SETD2 Deficiency and miR-21: Potent Therapeutic Targets in NUT Midline Carcinoma

BackgroundNuclear protein in testis (NUT) midline carcinoma (NMC) is a rare and highly aggressive tumor with the bromodomain containing 4 protein (BRD4)-NUT (NUTM1) gene fusion. Few targeted therapies are available for NMC, and novel therapeutic targets are required. The objectives of our study was to determine gene mutations and microRNA (miRNA) expression levels in NMC and to identify novel therapeutic targets for NMC. Methods Next-generation sequencing (NGS) was used to identify mutations in the NMC cell lines and the tumor sample from a NMC patient; we determined the BRD4-NUT fusion gene in the patient using a digital PCR assay. Trimethylation of lysine 36 on histone H3 expression (H3K36me3) was studied using western blotting. The efficacy of the WEE1 G2 checkpoint kinase (WEE1) inhibitor, AZD1775, was evaluated using the MTS assay. RNA sequencing was performed to determine miRNA expression levels in the NMC cell lines. TaqMan miRNA assays were used to analyze miR-21 expression. The efficacy of miR-21 inhibitor was evaluated using the MTS assay. Results A novel SETD2 mutation (p.Ser2382fs) was identified in the NMC cell lines and the patient tumor. H3K36me3 was depleted in the NMC cells, which was indicative of functional SETD2 loss. The NMC cells were sensitive to AZD1775, an inhibitor for SETD2-deficient cancer. miRNA analysis revealed that miR-21 expression was increased in the NMC cells resistant to the traditional BET-targeted therapy. The miR-21 inhibitor suppressed the proliferation of the NMC cells. ConclusionsSETD2 deficiency and miR-21 may serve as novel therapeutic targets for the treatment of NMC.Trial registrationIn this study, we analyzed the gene alterations in human tumor samples. This study was registered in the UMIN clinical trial registered system (UMIN000043147, January 27, 2021).