Epigenetic regulation in human melanoma: past and future

Abstract

The development and progression of melanoma have been attributed to independent or combined genetic and epigenetic events. There has been remarkable progress in understanding melanoma pathogenesis in terms of genetic alterations. However, recent studies have revealed a complex involvement of epigenetic mechanisms in the regulation of gene expression, including methylation, chromatin modification and remodeling, and the diverse activities of non-coding RNAs. The roles of gene methylation and miRNAs have been relatively well studied in melanoma, but other studies have shown that changes in chromatin status and in the differential expression of long non-coding RNAs can lead to altered regulation of key genes. Taken together, they affect the functioning of signaling pathways that influence each other, intersect, and form networks in which local perturbations disturb the activity of the whole system. Here, we focus on how epigenetic events intertwine with these pathways and contribute to the molecular pathogenesis of melanoma.

Keywords: 5hmC, 5-hydroxymethylcytosine; 5mC, 5-methylcytosine; ACE, angiotensin converting enzyme; ANCR, anti-differentiation non-coding RNA; ANRIL, antisense noncoding RNA in INK4 locus; ASK1, apoptosis signal-regulating kinase 1; ATRA, all-trans retinoic acid; BANCR, BRAF-activated non-coding RNA; BCL-2, B-cell lymphoma 2; BRAF, B-Raf proto-oncogene, serine/threonine kinase; BRG1, ATP-dependent helicase SMARCA4; CAF-1, chromatin assembly factor-1; CBX7, chromobox homolog 7; CCND1, cyclin D1; CD28, cluster of differentiation 28; CDK, cyclin-dependent kinase; CDKN2A/B, cyclin-dependent kinase inhibitor 2A/B; CHD8, chromodomain-helicase DNA-binding protein 8; CREB, cAMP response element-binding protein; CUDR, cancer upregulated drug resistant; Cdc6, cell division cycle 6; DNA methylation/demethylation; DNMT, DNA methyltransferase; EMT, epithelial-mesenchymal transition; ERK, extracellular signal-regulated kinase; EZH2, enhancer of zeste homolog 2; GPCRs, G-protein coupled receptors; GSK3a, glycogen synthase kinase 3 α; GWAS, genome-wide association study; HDAC, histone deacetylase; HOTAIR, HOX antisense intergenic RNA; IAP, inhibitor of apoptosis; IDH2, isocitrate dehydrogenase; IFN, interferon, interleukin 23; JNK, Jun N-terminal kinase; Jak/STAT, Janus kinase/signal transducer and activator of transcription; MAFG, v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G; MALAT1, metastasis-associated lung adenocarcinoma transcript 1; MAPK, mitogen-activated protein kinase; MC1R, melanocortin-1 receptor; MGMT, O6-methylguanine-DNA methyltransferase; MIF, macrophage migration inhibitory factor; MITF, microphthalmia-associated transcription factor; MRE, miRNA recognition element; MeCP2, methyl CpG binding protein 2; NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells; NOD, nucleotide-binding and oligomerization domain; PBX, pre-B-cell leukemia homeobox; PEDF, pigment epithelium derived factor; PI3K, phosphatidylinositol-4, 5-bisphosphate 3-kinase; PIB5PA, phosphatidylinositol-4, 5-biphosphate 5-phosphatase A; PKA, protein kinase A; PRC, polycomb repressor complex; PSF, PTB associated splicing factor; PTB, polypyrimidine tract-binding; PTEN, phosphatase and tensin homolog; RARB, retinoic acid receptor-β2; RASSF1A, Ras association domain family 1A; SETDB1, SET Domain, bifurcated 1; SPRY4, Sprouty 4; STAU1, Staufen1; SWI/SNF, SWItch/Sucrose Non-Fermentable; TCR, T-cell receptor; TET, ten eleven translocase; TGF β, transforming growth factor β; TINCR, tissue differentiation-inducing non-protein coding RNA; TOR, target of rapamycin; TP53, tumor protein 53; TRAF6, TNF receptor-associated factor 6; UCA1, urothelial carcinoma-associated 1; ceRNA, competitive endogenous RNAs; chromatin modification; chromatin remodeling; epigenetics; gene regulation; lncRNA, long ncRNA; melanoma; miRNA, micro RNA; ncRNA, non-coding RNA; ncRNAs; p14ARF, p14 alternative reading frame; p16INK4a, p16 inhibitor of CDK4; pRB, retinoblastoma protein; snoRNA, small nucleolar RNA; α-MSHm, α-melanocyte stimulating hormone.

