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The Mechanisms of Cancer Metastasis Based on Epigenetics and Epitranscriptomics: A Recent Insight

Cancer is a complex disease that is characterized by a series of genetic alterations and uncontrolled cell growth. These genetic changes, often referred to as "multi-hit" events, can involve mutations, deletions, insertions, or rearrangements of DNA sequences within the genome. These alterations can affect critical genes that regulate cell division, apoptosis (programmed cell death), DNA repair, and other cellular processes, leading to the development and progression of cancer.


The presence of genetic mutations is a hallmark of cancer initiation and progression. These mutations can disrupt the normal functioning of genes known as oncogenes and tumour suppressor genes, which play crucial roles in maintaining the balance between cell growth and cell death. Oncogenes are genes that, when mutated or activated, can promote excessive cell proliferation and survival. Conversely, tumour suppressor genes normally act as "brakes" on cell growth, preventing uncontrolled division and promoting programmed cell death. Mutations in tumour suppressor genes can result in their inactivation or loss of function, allowing cells to evade growth restrictions and accumulate genetic damage. However, when it comes to cancer metastasis, the process by which cancer cells spread from the primary tumour to distant sites in the body, the relationship with specific driver gene mutations becomes less clear. Unlike the well-established connection between genetic mutations and cancer initiation, the mechanisms underlying metastasis are more complex and involve a combination of genetic, epigenetic, and microenvironmental factors.


Indeed, there are no specific driver gene mutations linked to cancer metastasis[1], which refers to the movement of cancer cells from a primary site to progressively colonize distant organs. In fact, the sites of metastasis are determined by the intrinsic properties of cancer, host-organ microenvironment and organ-specific circulation pattern[2,3]. It indicates the existence of potential mechanisms between cancer cells and the environment, including epigenetics and epitranscriptomics. Instead of the underlying DNA sequence, epigenetics refers to other heritable changes of gene expression, mainly involving DNA methylation, histone modifications and non-coding RNA regulation. Epitranscriptomics refers to chemical modifications for RNA in a similar manner as epigenetics.

As a widely known epigenetic mechanism, DNA methylation is defined as the addition of a methyl group to cytosine nucleotides, especially when cytosines are followed by guanines (CpG sites). Aberrant DNA methylation shows large amounts of loss of DNA methylation (hypomethylation), which is regarded as a classic hallmark of cancer. It usually targets repetitive sequences, further giving rise to chromosomal instability, translocations and gene disruption [4,5]. Interestingly, hypermethylation of promoter-related CpG sites also plays a significant role in gene silencing of tumour suppressor genes [6,7].


Most importantly, there are many metastasis-specific methylation events in some cancer types. For instance, the expression of S100 calcium-binding protein A4 (S100A4) and cytohesin 1 interacting protein (CYTIP) increases when induced by promoter hypomethylation in clear cell renal cell carcinoma (ccRCC), which finally leads to metastasis colonization [8,9]. In detail, DNA hypomethylation drives HIF-mediated CYTIP expression, which inhibits death cytokine signals in cancer cells independently of VHL expression. Besides, downregulation of the PRC2 subunit SUZ12 causes loss of repressive histone methylation mark H3K27me3, leading to activated HIF-driven CXCR4 expression (Figure 1). Eventually, the action of chemotactic cell invasion is amplified [9].


Figure 1. The metastatic mechanisms are caused by DNA and histone hypomethylation events independently of VHL expression. The image is adapted from [9]


Histone post-translational modifications (PTMs) mainly contain methylation, acetylation, ubiquitination and phosphorylation. Disturbance of the histone code contributes to cancer initiation, progression and metastasis. For cancer metastasis, epithelial-to-mesenchymal transition (EMT) transcription factors can recruit histone-modifying complexes to chromatin in order to induce epigenetic silencing [10,11]. Enhancer of zest homolog 2 (EZH2) is the enzymatic subunit of PRC2, which can trimethylate histone H3 lysine 27 (H3K27me3) and mediate transcriptional silencing.


