Differentiation of NUT Midline Carcinoma by Epigenomic Reprogramming

Abstract

NUT midline carcinoma (NMC) is a lethal pediatric tumor defined by the presence of BRD-NUT fusion proteins that arrest differentiation. Here we explore the mechanisms underlying the ability of BRD4-NUT to prevent squamous differentiation. In both gain-of and loss-of-expression assays, we find that expression of BRD4-NUT is associated with globally decreased histone acetylation and transcriptional repression. Bulk chromatin acetylation can be restored by treatment of NMC cells with histone deacetylase inhibitors (HDACi), engaging a program of squamous differentiation and arrested growth in vitro that closely mimics the effects of siRNA-mediated attenuation of BRD4-NUT expression. The potential therapeutic utility of HDACi differentiation therapy was established in three different NMC xenograft models, where it produced significant growth inhibition and a survival benefit. Based on these results and translational studies performed with patientderived primary tumor cells, a child with NMC was treated with the FDA-approved HDAC inhibitor, vorinostat. An objective response was obtained after five weeks of therapy, as determined by positron emission tomography. These findings provide preclinical support for trials of HDACi in patients with NMC. Cancer Res; 71(7); 2686-96. Ó2011 AACR.

The Importance of Diagnosing NUT Midline Carcinoma

“…The findings have led to the recent treatment of pediatric patients with NMC using HDACi-containing regimens. Anecdotal results have been promising [16] (Fig. 3b).…”

“…2b) [15]. The paradox is that these large aggregates of hyperacetylated chromatin, BRD4-NUT, and p300, rather than leading to increased transcription, actually act as p300 sinks that globally decrease acetylation and transcription [16]. Thus, genes required for differentiation are not expressed.…”

“…This feed-forward mechanism can be reversed by treating cells with histone deacetylase inhibitors (HDACi), which artificially increase acetylation throughout the cell. HDACi treatment leads to globally increased transcription, differentiation, and arrested proliferation in NMC, both in vitro, and in animal models [16]. The findings have led to the recent treatment of pediatric patients with NMC using HDACi-containing regimens.…”

Ectopic protein interactions within BRD4–chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma

“…To this end, we induced expression of BioTAP-tagged BRD4-NUT (BRD4-NUT-BioTAP) or the short isoform of BRD4 (BRD4short-BioTAP), encoding only the portion of BRD4 included in the BRD4-NUT fusion oncoprotein (10). We expressed the epitopetagged proteins from single-copy transgenes integrated in a non-NMC cell line, 293T, the derivative of which we term 293TRex (3,11). 293TRex cells serve as a useful model, as they do not normally harbor the oncogenic fusion but, when induced to express BRD4-NUT, form de novo nuclear foci and hyperacetylated megadomains (3).…”

NUT midline carcinomas in the thymic region

“…Recently, therapeutic approaches for NMC have been developed involving inhibitors of BRD3 and BRD4 bromodomain (BETi). [22][23][24] Two phase I clinical trials with BETi (GSK 525762; Glaxo-Smith Kline and TEN-010; Tensha Therapeutics) (Clinical trials NCT01587703 & NCT01987362) are ongoing and open to NMC patients. In addition, HDACi demonstrated promising clinical response in pediatric patients.…”