Effects of super-enhancers in cancer metastasis: mechanisms and therapeutic targets

Abstract

Metastasis remains the principal cause of cancer-related lethality despite advancements in cancer treatment. Dysfunctional epigenetic alterations are crucial in the metastatic cascade. Among these, super-enhancers (SEs), emerging as new epigenetic regulators, consist of large clusters of regulatory elements that drive the high-level expression of genes essential for the oncogenic process, upon which cancer cells develop a profound dependency. These SE-driven oncogenes play an important role in regulating various facets of metastasis, including the promotion of tumor proliferation in primary and distal metastatic organs, facilitating cellular migration and invasion into the vasculature, triggering epithelial-mesenchymal transition, enhancing cancer stem cell-like properties, circumventing immune detection, and adapting to the heterogeneity of metastatic niches. This heavy reliance on SE-mediated transcription delineates a vulnerable target for therapeutic intervention in cancer cells. In this article, we review current insights into the characteristics, identification methodologies, formation, and activation mechanisms of SEs. We also elaborate the oncogenic roles and regulatory functions of SEs in the context of cancer metastasis. Ultimately, we discuss the potential of SEs as novel therapeutic targets and their implications in clinical oncology, offering insights into future directions for innovative cancer treatment strategies.

Keywords: Metastasis; Molecular mechanisms; Super-enhancers; Therapeutic targets.

Fig. 1

Structure and activity verification methods of super-enhancers (SEs). a Typical enhancers are DNA elements bound by transcription factor (TFs) that recruit a moderate amount of H3K27ac, BRD4, CDKs, Med1 and RNA polymerase II (Pol II), which contributes to the expression of target genes at normal levels. b SEs possess the same components as typical enhancers, yet in significantly higher density, consequently facilitating vigorous transcription of target genes. The stability of enhancer-promoter interaction is stabilized through the binding of CTCF and cohesin. c Selected enhancer regions within SE are cloned into a reporter vector. Subsequently, the enhancer activity is vitrificated through a dual luciferase reporter assay after constructing the plasmid. d CRISPR/Cas9 constructs containing specific small guide RNAs (sgRNAs) targeting the enhancer region are constructed to assess the function of SE by individually depleting each element. e The CRISPR activation system utilizes the catalytically deactivated Cas9 (dCas9) and sgRNAs to guide transcriptional activators (such as VP64 or the histone acetyltransferase p300) to specific genomic sites within SEs, facilitating effective transcriptional activation and enabling the assessment of SE activity. SAM, synergistic activation mediator. f The CRISPR inhibition complex contains the dCas9 and sgRNAs to guide transcriptional repressors (e.g. the KRAB repressor protein or histone demethylase LSD1, DNMT3A) to specific genomic loci, facilitating robust transcriptional suppression and allowing for the evaluation of SE activity

Fig. 2

Mechanisms responsible for the formation of SEs. aDe novo generation of TF binding sites through genomic rearrangements, sequence insertions/deletions, or translocations in the genome. b Structural variations or epigenetic dysregulation can modify the three-dimensional chromatin structure, causing abnormal interactions between SEs and promoters, consequently enhancing the expression of nearby oncogenes. c Specific proteins or TFs encoded by viruses (such as EBV, HTLV-I) promote the formation of SEs in infected cells. d Persistently active signaling pathways trigger the activation of effective TFs to bind to susceptible genomic regions, initiating the generation of SEs

Fig. 3

Gain or loss of SEs enhances malignant tumor metastasis through either upregulating oncogene expression or downregulating tumor suppressor gene expression. SEs can foster metastasis-related cellular characteristics by modulating key molecular factors associated with proliferation, migration, invasion, cancer stem cells (CSCs) formation, epithelial-mesenchymal transition (EMT), and the tumor microenvironment (TME)

Fig. 4

SEs regulate the tumor microenvironment. a SEs participate in immune response. a1 The transcription factor NF-κB, co-factor BRD4, and C/EBP can bind to the SE regions of multiple CXC chemokines to promote their transcription, thereby priming of neutrophils by inflammatory clear cell renal cell carcinoma (ccRCC) cells to facilitate lung metastasis; a2 A SE located between the CD274 and CD273 genes drives the expression of PD-L1 and PD-L2, leading to immune evasion and resistance to T cell-mediated killing; a3 NF-κB, BRD4, and RNA Pol II bind to the SE region of miR-146a and miR-155 to enhance their transcription. These microRNAs can be transported to tumor-associated macrophages through exosomes, stimulating M2-like macrophage polarization and promoting cancer progression. b ASPSCR1::TFE3, the fusion TF, orchestrates the angiogenic program to promote the development of cancer through enhancing SE activity at critical genes, such as Pdgfb, Rab27a, Sytl2, and Vwf. c SE orchestrates the transcription of PRRX1 gene, encoding a critical TF. The PRRX1 protein subsequently engages in autoregulatory interaction with its corresponding SE, thereby forming a critical regulatory loop, which is essential for initiating the transition of fibroblasts into a myofibroblastic phenotype and enhancing the deposition of the extracellular matrix

Fig. 5

Pharmacological targeting SE-driven transcriptional program in cancer. Inhibition of histone deacetylase enzymes (HDACs) with romidepsin or virinostat disrupts acetylation marks levels, impeding the interactions between SEs and promoters. Suppression of the enzymatic activity of histone acetyltransferases CBP/p300 with ICG-001 or CBP30 perturbs SE formation. Treatment with coactivator-associated arginine methyltransferase 1 (CARM1) inhibitor TP-064 hampers the methylation of BAF155, impairing the recruitment of BRD4 and the formation of SEs. Inhibition of the H3K27 demethylase KDM6 with GSK-J4 leads to widespread enhancer reorganization, particularly affecting stemness genes regulated by SEs. JQ1 and OTX015 specifically target BRD4, leading to a reduction in the recruitment of Mediator, BRD4, and RNA Pol II at SE sites. Inhibitors targeting CDKs, upregulate or downregulate the transcription of SE-associated genes through affecting phosphorylation C-terminal domain (CTD) of RNA Pol II. Proteolysis-targeting chimeras (PROTACs) can selectively hijack BRD4, CDKs and TFs into the ubiquitin-proteasome system to elicit its degradation, resulting to interruption of SE-driven transcriptional program. CRISPR/Cas9-mediated genetic perturbation can directly targeting individual components within SEs