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Trends in Cancer
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Epigenetic basis and targeting of cancer metastasis

Published:December 21, 2021DOI:https://doi.org/10.1016/j.trecan.2021.11.008

      Highlights

      • Epigenetic regulators play a key role in the transition from primary to metastatic cancer.
      • The advent of CRISPR-based epigenomic editing tools provides a range of novel approaches to directly investigate epigenetic drivers of cancer metastasis.
      • Epigenomic editing tools have now been used to establish causal roles for epigenetic regulators in tumourigenesis; however, their application to specific models of metastasis remains limited.
      • Utilising these tools for detailed investigation of metastasis-associated epigenetic changes may yield a plethora of downstream applications, including improving our fundamental understanding of the metastatic cascade; the identification of novel biomarkers to support clinical diagnosis, prognostication, and monitoring; and aiding the development of innovative therapeutic approaches to enhance clinical outcomes in advanced malignancy.
      Despite the development of novel therapeutic approaches and improved clinical management, survival from metastatic disease remains poor. Indeed, metastasis accounts for the vast majority of cancer-related deaths. The metastatic cascade comprises a complex range of molecular events that cannot be explained by genetic aberrations alone; dynamic, epigenetic regulatory mechanisms are now being implicated as key drivers of successful metastasis. With the emergence of CRISPR-based epigenomic editing, it is now possible to investigate the direct role of locus-specific epigenetic alterations in metastatic progression. Here, we review the role of epigenetic mechanisms in cancer metastasis, explore recent developments in technologies for epigenomic investigation, and highlight the emerging applications of epigenomic editing technologies in the clinical management of cancer.

      Keywords

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      Glossary

      Antisense oligonucleotides (ASOs)
      antisense-based inhibitors designed to bind to and disrupt the activity of specific RNA molecules in a targeted fashion; they are an emerging therapeutic option for pathologies involving disordered RNA expression, including noncoding RNAs.
      Cas9
      CRISPR-associated protein 9 is an RNA-guided endonuclease derived from type II CRISPR-Cas systems, which induces double-stranded DNA breaks at the locus at which it binds.
      Casilio-ME
      the Casilio system utilises a multimerisation approach for gene editing consisting of a dCas9 protein, an sgRNA tagged with Pumilio/FBF (PUF) binding sites, and a PUF-tagged effector. The Casilio-ME platforms were developed as a panel of epigenetic editing tools that provided enhanced TET1-induced DNA demethylation via co-delivery of the base excision repair-associated protein GADD45A or NEIL2, which are major components of the TET demethylation process.
      Cas9n
      Cas9 nickase, a modified variant of Cas9 with only single-stranded catalytic activity at the specific strand at which it binds; Cas9n is generally characterised by an introduced D10A mutation in the RuvC domain.
      CRISPR
      clustered regularly interspaced short palindromic repeats are a family of clustered genomic repeat sequences found in prokaryotes and which provide an adaptive immune response against invading pathogens. CRISPR and associated Cas protein systems have now been repurposed for targeted editing of the genome and epigenome in a variety of organisms.
      CRISPRa
      CRISPR-activation approaches use dCas9 fused to transcriptional activators (e.g., dCas9-VP64, dCas9-SAM) in order to increase gene expression at a target locus.
      CRISPRi
      CRISPR-interference approaches use dCas9 fused to transcriptional repressors (e.g., dCas9-KRAB, dCas9-MXD1) in order to decrease gene expression at a target locus.
      dCas9
      deactivated or ‘dead’ Cas9, a modified variant of the Cas9 nuclease that has targeted DNA-binding activity but no catalytic activity; dCas9 is inactivated via mutations in the HNH and RuvC-like domains.
      DNA methylation
      refers to the addition of a 5′ methyl group to cytosine residues to form 5-methylcytosine, the most stable and well-characterised epigenetic modification. Here, we use DNA methylation to refer to methylation of CpG residues specifically, as methylation almost exclusively occurs at CpG sites in mammals; though non-CpG cytosine methylation has been described, including in the context of human cancers, it remains rare, and understanding its functional relevance is limited in this context.
      DNA methylome
      refers to the pattern of DNA methylation across the entire genome.
      DNMT
      DNA methyltransferase enzymes transfer a methyl group from the donor molecule S-adenosylmethionine to cytosine, thereby generating 5-methylcytosine. DNMT1 is a maintenance DNMT that facilitates stable DNA methylation during replication; DNMT3A and DNMT3B are de novo DNMTs that can actively methylate unmethylated cytosine residues; DNMT3L is an accessory enzyme that stimulates DNMT3A de novo methylation.
      Epithelial to mesenchymal transition (EMT)
      describes a shift from epithelial cell-type features to a more mesenchymal stem cell phenotype; this is a commonly characterised phenomenon in tumourigenesis that facilitates the gain of specific cell functions required for tumour progression and metastasis, including loss of cell polarity and cell–cell adhesion, gain of migratory properties, and increased invasive capabilities.
      HAT
      histone acetyltransferases add acetyl groups to specific residues of histone tails.
      HDAC
      histone deacetylases remove histone tail acetyl groups.
      HDM
      histone demethylases remove methyl groups from histone tails.
      Histone modifications
      refers to the wide range of post-translational modifications that occur on histone tails, including acetylation and methylation, which we largely focus on in this review.
      HMT
      histone methyltransferases transfer methyl groups from S-adenosylmethionine to lysine or arginine residues on histone tails.
      Noncoding RNA (ncRNA)
      sequences of the genome that are not protein-coding but are actively transcribed; ncRNA has numerous regulatory roles and interactions with other genomic elements, RNA, and proteins.
      Repeat elements
      repeated sequences or repetitive elements are noncoding DNA sequences that are found multiple times throughout the genome and often have unknown functions; in the context of malignancy, altered expression of repeat elements is associated with genomic instability.
      siRNA
      short, double-stranded RNA molecules that can disrupt gene expression through the post-translational degradation of mRNA transcripts.
      SunTag
      the supernova tagging system is a protein multimerisation system that has been adapted for epigenetic editing to maximise effector protein recruitment; CRISPR-dCas9-SunTag modules consist of a modified dCas9 construct with an appended epitope-based protein scaffold, facilitating the recruitment of multiple copies of an antibody-tagged effector enzyme.
      TET
      ten-eleven translocation family dioxygenases, TET1, TET2, and TET3, actively catalyse the progressive oxidation of 5-methylcytosine to unmethylated cytosine via a series of intermediates.
      VX809
      an agent used in the management of cystic fibrosis patients with F508del mutation via correcting folding defects in the cystic fibrosis transmembrane conductance regulator (CFTR).