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Updated: Nov 5, 2025
Methyl-binding DNA capture Sequencing for Patient Tissues
Published on: October 31, 2016
Clinically relevant aberrant Filip1l DNA methylation detected in a murine model of cutaneous squamous cell carcinoma
Kevin Roth1, Louis Coussement2, Elena V Knatko1
1Jacqui Wood Cancer Centre, Division of Cellular Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, United Kingdom.
Background:
Cutaneous squamous cell carcinomas (cSCC) are among the most common and highly mutated human malignancies. Understanding the impact of DNA methylation in cSCC may provide avenues for new therapeutic strategies.
Methods:
We used reduced-representation bisulfite sequencing for DNA methylation analysis of murine cSCC. Differential methylation was assessed at the CpG level using limma. Next, we compared with human cSCC Infinium HumanMethylation BeadArray data. Genes were considered to be of major relevance when they featured at least one significantly differentially methylated CpGs (RRBS) / probes (Infinium) with at least a 30% difference between tumour vs. control in both a murine gene and its human orthologue. The human EPIC Infinium data were used to distinguish two cSCC subtypes, stem-cell-like and keratinocyte-like tumours.
Findings:
We found increased average methylation in mouse cSCC (by 12.8%, p = 0.0011) as well as in stem-cell like (by 3.1%, p=0.002), but not keratinocyte-like (0.2%, p = 0.98), human cSCC. Comparison of differentially methylated genes revealed striking similarities between human and mouse cSCC. Locus specific methylation changes in mouse cSCC often occurred in regions of potential regulatory function, including enhancers and promoters. A key differentially methylated region was located in a potential enhancer of the tumour suppressor gene Filip1l and its expression was reduced in mouse tumours. Moreover, the FILIP1L locus showed hypermethylation in human cSCC and lower expression in human cSCC cell lines.
Interpretation:
Deregulation of DNA methylation is an important feature of murine and human cSCC that likely contributes to silencing of tumour suppressor genes, as shown for Filip1l.
Funding:
British Skin Foundation, Cancer Research UK.
Insights
DNA methylation changes are crucial in cutaneous squamous cell carcinoma (cSCC), a common skin cancer. This study reveals similarities in methylation patterns between mouse and human cSCC, highlighting potential therapeutic targets like the tumor suppressor gene Filip1l.
Area of Science:
- Oncology
- Epigenetics
- Dermatology
Background:
- Cutaneous squamous cell carcinoma (cSCC) is a prevalent and highly mutated human skin cancer.
- Understanding DNA methylation's role in cSCC is vital for developing novel therapeutic strategies.
Purpose of the Study:
- To investigate DNA methylation patterns in murine and human cSCC.
- To identify conserved differentially methylated genes between species.
- To explore the potential of DNA methylation as a therapeutic target in cSCC.
Main Methods:
- Reduced-representation bisulfite sequencing (RRBS) for DNA methylation analysis in murine cSCC.
- Differential methylation assessment at the CpG level using limma.
- Comparison with human cSCC Infinium HumanMethylation BeadArray data.
- Identification of highly relevant genes with significant methylation differences in both murine and human orthologues.
- Distinguishing cSCC subtypes using human EPIC Infinium data.
Main Results:
- Increased average DNA methylation observed in mouse cSCC and stem-cell-like human cSCC, but not keratinocyte-like cSCC.
- Striking similarities in differentially methylated genes between human and mouse cSCC.
- Locus-specific methylation changes in mouse cSCC occurred in regulatory regions like enhancers and promoters.
- A key differentially methylated region in a Filip1l enhancer led to reduced gene expression in mouse tumors.
- The FILIP1L locus exhibited hypermethylation and lower expression in human cSCC cell lines.
Conclusions:
- Deregulation of DNA methylation is a significant characteristic of both murine and human cSCC.
- Aberrant DNA methylation likely contributes to the silencing of tumor suppressor genes, exemplified by Filip1l.
- These findings underscore the importance of epigenetic alterations in cSCC pathogenesis and suggest potential therapeutic avenues.
