Elevated NSD3 Histone Methylation Activity Drives Squamous Cell Lung Cancer

Amplification of chromosomal region 8p11-12 is a frequent genetic alteration implicated in the etiology of lung squamous cell carcinoma (LUSC)(1-3). FGFR1 (fibroblast growth factor receptor 1) is the main candidate driver within this region(4). However, clinical trials evaluating FGFR1 inhibition as a targeted therapy have been unsuccessful(5). Here we identify the H3K36 methyltransferase NSD3 (nuclear receptor binding SET domain protein 3), an 8p11-12-localized gene, as a key regulator of LUSC tumorigenesis. In contrast to other 8p11-12 candidate LUSC drivers, increased NSD3 expression strongly correlates with its gene amplification. Ablation of NSD3, but not FGFR1, attenuates tumor growth and extends survival in a potent LUSC mouse model. We identify NSD3(T1232A) as an LUSC-associated variant that increases H3K36 dimethylation (H3K36me2) catalytic activity in vitro and in vivo. Structural dynamic analyses reveal that the T1232A substitution elicits localized mobility changes throughout NSD3’s catalytic domain to relieve auto-inhibition and increase H3 substrate accessibility. NSD3(T1232A) expression in vivo accelerates tumorigenesis and decreases overall survival in LUSC mouse models. Pathologic H3K36me2 generation by NSD3(T1232A) rewires the chromatin landscape to promote oncogenic gene expression programming. Further, NSD3’s catalytic activity promotes human tracheobronchial cell transformation and xenograft growth of human 8p11-12-amplified LUSC cell lines. NSD3 depletion in patient-derived xenografts (PDXs) from primary LUSC harboring NSD3 amplification or the NSD3(T1232A) variant attenuates neoplastic growth. Finally, NSD3-regulated LUSC PDXs are markedly sensitive to bromodomain inhibition (BETi). Together, our work identifies NSD3 as a principal 8p11-12 amplicon-associated oncogenic driver in LUSC and suggests that NSD3-dependency renders LUSC therapeutically vulnerable to BETi.