DNA methylation profiling at base-pair resolution reveals unique epigenetic features of early-onset colorectal cancer in underrepresented populations
Abstract Background The incidence of early-onset colorectal cancer (EOCRC) has been rising at an alarming rate in the USA, and EOCRC disproportionately affects racial/ethnic minorities. Here, we construct comprehensive profiles of EOCRC DNA methylomes at base-pair resolution for a cohort of Hispanic...
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BMC
2025-01-01
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| Series: | Clinical Epigenetics |
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| Online Access: | https://doi.org/10.1186/s13148-025-01817-z |
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| author | Jason Sheng Li Karen Riggins Li Yang Chaorong Chen Patricia Castro Wedad Alfarkh Neda Zarrin-Khameh Michael E. Scheurer Chad J. Creighton Benjamin Musher Wei Li Lanlan Shen |
| author_facet | Jason Sheng Li Karen Riggins Li Yang Chaorong Chen Patricia Castro Wedad Alfarkh Neda Zarrin-Khameh Michael E. Scheurer Chad J. Creighton Benjamin Musher Wei Li Lanlan Shen |
| author_sort | Jason Sheng Li |
| collection | DOAJ |
| description | Abstract Background The incidence of early-onset colorectal cancer (EOCRC) has been rising at an alarming rate in the USA, and EOCRC disproportionately affects racial/ethnic minorities. Here, we construct comprehensive profiles of EOCRC DNA methylomes at base-pair resolution for a cohort of Hispanic and African American patients. Results We show the epigenetic landscape of these EOCRC patients differs from that of late-onset colorectal cancer patients, and methylation canyons in EOCRC tumor tissue preferentially overlapped genes in cancer-related pathways. Furthermore, we identify epigenetic alterations in metabolic genes that are specific to our racial/ethnic minority EOCRC cohort but not Caucasian patients from TCGA. Top genes differentially methylated between these cohorts included the obesity-protective MFAP2 gene as well as cancer risk susceptibility genes APOL3 and RNASEL. Conclusions In this study, we provide to the scientific community high-resolution DNA methylomes for a cohort of EOCRC patients from underrepresented populations. Our exploratory findings in this cohort highlight epigenetic mechanisms underlying the pathogenesis of EOCRC and nominate novel biomarkers for EOCRC in underrepresented populations. |
| format | Article |
| id | doaj-art-5dd4d3b327bb479b811c9a9af0f32af6 |
| institution | Kabale University |
| issn | 1868-7083 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Clinical Epigenetics |
| spelling | doaj-art-5dd4d3b327bb479b811c9a9af0f32af62025-01-26T12:39:15ZengBMCClinical Epigenetics1868-70832025-01-0117111310.1186/s13148-025-01817-zDNA methylation profiling at base-pair resolution reveals unique epigenetic features of early-onset colorectal cancer in underrepresented populationsJason Sheng Li0Karen Riggins1Li Yang2Chaorong Chen3Patricia Castro4Wedad Alfarkh5Neda Zarrin-Khameh6Michael E. Scheurer7Chad J. Creighton8Benjamin Musher9Wei Li10Lanlan Shen11Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of CaliforniaDepartment of Medicine, Hematology and Oncology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of MedicineDepartment of Pediatrics, USDA Children’s Nutrition Research Center, Baylor College of MedicineDivision of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of CaliforniaDepartment of Pathology and Immunology, Baylor College of MedicineDepartment of Pathology and Immunology, Baylor College of MedicineDepartment of Pathology and Immunology, Baylor College of MedicineDepartment of Pediatrics, Center for Epidemiology and Population Health, Baylor College of MedicineDepartment of Medicine and Dan L Duncan Comprehensive Cancer Center, Baylor College of MedicineDepartment of Medicine, Gastrointestinal Medical Oncology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of MedicineDivision of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of CaliforniaDepartment of Pediatrics, USDA Children’s Nutrition Research Center, Baylor College of MedicineAbstract Background The incidence of early-onset colorectal cancer (EOCRC) has been rising at an alarming rate in the USA, and EOCRC disproportionately affects racial/ethnic minorities. Here, we construct comprehensive profiles of EOCRC DNA methylomes at base-pair resolution for a cohort of Hispanic and African American patients. Results We show the epigenetic landscape of these EOCRC patients differs from that of late-onset colorectal cancer patients, and methylation canyons in EOCRC tumor tissue preferentially overlapped genes in cancer-related pathways. Furthermore, we identify epigenetic alterations in metabolic genes that are specific to our racial/ethnic minority EOCRC cohort but not Caucasian patients from TCGA. Top genes differentially methylated between these cohorts included the obesity-protective MFAP2 gene as well as cancer risk susceptibility genes APOL3 and RNASEL. Conclusions In this study, we provide to the scientific community high-resolution DNA methylomes for a cohort of EOCRC patients from underrepresented populations. Our exploratory findings in this cohort highlight epigenetic mechanisms underlying the pathogenesis of EOCRC and nominate novel biomarkers for EOCRC in underrepresented populations.https://doi.org/10.1186/s13148-025-01817-zCancer epigeneticsEarly-onset colorectal cancerDNA methylationCancer disparity |
| spellingShingle | Jason Sheng Li Karen Riggins Li Yang Chaorong Chen Patricia Castro Wedad Alfarkh Neda Zarrin-Khameh Michael E. Scheurer Chad J. Creighton Benjamin Musher Wei Li Lanlan Shen DNA methylation profiling at base-pair resolution reveals unique epigenetic features of early-onset colorectal cancer in underrepresented populations Clinical Epigenetics Cancer epigenetics Early-onset colorectal cancer DNA methylation Cancer disparity |
| title | DNA methylation profiling at base-pair resolution reveals unique epigenetic features of early-onset colorectal cancer in underrepresented populations |
| title_full | DNA methylation profiling at base-pair resolution reveals unique epigenetic features of early-onset colorectal cancer in underrepresented populations |
| title_fullStr | DNA methylation profiling at base-pair resolution reveals unique epigenetic features of early-onset colorectal cancer in underrepresented populations |
| title_full_unstemmed | DNA methylation profiling at base-pair resolution reveals unique epigenetic features of early-onset colorectal cancer in underrepresented populations |
| title_short | DNA methylation profiling at base-pair resolution reveals unique epigenetic features of early-onset colorectal cancer in underrepresented populations |
| title_sort | dna methylation profiling at base pair resolution reveals unique epigenetic features of early onset colorectal cancer in underrepresented populations |
| topic | Cancer epigenetics Early-onset colorectal cancer DNA methylation Cancer disparity |
| url | https://doi.org/10.1186/s13148-025-01817-z |
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