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Liu X, Xi R, Du X, Wang Y, Cheng L, Yan G, Zhu J, Liu T, Li F. DNA methylation of microRNA-365-1 induces apoptosis of hair follicle stem cells by targeting DAP3. Noncoding RNA Res 2024; 9:901-912. [PMID: 38616861 PMCID: PMC11010783 DOI: 10.1016/j.ncrna.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 04/16/2024] Open
Abstract
Background DNA methylation is a crucial epigenetic alteration involved in diverse biological processes and diseases. Nevertheless, the precise role of DNA methylation in chemotherapeutic drug-induced alopecia remains unclear. This study examined the role and novel processes of DNA methylation in regulating of chemotherapeutic drug-induced alopecia. Methods A mouse model of cyclophosphamide (CTX)-induced alopecia was established. Hematoxylin-eosin staining and immunohistochemical staining for the Ki67 proportion and a mitochondrial membrane potential assay (JC-1) were performed to assess the structural integrity and proliferative efficiency of the hair follicle stem cells (HFSCs). Immunofluorescence staining and real-time fluorescence quantitative PCR (RT-qPCR) were performed to determine the expression levels of key HFSC markers, namely Lgr5, CD49f, Sox9, CD200, and FZD10. Differential DNA methylation levels between the normal and CTX-induced model groups were determined through simple methylation sequencing and analyzed using bioinformatics tools. The expression levels of miR-365-1, apoptosis markers, and DAP3 were detected through RT-qPCR and western blotting. In parallel, primary mouse HFSCs were extracted and used as a cell model, which was constructed using 4-hydroperoxycyclophosphamide. The luciferase reporter gene assay was conducted to confirm miR-365-1 binding to DAP3. To measure the expression of relevant indicators, superoxide dismutase (SOD) and malondialdehyde (MDA) kits were used. Methylation-specific PCR (MS-PCR) was performed to determine DNA methylation levels. The regulatory relationship within HFSCs was confirmed through plasmid overexpression of miR-365-1 and DAP3. Result In the alopecia areata model, a substantial number of apoptotic cells were observed within the hair follicles on the mouse backs. Immunofluorescence staining revealed that the expression of HFSC markers significantly reduced in the CTX group. Both RT-qPCR and western blotting demonstrated a noteworthy difference in DNA methyltransferase expression. Simple methylation sequencing unveiled that DNA methylation substantially increased within the dorsal skin of the CTX group. Subsequent screening identified miR-365-1 as the most differentially expressed miRNA. miR-365-1 was predicted and confirmed to bind to the target gene DAP3. In the CTX group, SOD and ATP expression markedly reduced, whereas MDA levels were significantly elevated. Cellular investigations revealed 4-HC-induced cell cycle arrest and decreased expression of HFSC markers. MS-PCR indicated hypermethylation modification of miR-365-1 in the 4-HC-induced HFSCs. The luciferase reporter gene experiment confirmed the binding of miR-365-1 to the DAP3 promoter region. miR-365-1 overexpression dramatically reduced apoptotic protein expression in the HFSCs. However, this effect was slightly reversed after DAP3 overexpression in lentivirus. Conclusion This study explored the occurrence of miR-365-1 DNA methylation in chemotherapeutic drug-induced alopecia. The results unveiled that miR-365-1 reduces cell apoptosis by targeting DAP3 in HFSCs, thereby revealing the role of DNA methylation of the miR-365-1 promoter in chemotherapeutic drug-induced alopecia.
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Affiliation(s)
- Xin Liu
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Ruofan Xi
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Xinran Du
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Yi Wang
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Linyan Cheng
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Ge Yan
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Jianyong Zhu
- Department of Pharmacy Research, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Te Liu
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200031, China
| | - Fulun Li
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
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Li J, Li Y, Li W, Luo H, Xi Y, Dong S, Gao M, Xu P, Zhang B, Liang Y, Zou Q, Hu X, Peng L, Zou D, Wang T, Yang H, Jiang C, Peng S, Wu F, Yu W. Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks. Genome Res 2019; 29:270-280. [PMID: 30670627 PMCID: PMC6360814 DOI: 10.1101/gr.240606.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 12/18/2018] [Indexed: 01/05/2023]
Abstract
Aberrant DNA methylation is a distinguishing feature of cancer. Yet, how methylation affects immune surveillance and tumor metastasis remains ambiguous. We introduce a novel method, Guide Positioning Sequencing (GPS), for precisely detecting whole-genome DNA methylation with cytosine coverage as high as 96% and unbiased coverage of GC-rich and repetitive regions. Systematic comparisons of GPS with whole-genome bisulfite sequencing (WGBS) found that methylation difference between gene body and promoter is an effective predictor of gene expression with a correlation coefficient of 0.67 (GPS) versus 0.33 (WGBS). Moreover, Methylation Boundary Shift (MBS) in promoters or enhancers is capable of modulating expression of genes associated with immunity and tumor metabolism. Furthermore, aberrant DNA methylation results in tissue-specific enhancer switching, which is responsible for altering cell identity during liver cancer development. Altogether, we demonstrate that GPS is a powerful tool with improved accuracy and efficiency over WGBS in simultaneously detecting genome-wide DNA methylation and genomic variation. Using GPS, we show that aberrant DNA methylation is associated with altering cell identity and immune surveillance networks, which may contribute to tumorigenesis and metastasis.
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Affiliation(s)
- Jin Li
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, 200032, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yan Li
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, 200032, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Wei Li
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, 200032, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Huaibing Luo
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, 200032, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yanping Xi
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, 200032, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Shihua Dong
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, 200032, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Ming Gao
- College of Computer Science and Electronic Engineering and National Supercomputing Centre in Changsha, Hunan University, Changsha 410082, China.,School of Computer Science, National University of Defense Technology, Changsha, 410073, China
| | - Peng Xu
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, 200032, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Baolong Zhang
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, 200032, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Ying Liang
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, 200032, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Qingping Zou
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, 200032, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Xin Hu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Lina Peng
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, 200032, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Dan Zou
- College of Computer Science and Electronic Engineering and National Supercomputing Centre in Changsha, Hunan University, Changsha 410082, China.,School of Computer Science, National University of Defense Technology, Changsha, 410073, China
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA.,Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA.,Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Cizhong Jiang
- Institute of Translational Research, Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, the Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, 200092, China
| | - Shaoliang Peng
- College of Computer Science and Electronic Engineering and National Supercomputing Centre in Changsha, Hunan University, Changsha 410082, China.,School of Computer Science, National University of Defense Technology, Changsha, 410073, China
| | - Feizhen Wu
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Wenqiang Yu
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Department of Biochemistry and Molecular Biology, Shanghai Medical College, Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, 200032, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
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