Therefore, overexpression of EZH2 in various cancer types such as prostate cancer and breast cancer will provoke silencing via H3K27me3 and further induce cell invasion and metastasis [12-14]. Moreover, EZH2 induces transcriptional silencing of the metastasis suppressor gene RKIP in prostate cancer and breast cancer via H3K27 and H3K9me3 modifications. It also makes EZH2 expression negatively associate with relapse-free survival of cancer patients [15]. Last but not least, EZH2 can also regulate EMT and metastasis through gene silencing of tumour suppressors such as DAB2IP in colorectal cancer (CRC) [16] (Figure 2).



Figure 2. The metastatic mechanisms are caused by EZH2-mediated transcriptional or genetic silencing. Image source: Peiyi Luo (2023).


Non-coding RNAs (ncRNAs) refer to specific RNA molecules transcribed by the genome which code for proteins, including housekeeping and regulatory ncRNAs. Housekeeping ncRNAs are classified into rRNA, tRNA, snRNA and so on. Regulatory ncRNAs are divided into long non-coding RNA (lncRNA), microRNA (miRNA), circular RNA (circRNA) etc. in particular, miRNA, which is a kind of single-strand small molecules, can regulate post-transcriptional genetic expression. miRNA will be paired by complementary sequences of 3’ UTR on target mRNA transcripts, leading to genetic silencing. For example, miR-149 initiates epigenetic silencing in cancer-associated fibroblasts in the context of gastric cancer [17]. For another example, miR-149 is epigenetically silenced in glioblastoma.


Furthermore, the restoration of miR-149 decreases the expression of AKT1 and cyclin D1, further causing inhibited proliferative activities of glioma cells. Remarkably, these actions seemingly have no correlation with metastasis potential [18]. However, we must pay more attention to cancer metastatic mechanisms induced by ncRNAs regulation. miR-491-5p can directly target a histone demethylase JMJD2B/KDM4B, which have the potential oncogenic effect. This gives rise to downstream epigenetic-mediated tumour suppressor effects [19]. miR-149 can directly target GIT ArfGAP 1 (GIT1) and inhibit integrin signalling, further suppressing metastasis [20](Figure 3). Hypermethylated miR-491-5p and miR-149 cause decreased expression in breast cancer. Tumour suppressor effects are reduced and integrin signalling is activated respectively, finally promoting cancer progression and metastasis [19,20]. The expression of miR-491-5p is also decreased in oral squamous cell carcinoma (OSCC). It induces overexpression of GIT1, and provokes migration, invasion as well as metastasis of OSCC cells in a similar manner as breast cancer [21].



Figure 3. miR-149-GIT1 regulation pathways in regulating breast cancer metastasis. Image is adapted from [20].


Epitranscriptome refers to chemical modifications for RNA molecules. They are mainly associated with ncRNAs, such as rRNA, tRNA, snRNA as well as messenger RNA (mRNA). The N6-methyladenosine (m6A) deposition on mRNA is a widely known epitranscriptomic modification driven by METTL3. METTL3 can mediate m6A modification of SOX2 and stimulate the malignant progression of breast cancer [22]. MELLT3 can also stabilize SOX2 mRNA, induce drug resistance and provoke lung metastasis in CRC [23]. Last but not least, research shows that METTL3 can promote KRT7-AS methylation in order to amplify expression. METTL3 and KRT7 mRNA will form duplexes with each other to increase stability and expression of KRT7 through recruitment of the IGF2BP1/HuR complex in the breast cancer lung metastasis model [24].

In conclusion, chemical alternations in both epigenetics and epitranscriptomics will affect cancer metastasis via DNA methylation, histone modifications, ncRNAs regulation as well as RNA changes Gaining a comprehensive understanding of these mechanisms is crucial due to their substantial clinical relevance in preventing advanced metastasis. These epi-alternations can be targeted by small molecules or inhibitors of epi-modifiers, which is regarded as a therapeutic strategy based on precision oncology.

This article is written by Peiyi Luo, Queen Mary University of London, UK.


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