Table 2.
Overview of super-enhancer DNA methylation on various cancers.
| Cancer | Study | Gene | Mechanism | Description | Ref. |
|---|---|---|---|---|---|
| Chronic lymphocytic leukemia (CLL) | Clinical | ENO2, SEPT9, RXRA, and CCR7 | FCER2 and PDCD1 | Hypomethylation in the super-enhancers of B cells triggered the upregulation of immune and metabolic genes, which are crucial for the progression of CLL. | (69) |
| Acute lymphoblastic leukemia (ALL), acute megakaryoblastic leukemia | Clinical | RUNX1 | - | In Down syndrome (DS), the RUNX1 locus was found to be hypermethylated, especially within a super-enhancer specific to hematopoietic stem cells (HSCs). The methylation level of the RUNX1 super-enhancer was significantly higher in DS compared to control samples. | (107) |
| B lymphoma | In vitro | Chemokine (C-X-C motif) ligand 13 (CXCL13) | CTCFs | MBD1-mediated DNA methylation of super-enhancers played a crucial role in repressing CXCL13 expression. This regulation was influenced by stress conditions, CTCF, and the DNA methylation status of the promoter, emphasizing the complex interaction of DNA modifications in controlling immune-related genes in cancer. | (108) |
| CLL | Clinical | BCL2 | H3K27ac | In CLL, super-enhancers located near critical genes like BCL2, LEF1, and CTLA4, which are involved in lymphocyte proliferation and differentiation, exhibited elevated levels of H3K27ac. | (109) |
| CLL | Clinical | CD5, CLLU1, and IRF2 | - | DNA methylation specific to CLL, especially in class A and C CpG sites, was enriched within super-enhancer regions. These super-enhancers were categorized into “stable” (shared with normal B cells) and “gained” (newly acquired in CLL). | (110) |
| Multiple Myeloma (MM) | Clinical | ARID5A | CTCF | Super-enhancer-CTCF loops at H3K27ac-enriched differentially methylated regions (DMRs) were responsible for regulating the overexpression of specific genes or gene clusters. | (111) |
| MM | Clinical | ITGB7 | H3K36me3 | Targeted induction of DNA methylation at intragenic enhancers, such as those in ITGB7, promoted gene expression, likely through interactions with other epigenetic modifications like H3K36me3. Induced methylation at DMRs overlapping with super-enhancer regions in ITGB7, leading to a marked increase in gene expression. | (55) |
| Colorectal cancer (CRC), Breast cancer, Glioblastoma, Lung cancer | Clinical | MYC and RNF43 | Transcription factor (FOXA2, FOXP1, and FOXQ1) binding | DNA methylation changes in super-enhancers, influenced by histone modifications such as H3K27ac and H3K4me1, were associated with cancer-specific alterations. These methylation changes contributed to the silencing of tumor suppressor genes like MIRLET7 and RUNX1, while promoting the activation of oncogenes such as MYC and RNF43. | (13) |
| Gastric adenocarcinoma | Clinical and in vitro | CLDN4 and ELF3 | ABLIM2, SLC1A2 | Super-enhancers with somatic gain exhibited hypomethylation, while those with somatic loss showed hypermethylation. This was confirmed by analyzing loci like ABLIM2 and SLC1A2, highlighting the link between super-enhancer methylation changes and cancer progression. | (50) |
| Oropharyngeal carcinoma | Clinical | SMAGP, and GPR107 | - | Hypermethylation of super-enhancers was linked to the suppression of tumor suppressor genes, such as the reduced expression of SMAGP, a gene important for epithelial cell adhesion. | (112) |
| Oesophageal squamous cell carcinoma (OSCC) | Clinical | ZFP36L2 | H3K27ac | The study observed frequent hypermethylation of the ZFP36L2 super-enhancer region in OSCC. Methylation at specific CpG sites was negatively associated with the expression of ZFP36L2, suggesting epigenetic silencing of the gene. | (113) |
