Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation

Murcott, Ben; Honig, Floris; Halliwell, Dominic Oliver; Tian, Yuan; Robson, James Lawrence; Manasterski, Piotr; Pinnell, Jennifer; Dix-Peek, Thérèse; Uribe-Lewis, Santiago; Ibrahim, Ashraf E. K.; Sero, Julia; Gurevich, David; Nikolaou, Nikolas; Murrell, Adele

Abstract

Background: Colorectal cancer (CRC) progression from adenoma to adenocarcinoma is associated with global reduction in 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). DNA hypomethylation continues upon liver metastasis. Here we examine 5hmC changes upon progression to liver metastasis. Results: 5hmC is increased in metastatic liver tissue relative to the primary colon tumour and expression of TET2 and TET3 is negatively correlated with risk for metastasis in patients with CRC. Genes associated with increased 5-hydroxymethylcytosine show KEGG enrichment for adherens junctions, cytoskeleton and cell migration around a core cadherin (CDH2) network. Overall, the 5-hydroxymethylcyosine profile in the liver metastasis is similar to normal colon appearing to recover at many loci where it was originally present in normal colon and then spreading to adjacent sites. The underlying sequences at the recover and spread regions are enriched for SALL4, ZNF770, ZNF121 and PAX5 transcription factor binding sites. Finally, we show in a zebrafish migration assay using SW480 CRISPR-engineered TET knockout and rescue cells that reduced TET expression leads to a reduced migration frequency. Conclusions: Together these results suggest a biphasic trajectory for 5-hydroxymethyation dynamics that has bearing on potential therapeutic interventions aimed at manipulating 5-hydroxymethylcytosine levels.

• Journal Article Type: Article
• Acceptance Date: Apr 3, 2025
• Online Publication Date: Apr 16, 2025
• Publication Date: Apr 16, 2025
• Deposit Date: Apr 28, 2025
• Publicly Available Date: Apr 29, 2025
• Journal: BMC Biology
• Electronic ISSN: 1741-7007
• Publisher: BioMed Central
• Peer Reviewed: Peer Reviewed
• Volume: 23
• Issue: 1
• Article Number: 100
• DOI: https://doi.org/10.1186/s12915-025-02205-y
• Keywords: 5-Hydroxymethylcytosine, Epigenetics, Ten-eleven-translocation (TET), Colorectal cancer progression to metastasis, Zebrafish assay
• Public URL: https://uwe-repository.worktribe.com/output/14319390