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

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

doi:10.1186/s12915-025-02205-y

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

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

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	100
Journal	BMC Biology
Volume	23
Issue number	1
Early online date	16 Apr 2025
DOIs	https://doi.org/10.1186/s12915-025-02205-y
Publication status	Published - 16 Apr 2025

Data Availability Statement

All data generated or analysed during this study are included in this published article, its supplementary information files, and publicly available repositories. The datasets generated and analysed during the current study are available in the GEO database repository, BioProject accession PRJNA206436 and GEO Series GSE268934 [79]. URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE268934. Supporting data values for figures are included in Additional File 6.

Funding

UKRI: Medical Research Council London GB Grant numbers MR/T000481/1 and MR/P000711/1; Engineering and Physical Research Council Grant number 259868, Biotechnology and Biological Sciences Research Council 2598658. Wellcome Trust Sir Henry Dale fellowship, number 220188/A/20/Z. Royal Society RG|/R2/232121. The Academy of Medical Sciences Springboard Award SBF008/1073. Cancer Research at Bath CR@B network; The University of Cambridge, Cancer Research UK (CRUK SEB-Institute Group Award A ref10182). UKRI: Medical Research Council London GB Grant numbers MR/T000481/1 and MR/P000711/1; Engineering and Physical Research Council Grant number 259868, Biotechnology and Biological Sciences Research Council 2598658. Wellcome Trust Sir Henry Dale fellowship, number 220188/A/20/Z. Royal Society RG|/R2/232121. The Academy of Medical Sciences Springboard Award SBF008/1073.\u00A0Cancer Research at Bath CR@B network; The University of Cambridge, Cancer Research UK (CRUK SEB-Institute Group Award A ref10182).

Funders	Funder number
Sir Henry Dale fellowship
Cancer Research UK
University of Cambridge
Wellcome Trust	220188/A/20/
Academy of Medical Sciences	SBF008/1073
Royal Society	RG\|/R2/232121
Biotechnology and Biological Sciences Research Council	2598658
Medical Research Council London GB	MR/P000711/1, MR/T000481/1
Engineering and Physical Sciences Research Council	259868

Keywords

5-Hydroxymethylcytosine
Colorectal cancer progression to metastasis
Epigenetics
Ten-eleven-translocation (TET)
Zebrafish assay

ASJC Scopus subject areas

Biotechnology
Structural Biology
Ecology, Evolution, Behavior and Systematics
Physiology
General Biochemistry,Genetics and Molecular Biology
General Agricultural and Biological Sciences
Plant Science
Developmental Biology
Cell Biology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1186/s12915-025-02205-yLicence: CC BY

Cite this

Murcott, B., Honig, F., Halliwell, D. O., Tian, Y., Robson, J. L., Manasterski, P., Pinnell, J., Dix-Peek, T., Uribe-Lewis, S., Ibrahim, A. E. K., Sero, J., Gurevich, D., Nikolaou, N., & Murrell, A. (2025). Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation. BMC Biology, 23(1), Article 100. https://doi.org/10.1186/s12915-025-02205-y

Murcott, B , Honig, F , Halliwell, DO, Tian, Y, Robson, JL, Manasterski, P, Pinnell, J, Dix-Peek, T, Uribe-Lewis, S, Ibrahim, AEK, Sero, J , Gurevich, D, Nikolaou, N & Murrell, A 2025, 'Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation', BMC Biology, vol. 23, no. 1, 100. https://doi.org/10.1186/s12915-025-02205-y

@article{c7c0c4aac52242679db75618e0682322,

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

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. ",

keywords = "5-Hydroxymethylcytosine, Colorectal cancer progression to metastasis, Epigenetics, Ten-eleven-translocation (TET), Zebrafish assay",

author = "Ben Murcott and Floris Honig and Halliwell, {Dominic Oliver} and Yuan Tian and Robson, {James Lawrence} and Piotr Manasterski and Jennifer Pinnell and Therese Dix-Peek and Santiago Uribe-Lewis and Ibrahim, {Ashraf E K} and Julia Sero and David Gurevich and Nikolas Nikolaou and Adele Murrell",

year = "2025",

month = apr,

day = "16",

doi = "10.1186/s12915-025-02205-y",

language = "English",

volume = "23",

journal = "BMC Biology",

issn = "1741-7007",

publisher = "BioMed Central",

number = "1",

}

TY - JOUR

T1 - Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation

AU - Murcott, Ben

AU - Honig, Floris

AU - Halliwell, Dominic Oliver

AU - Tian, Yuan

AU - Robson, James Lawrence

AU - Manasterski, Piotr

AU - Pinnell, Jennifer

AU - Dix-Peek, Therese

AU - Uribe-Lewis, Santiago

AU - Ibrahim, Ashraf E K

AU - Sero, Julia

AU - Gurevich, David

AU - Nikolaou, Nikolas

AU - Murrell, Adele

PY - 2025/4/16

Y1 - 2025/4/16

N2 - 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.

AB - 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.

KW - 5-Hydroxymethylcytosine

KW - Colorectal cancer progression to metastasis

KW - Epigenetics

KW - Ten-eleven-translocation (TET)

KW - Zebrafish assay

UR - http://www.scopus.com/inward/record.url?scp=105002734662&partnerID=8YFLogxK

U2 - 10.1186/s12915-025-02205-y

DO - 10.1186/s12915-025-02205-y

M3 - Article

SN - 1741-7007

VL - 23

JO - BMC Biology

JF - BMC Biology

IS - 1

M1 - 100

ER -

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

Abstract

Data Availability Statement

Funding

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this