Dino Is a DNA Damage-Induced Tumor Suppressing Long Noncoding RNA

Abstract

While the CKDN1A locus is frequently suppressed in human cancers, the mechanism by which this finding contributes to tumor suppression has not been fully elucidated. We hypothesized that DINO, a novel DNA damage-induced long noncoding RNA encoded in the CDKN1A promoter, is essential to p53-dependent tumor suppression. We used a combination of in vivo mouse models, cell culture experiments and human tumor profiling to examine the contribution of DINO to p53-dependent tumor suppression. We crossed a Dino loss of function mouse to the E-mu-Myc model of B-cell lymphoma to examine p53-dependent, p21-independent tumor suppression. Rescue experiments to restore Dino function in Dino-/- lymphoma cells were performed to confirm its contribution to growth suppression. Finally, we analyzed methylation patterns of the DINO/CDKN1A locus in TCGA datasets to investigate the relationship of DINO inactivation and TP53 mutation in human cancers. We find that loss of Dino significantly accelerates tumorigenesis in the E-mu-Myc mouse model of B-cell lymphoma in a haplo-insufficient manner, while previous studies have shown that loss of Cdkn1a does not impact tumor development. Complementation with Dino suppresses growth of isolated Dino-/-, E-mu-Myc lymphoma cells and delays tumor development when re-engrafted into mice. We show that each of these effects requires an intact p53 signaling pathway. Human DINO and mouse Dino can each functionally restore growth suppression in cell culture, suggesting functional conservation through mammalian evolution. Finally, we find that DINO is hypermethylated in multiple types of human cancer and that DINO hypermethylation is correlated to DINO expression, but not CDNK1A expression. Hypermethylation of DINO is mutually exclusive with TP53 alteration in several specific human cancers. We provide direct evidence that the long noncoding RNA DINO is a tumor suppressor transcribed from the CDKN1A promoter. These findings provide insight into a mechanism by which human tumors inactivate p53-dependent functions and describe a novel mechanism of tumor suppression by a long noncoding RNA. We suggest that inactivation of DINO presents a potential biomarker of tumors with altered p53 function, and provides a future basis for targeted therapy and personalized treatment.