| Nasopharyngeal carcinoma | In vitro and in vitro | TRIB1 | R-loop | In cell lines like K562 and GM12878, the super-enhancer regions near TRIB1 exhibited hypomethylation, while the exons of the TRIB1 gene showed hypermethylation. The hypomethylation in the super-enhancer regions was linked to R-loop formation, which in turn triggered gene activation. | (114) |
| Lung cancer | In vitro | MYC, E2F6, and IRF1 | TF binding and RNA polymerase II recruitment | Hypomethylation of G4 structures in super-enhancers, overlapping with CpG islands, enhances super-enhancer activity and gene expression in cancer. In contrast, methylation of these regions reduces their regulatory function, affecting downstream gene activity. | |
| Leukemia, CRC, Breast cancer, Chronic myeloid leukemia |
In vitro | MYC | CTCF | Methylation of the enhancer-docking CTCF site disrupts CTCF binding, reducing MYC expression and cellular proliferation, highlighting its key role in cancer development. | (115) |
| Prostate cancer | Clinical | KRT5, and KRT14 | TRIM29, TP63 | Methylation of specific CpG sites within super-enhancers was closely associated with epigenetic changes and transcriptional disruptions specific to PRAD. | (116) |
| Prostate cancer, Breast cancer | Clinical | - | H3K27ac, TCF4, YY-1 | Super-enhancers exhibited more significant methylation compared to regular enhancers, with the H3K27ac mark still present. | (12) |
| Breast Cancer | Clinical | USF1, SOX4, and MYBL2 | Core transcriptional regulatory circuitry | Super-enhancer regions had lower methylation levels than random genomic areas, with cancer samples showing even lower methylation compared to normal tissues. ChIP-seq analysis revealed that super-enhancer regions were enriched with active chromatin marks (H3K4me1, H3K4me2, H3K27ac, EP300), transcriptional marks (H3K4me3), and exhibited greater chromatin accessibility compared to random regions. | (98) |
| Breast cancer | Clinical and in vitro | ESR1, ERBB2, FBLN2, CEBPA, and FAT4 | - | Key hypomethylation sites in enhancer regions and hypermethylation sites in CpG islands (CGIs) were identified as regulators of critical genes. These included oncogenes ESR1 and ERBB2, as well as tumor suppressor genes FBLN2, CEBPA, and FAT4. | (117) |
| Breast cancer | Clinical | ADM2, TGFBR2, JUN, EGFR, and GATA3 | H3K27ac | Several differentially methylated sites (DMS) were found in breast-tissue-specific super-enhancer regions, including the SE-ID-36299 and SE-ID-30649537 regions, which contained 49 and 45 DMS, respectively. | (118) |
| Breast cancer | Clinical | HOXB2 | H3K27ac | Hypermethylation at the CpG site cg20401567, situated downstream of the HOXB2 gene, was linked to reduced expression of HOXB2 and other genes in the HOXB family. | (119) |
| Breast, Myeloid leukemia, MM, Acute promyelocytic leukemia (APL), nasopharyngeal carcinoma (NPC), plasmacytoma tumor, urothelial cell carcinoma (UCC), uveal melanoma | In silico | MIXL1, BLK, PLEKHA2, ACY3, PTPRCAP, TBC1D10C, PLEKHA2, HAND2, HPGD, EHD3, CD163L1, CD27, LPAR5, RBP5, KCNN3, PBXIP1, CCDC152, LOC153684, ERMN, C16orf54, CORO1A, ITGAL, LOC606724, and MAPK3 | - | The study identified 159 differentially methylated super-enhancers, with 87 actively regulating 150 genes. Pathway analysis showed these genes were associated with carcinogenesis in nasopharyngeal, breast, melanoma, and bladder cancers, and were regulated by the epigenetic landscape in these cancers. | (112) |
| Lung cancer | Clinical and in vitro | SFTPA2, SMDP4, SFTPD, and SFTA3 | – | Hypomethylated and hypermethylated F-seDMRs were enriched in the Reactome pathways for “keratinization” and “surfactant metabolism,” respectively. This suggests that enhancer region methylation, rather than promoter methylation, is more influential in regulating tumorigenesis and immune infiltration in lung squamous cell carcinoma (LUSC). | (85) |
