Imprinted CDKN1C Is a Tumor Suppressor in Rhabdoid Tumor and Activated by Restoration of SMARCB1 and Histone Deacetylase Inhibitors

Abstract

SMARCB1 is deleted in rhabdoid tumor, an aggressive paediatric malignancy affecting the kidney and CNS. We hypothesized that the oncogenic pathway in rhabdoid tumors involved epigenetic silencing of key cell cycle regulators as a consequence of altered chromatin-remodelling, attributable to loss of SMARCB1, and that this hypothesis if proven could provide a biological rationale for testing epigenetic therapies in this disease. We used an inducible expression system to show that the imprinted cell cycle inhibitor CDKN1C is a downstream target for SMARCB1 and is transcriptionally activated by increased histone H3 and H4 acetylation at the promoter. We also show that CDKN1C expression induces cell cycle arrest, CDKN1C knockdown with siRNA is associated with increased proliferation, and is able to compete against the anti-proliferative effect of restored SMARCB1 expression. The histone deacetylase inhibitor (HDACi), Romidepsin, specifically restored CDKN1C expression in rhabdoid tumor cells through promoter histone H3 and H4 acetylation, recapitulating the effect of SMARCB1 on CDKNIC allelic expression, and induced cell cycle arrest in G401 and STM91-01 rhabdoid tumor cell lines. CDKN1C expression was also shown to be generally absent in clinical specimens of rhabdoid tumor, however CDKN1A and CDKN1B expression persisted. Our observations suggest that maintenance of CDKN1C expression plays a critical role in preventing rhabdoid tumor growth. Significantly, we report for the first time, parallels between the molecular pathways of SMARCB1 restoration and Romidepsin treatment, and demonstrate a biological basis for the further exploration of histone deacetylase inhibitors as relevant therapeutic reagents in the treatment of rhabdoid tumor.

Low-Dose Histone Deacetylase Inhibitor Treatment Leads to Tumor Growth Arrest and Multi-Lineage Differentiation of Malignant Rhabdoid Tumors

“…We have previously shown that several HDACi can mimic the histone acetylation function of SWI/SNF complexes in SMARCB1-null cells and also provided evidence for direct epigenetic regulation of target gene promoters by SMARCB1 (8)(9)(10).…”

Epigenetic modification in chromatin machinery and its deregulation in pediatric brain tumors: Insight into epigenetic therapies

“…63 In addition, the SNF5 protein has a role in histone acetylation. 64,65 Inhibition of histone deacetylases (HDACs) has been found to specifically restore normal expression of proteins involved in cell cycle, originally altered in ATRT cells, through promoter histone H3 and H4 acetylation, recapitulating the effect of SNF5 restoration in ATRT cells. 65 …”

p57Kip2 and Cancer: Time for a Critical Appraisal

“…In the context of epigenetic control, the proteins SMARCB1 (SWI/SNF-related, matrix-associated, actindependent regulator of chromatin, subfamily B, member 1) and CITP2 (chicken ovalbumin upstream promoter transcription factor interacting protein 2) have been reported to increase (SMARCB1) or decrease (CITP2) CDKN1C expression by chromatin structure remodeling (13,14). Intriguingly, SMARCB1 has been reported to be absent (mostly by gene deletion) in rhabdoid tumor, an aggressive pediatric malignancy that affects the kidney and central nervous system.…”

“…Moreover, it was shown that another HDACI molecule, romidepsin, specifically restored CDKN1C expression in rhabdoid tumor cells through promoter histone H3 and H4 acetylation, inducing cell cycle arrest (13). The proposed mechanism of romidepsin's action was particularly complex.…”