutions), suggesting that NMCs may arise from actively proliferating normal cells.ConclusionTaken together, our findings suggest that a single catastrophic event in proliferating normal cells could be sufficient for neoplastic transformation into NMCs.

Clinicopathological and Preclinical Findings of NUT Carcinoma: A Multicenter Study

“…The NUT gene translocation pattern was simple in the FISH assay in all cases except NC13, which showed NUT gene gains with an isolated red signal in addition to paired green and red signals. Consistently, it was previously reported that chromosomal alterations underlying the simple BRD4 / BRD3 ‐ NUT transcript can be highly sophisticated and even harbor hyperdiploidy .…”

“…We observed high and frequent overexpression of p53 in NUT carcinoma cases. The reason for this finding is uncertain because chromosomal rearrangement or somatic mutation of p53 was not found in the SNU‐2972‐1 or SNU‐317S cell line in our previous study . p300 HAT is sequestered to the NUT moiety BRD4‐NUT, which, in turn, acetylates p53 and binds it to the BRD4‐NUT foci of the chromatin .…”

NUT Carcinoma: Clinicopathologic features, pathogenesis, and treatment

“…The extensive work done by this group in Korea indicates that the reciprocal translocation involving NUTM1 results from complex multiple chromosomal rearrangements, termed chromoplexy, that ultimately give rise to a single reciprocal translocation and the simple t(15;19) karyotype. The majority of mutations in three early passage NC cell lines tested in the study had a clock‐like molecular signature, consistent with those predicted from a tumor that arises from a normal somatic cell . The findings suggest that NC may arise from a single catastrophic chromosomal event in an otherwise healthy dividing cell.…”

“…While it is not unusual for an NC patient to have a smoking history, there is no evidence that smoking or any other etiology (environmental or viral) is associated with NC. Nevertheless, due to small numbers of patients, no epidemiologic study has been conducted that has rigorously analyzed etiologic factors, thus the current thought, which is supported by NGS data, is that the BRD4‐NUTM1 translocation occurs within a somatic cell as a single catastrophic event due to chance alone …”

Renal NUT carcinoma: a case report

“…The breakpoint in NUTM1 was upstream of exon 1 and not exon 2. Exon 1 breakpoints have been reported and are quite frequent . Unlike exon 2, exon 1 lacks a splice acceptor site and hence is not included in the transcript.…”