A qualitative prognostic biomarker for melanoma based on the relative methylation orderings of CpG loci
Skin cutaneous melanoma (SKCM) is an aggressive tumor with a poor prognosis. We developed SKCM-P8, a novel qualitative prognostic biomarker based on the relative methylation orderings of eight pairs of loci. Analysis of a training cohort and two independent validation datasets revealed a significant...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2025-12-01
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| Series: | Epigenetics |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/15592294.2025.2487316 |
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| author | Yue Huo Yaru Gao Jiayi Ruan Lingli Wang Hongdong Li Guini Hong |
| author_facet | Yue Huo Yaru Gao Jiayi Ruan Lingli Wang Hongdong Li Guini Hong |
| author_sort | Yue Huo |
| collection | DOAJ |
| description | Skin cutaneous melanoma (SKCM) is an aggressive tumor with a poor prognosis. We developed SKCM-P8, a novel qualitative prognostic biomarker based on the relative methylation orderings of eight pairs of loci. Analysis of a training cohort and two independent validation datasets revealed a significant difference in overall survival between high- and low-risk groups stratified by SKCM-P8 (p < 0.05, log-rank test), with average area under the curve values of 0.83, 0.80, and 0.61, respectively. The differential methylation loci between high- and low-risk patients were enriched in immune-related biological processes and signaling pathways. Furthermore, low-risk patients exhibited higher CD8+ T cells and B levels, while high-risk patients had higher monocytes. The methylation levels of SKCM-P8 were also correlated with immune cell levels, indicating that they can reflect prognosis-related immune information. The low-risk group had a significantly higher mutation burden (p < 0.05, Wilcoxon test), suggesting potential benefits from immune checkpoint inhibitors. Patients stratified by SKCM-P8 displayed differential responses to therapy and immunotherapy (p < 0.05, Wilcoxon test), with low-risk patients showing better sensitivity and response. Furthermore, SKCM-P8 demonstrated super-predictive accuracy compared to six published models. Overall, SKCM-P8 offers a promising tool for predicting prognosis and guiding therapeutic decisions in SKCM. |
| format | Article |
| id | doaj-art-1c42b6e620ed4e319558db11df67a487 |
| institution | OA Journals |
| issn | 1559-2294 1559-2308 |
| language | English |
| publishDate | 2025-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Epigenetics |
| spelling | doaj-art-1c42b6e620ed4e319558db11df67a4872025-08-20T01:51:39ZengTaylor & Francis GroupEpigenetics1559-22941559-23082025-12-0120110.1080/15592294.2025.2487316A qualitative prognostic biomarker for melanoma based on the relative methylation orderings of CpG lociYue Huo0Yaru Gao1Jiayi Ruan2Lingli Wang3Hongdong Li4Guini Hong5School of Public Health and Health Management, Gannan Medical University, Ganzhou, ChinaSchool of Public Health and Health Management, Gannan Medical University, Ganzhou, ChinaSchool of Medical Information Engineering, Gannan Medical University, Ganzhou, ChinaSchool of Medical Information Engineering, Gannan Medical University, Ganzhou, ChinaSchool of Medical Information Engineering, Gannan Medical University, Ganzhou, ChinaSchool of Medical Information Engineering, Gannan Medical University, Ganzhou, ChinaSkin cutaneous melanoma (SKCM) is an aggressive tumor with a poor prognosis. We developed SKCM-P8, a novel qualitative prognostic biomarker based on the relative methylation orderings of eight pairs of loci. Analysis of a training cohort and two independent validation datasets revealed a significant difference in overall survival between high- and low-risk groups stratified by SKCM-P8 (p < 0.05, log-rank test), with average area under the curve values of 0.83, 0.80, and 0.61, respectively. The differential methylation loci between high- and low-risk patients were enriched in immune-related biological processes and signaling pathways. Furthermore, low-risk patients exhibited higher CD8+ T cells and B levels, while high-risk patients had higher monocytes. The methylation levels of SKCM-P8 were also correlated with immune cell levels, indicating that they can reflect prognosis-related immune information. The low-risk group had a significantly higher mutation burden (p < 0.05, Wilcoxon test), suggesting potential benefits from immune checkpoint inhibitors. Patients stratified by SKCM-P8 displayed differential responses to therapy and immunotherapy (p < 0.05, Wilcoxon test), with low-risk patients showing better sensitivity and response. Furthermore, SKCM-P8 demonstrated super-predictive accuracy compared to six published models. Overall, SKCM-P8 offers a promising tool for predicting prognosis and guiding therapeutic decisions in SKCM.https://www.tandfonline.com/doi/10.1080/15592294.2025.2487316Melanomaprognosisrelative methylation orderings |
| spellingShingle | Yue Huo Yaru Gao Jiayi Ruan Lingli Wang Hongdong Li Guini Hong A qualitative prognostic biomarker for melanoma based on the relative methylation orderings of CpG loci Epigenetics Melanoma prognosis relative methylation orderings |
| title | A qualitative prognostic biomarker for melanoma based on the relative methylation orderings of CpG loci |
| title_full | A qualitative prognostic biomarker for melanoma based on the relative methylation orderings of CpG loci |
| title_fullStr | A qualitative prognostic biomarker for melanoma based on the relative methylation orderings of CpG loci |
| title_full_unstemmed | A qualitative prognostic biomarker for melanoma based on the relative methylation orderings of CpG loci |
| title_short | A qualitative prognostic biomarker for melanoma based on the relative methylation orderings of CpG loci |
| title_sort | qualitative prognostic biomarker for melanoma based on the relative methylation orderings of cpg loci |
| topic | Melanoma prognosis relative methylation orderings |
| url | https://www.tandfonline.com/doi/10.1080/15592294.2025.2487316 |
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