Super-enhancer landscape regulated by CDK12 drives retinoblastoma progression

BACKGROUND: Retinoblastoma (RB) lacks effective targeted therapies. Super-enhancers (SEs) are crucial for tumorigenesis, yet their role in RB was unclear. METHODS: We profiled active SEs in RB cells using chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq). qRT-PCR, single-cell RNA sequencing (scRNA-Seq) and immunohistochemistry (IHC) were employed to identify the critical regulator of SE activity. The anti-tumour effect of targeted blockade of SE regulator, achieved via pharmacological degradation and specific lentiviruses, was investigated in vitro and in preclinical models of subcutaneous, intraocular, and central nervous system (CNS)-metastatic RB. RESULTS: Cyclin-dependent kinase 12 (CDK12) was identified as a key SE regulator. SE-driven oncogenic transcription was suppressed by CDK12 inhibition, leading to eliminated tumour outgrowth and metastasis. In addition, SE-associated oncogenes BIRC5 and PTPRC were identified as essential for RB cell survival and stemness. Furthermore, PTPRC overexpression rescued the anti-tumour effect of BSJ-4-116. CONCLUSIONS: This study defines CDK12 as a master regulator of oncogenic SEs in RB. Targeting the CDK12-SE axis, via CDK12 or downstream effectors like BIRC5/PTPRC, presents a novel therapeutic strategy.