Figure 1.

Schematic of pathways that play important roles in melanocyte and melanoma development. (A) Schematic of melanocyte differentiation through the MITF axis. KIT receptor and kit ligand are essential for melanocyte development. NRAS, BRAF and MITF are activated by the KIT receptor. The expression of the MITF transcription factor is regulated by α-MSH that binds to MC1R. MITF is phosphorylated by ERK. Activation of MITF controls expression of genes that help regulate melanocyte proliferation, differentiation, pigmentation and survival. Mutant MITF, NRAS, BRAF and KIT are known melanoma oncogenes. (B) Schematic of the EGFR signaling pathway. Signaling is activated by a ligand binding to EGFR receptor that leads to its dimerization. Downstream pathways through RAS and PI3K are activated. RAS signaling occurs via MEK, ERK and p38; PI3K via PIP3 and AKT. Both pathways regulate cellular functions such as metastasis and apoptosis which are vital for melanoma progression. Mutations in EGFR, RAS, RAF, PTEN and PI3K occur in melanoma. (C) Diagram showing the CDKN2A/B locus and its signaling pathway. The top panel illustrates the genomic organization of the CDKN2A/B locus. CDKN2A encodes for 2 proteins, p14^ARF and p16^INK4a, which have identical DNA sequence in exons 2 and 3, while their first exons (E1a and E1b) are different. These proteins have different open reading frames and act in separate pathways. CDKN2B is located upstream of CDKN2A and encodes p15. p16^INK4a and p15 are inhibitors of CDK4 and CDK6, which phosphorylate pRB, leading to progression from G1 to S phase. p14^ARF acts as an inhibitor for HDM2 which regulates p53. The suppression of p16^INK4A at this locus is the most common event reported in melanoma.

Figure 2.

Schematic illustrating different functions proposed for lncRNAs. A-D indicate functions regulating transcription, while E-I show posttranscriptional regulatory mechanisms. (A) lncRNAs can suppress transcription by interacting with PRCs or other chromatin modifying proteins. This leads to heterochromatin formation and gene suppression. (B) Trithorax complexes interact with lncRNA and induce transcription. Chromatin is retained in its euchromatin, actively transcribed state. (C) lncRNAs may be transcribed at enhancer regions, and establish and maintain enhancer-promoter looping and gene induction. (D) lncRNAs, e.g., those with decoy function, may bind to transcription factors and suppress their activities, leading to diverse changes in cells. (E) lncRNAs regulate alternative splicing by interacting with the spliceosomal machinery or mRNA. (F) Intronic regions of many lncRNAs encode snoRNAs. The processed lncRNA may be exported to the cytoplasm and perform roles as yet undefined. The snoRNAs remain in the nucleus. (G) Many lncRNAs are located in the cytoplasm and most of them are associated with polysomes. (H) lncRNAs, either as linear or as circular molecules, may sequester and inactivate miRNAs or mRNAs. The functions of many ribosome-associated lncRNAs are not known; but antisense lncRNAs, such as UCHL1AS, regulate the translation of their associated mRNAs. (I) Decoy lncRNAs, present in the cytoplasm, may bind to proteins and regulate their functions.

Figure 3.

Epigenetic regulators as central components in melanoma signaling. (A) Epigenetic networks. Chromatin modifications are integral to gene regulation at the transcriptional level and are guided by lncRNAs acting as specific sequence identifiers or scaffolds. PRC and trithorax complexes respectively suppress (red) and induce (green) gene expression. Chromatin-modifying enzymes are also regulated by miRNA. DNA methylation and demethylation are late events in DNA modification. In the cytoplasm, lncRNAs can regulate gene expression by acting as decoys or by undefined mechanisms involving ribosome interaction. miRNAs also act as key regulatory molecules in the cytoplasm. Each of these transcripts can be regulated through epigenetic events and contributes to feedback regulatory loops. (B) Example of an epigenetic intertwine in the melanoma signaling pathway. The lncRNA ANRIL may be a transcriptional target of oncogenic receptor tyrosine kinase-NRAS-BRAF signaling. ANRIL may recruit PRC2 and PCR1 to reduce the expression of tumor suppressor miR-449a and miR-99a. Other miRNAs counteract the actions of PRC2-associated EZH2 (miR-101) and DNMT3 (miR-29), and of PRC1-associated BMI1 (miR-200c). EZH2 and miR-31 engage in mutual suppression.