Abstract
BackgroundSuper-enhancers (SEs) play a crucial role in cancer, which is often associate with activated oncogenes. However, little is known about how SEs facilitate tumour suppression. Individuals with Down syndrome exhibit a remarkably reduced incidence of breast cancer (BC), moving the search for tumor suppressor genes on human chromosome 21 (HSA21). In this study, we aim to identify and explore potential mechanisms by which SEs are established for tumor suppressor RCAN1.4 on HSA21 in BC.MethodsIn silico analysis and immunohistochemical staining were used to assess the expression and clinical relevance of RCAN1.4 and RUNX3 in BC. Function experiments were performed to evaluate the effects of RCAN1.4 on the malignancy of breast carcinoma in vitro and in vivo. ChIP-seq data analysis, ChIP-qPCR, double-CRISPR genome editing, and luciferase reporter assay were utilized to confirm RUNX3 was involved in regulating RCAN1.4-associated SE in BC. The clinical value of co-expression of RCAN1.4 and RUNX3 was evaluated in BC patients.ResultsHere, we characterized RCAN1.4 as a potential tumour suppressor in BC. RCAN1.4 loss promoted tumour metastasis to bone and brain, and its overexpression inhibited tumour growth by blocking the calcineurin-NFATc1 pathway. Unexpectedly, we found RCAN1.4 expression was driven by a ~ 23 kb-long SE. RCAN1.4-SEdistal was sensitive to BRD4 inhibition, and its deletion decreased RCAN1.4 expression by over 90% and induced the malignant phenotype of BC cells. We also discovered that the binding sites in the SE region of RCAN1.4 were enriched for consensus sequences of transcription factor RUNX3. Knockdown of RUNX3 repressed the luciferase activity and also decreased H3K27ac enrichment binding at the SE region of RCAN1.4. Furthermore, abnormal SE-driven RCAN1.4 expression mediated by RUNX3 loss could be physiologically significant and clinically relevant in BC patients. Notably, we established a prognostic model based on RCAN1.4 and RUNX3 co-expression that effectively predicted the overall survival in BC patients.ConclusionsThese findings reveal an important role of SEs in facilitating tumour suppression in BC. Considering that the combination of low RCAN1.4 and low RUNX3 expression has worse prognosis, RUNX3-RCAN1.4 axis maybe a novel prognostic biomarker and therapeutic target for BC patients.
Highlights
Super-enhancers (SEs) play a crucial role in cancer, which is often associate with activated oncogenes
Regulator of calcineurin 1 (RCAN1).4-SEdistal was sensitive to BRD4 inhibition, and its deletion decreased RCAN1.4 expression by over 90% and induced the malignant phenotype of breast cancer (BC) cells
We discovered that the binding sites in the SE region of RCAN1.4 were enriched for consensus sequences of transcription factor RUNX family transcription factor 3 (RUNX3)
Summary
Super-enhancers (SEs) play a crucial role in cancer, which is often associate with activated oncogenes. Novel causative genes and molecular pathways underlying breast cancer progression and metastasis need to be identified and validated. Super-enhancers (SEs) are large clusters of transcriptional enhancers, including populations of transcription factors (TFs), cofactors, chromatin regulators, and transcription apparatus occupying super-enhancers, that drive the expression of genes that define cell identity [4]. Accumulating evidence shows that breast cancer cells generate super-enhancers at oncogenes during tumour pathogenesis. Whereas triple-negative breast cancer cells rely on a specific gene cluster of oncogenic TFs driven by SEs to sustain proliferation and survival [9]. There is little known about how super-enhancers are established for tumour suppression in breast cancer
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