| Lung cancer | Clinical and in vitro | Cytohesin 1 Interacting Protein (CYTIP), TNF superfamily member 8 (TNFSF8, Programmed cell death protein (PD)-1 | – | The hypomethylation of DMRs in CYTIP and TNFSF8 was found to be a stronger predictor of response to anti-PD-1 treatment, as well as progression-free survival (PFS) and overall survival, compared to PD-L1 expression. | (120) |
| Lung cancer | In vitro | MYC, E2F6, and IRF1 | TF binding and RNA polymerase II recruitment | Hypomethylation of G4 structures in super-enhancer-associated CGIs boosts super-enhancer activity and gene expression in cancer, while methylation reduces their regulatory impact on gene activity. | (121) |
| Lung cancer | Clinical | NEUROD1, and MYC | - | Genes covered by these super-enhancers, such as NEUROD1, FOXA1/2, and NKX2-1, exhibited a negative correlation between gene body methylation and gene expression. | (122) |
| Lung cancer | In vivo | KMT2D | - | Loss of Kmt2d notably reduced enhancer and super-enhancer activity, as evidenced by a global decrease in H3K4me1 and H3K27ac signals, without affecting H3K4me3 and H3K27me3 levels. | (87) |
| Lung cancer | Clinical | SFTPA2, SFTA3, and SFTPD | - | The findings highlight the critical role of super-enhancer methylation in tumor progression in LUSC, particularly by downregulating genes related to surfactant metabolism and keratinization, suggesting that super-enhancer methylation could be a key epigenetic mechanism driving tumorigenesis. | (85) |
| Pancreatic cancer | In vivo | ΔNp63, MYC, and RUNX3 | KDM6A | Downregulation of UTY is linked to CpG island methylation or Yq11 deletions. Additionally, changes in H3K4me1/H3K27ac and an increase in super-enhancer size, especially in knockout females, suggest that KDM6A regulates super-enhancer delimitation via the COMPASS complex. | (54) |
| Blader cancer | Clinical | PI3K-Akt | lncRNA | The study found a connection between DNA methylation changes and lncRNA expression in bladder cancer, specifically showing reduced 5mC levels in the super-enhancer regions of lncRNA genes in tumor tissues. | (123) |
| Retinoblastoma | Clinical and in vivo | Ascl1, and Crx | H3K27Ac | During retinal development, super-enhancers associated with genes like Ascl1 and Crx exhibited dynamic changes in activity and DNA methylation. These super-enhancers were identified as crucial regulators of genes that control retinal progenitor cell maintenance and differentiation into photoreceptors. | (124) |
| Glioma | Clinical | DICER1 | CTCF | The findings reveal that abnormal methylation of super-enhancers and associated regulatory elements, marked by altered 5hmC and 5mC levels, plays a crucial role in cancer. These epigenetic changes impact key pathways, including WNT signaling and RNA regulation, driving tumor development and progression. | (125) |
| Neuroblastoma | In vitro | MYCN | CTCF | Core Regulatory Circuit-driven super-enhancers surrounding MYCN demonstrated active regulation through hypomethylation. | (126) |
| Neuroendocrine carcinoma (NEC) | In vitro | ELF3 | ASCL1 | The DNA methylation status of super-enhancer regions was found to regulate ELF3 overexpression in ASCL1-positive NEC, emphasizing an epigenetic mechanism over transcriptional regulation by ASCL1. | (127) |
| Hepatocellular carcinoma (HCC) | Clinical | HGS, CEP131, MAFG, MAFG-DT, FOXK2, and SIRT7 | - | A total of 2,051 aberrant enhancer-associated DEGs were identified, with upregulated genes linked to cell cycle, DNA repair, and replication, and downregulated genes associated with immune response and metabolism. | (128) |