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Peng J, Li H, Tong F, Hu J, Li M, Chen G, Liu D, Liu J, Wang R, Xu H, Li X, Zhong X, Yao J, Cao B. Methylation changes of liver DNA during the formation of gallstones. Epigenomics 2024; 16:529-547. [PMID: 38444389 PMCID: PMC11160444 DOI: 10.2217/epi-2023-0391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/20/2024] [Indexed: 03/07/2024] Open
Abstract
Aim: To explore the overall methylation changes in liver tissues during the formation of gallstones, as well as the key pathways and genes involved in the process. Methods: Reduced-representation bisulfite sequencing and RNA sequencing were conducted on the liver tissues of mice with gallstones and control normal mice. Results: A total of 8705 differentially methylated regions in CpG and 1410 differentially expressed genes were identified. The joint analysis indicated that aberrant DNA methylation may be associated with dysregulated gene expression in key pathways such as cholesterol metabolism and bile secretion. Conclusion: We propose for the first time that methylation changes in some key pathway genes in liver tissue may be involved in the formation of gallstones.
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Affiliation(s)
- Junbin Peng
- Medical School of Anhui University Of Science & Technology, Huainan, 232001, Anhui, China
| | - Haojie Li
- Medical School of Anhui University Of Science & Technology, Huainan, 232001, Anhui, China
| | - Fang Tong
- Medical School of Anhui University Of Science & Technology, Huainan, 232001, Anhui, China
| | - Jinlong Hu
- Department of General Surgery, Anhui No.2 Provincial People’s Hospital, Hefei, 230041, Anhui, China
- Anhui Province Key Laboratory of Occupational Health, Anhui No.2 Provincial People’s Hospital, Hefei, 230041, China
| | - Min Li
- Department of General Surgery, Anhui No.2 Provincial People’s Hospital, Hefei, 230041, Anhui, China
| | - Gan Chen
- Department of General Surgery, Anhui No.2 Provincial People’s Hospital, Hefei, 230041, Anhui, China
| | - Dongquan Liu
- Department of General Surgery, Anhui No.2 Provincial People’s Hospital, Hefei, 230041, Anhui, China
| | - Jinshan Liu
- Anhui Medical University, Hefei, 230032, Anhui, China
| | - Rui Wang
- Bengbu Medical College, Bengbu, 233030, Anhui, China
| | - Hongyu Xu
- Anhui Medical University, Hefei, 230032, Anhui, China
| | - Xuanxuan Li
- Bengbu Medical College, Bengbu, 233030, Anhui, China
| | - Xinguo Zhong
- Department of General Surgery, Anhui No.2 Provincial People’s Hospital, Hefei, 230041, Anhui, China
| | - Jiaming Yao
- Department of General Surgery, Anhui No.2 Provincial People’s Hospital, Hefei, 230041, Anhui, China
| | - Baoqiang Cao
- Medical School of Anhui University Of Science & Technology, Huainan, 232001, Anhui, China
- Department of General Surgery, Anhui No.2 Provincial People’s Hospital, Hefei, 230041, Anhui, China
- Anhui Province Key Laboratory of Occupational Health, Anhui No.2 Provincial People’s Hospital, Hefei, 230041, China
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Macías M, Acha B, Corroza J, Urdánoz-Casado A, Roldan M, Robles M, Sánchez-Ruiz de Gordoa J, Erro ME, Jericó I, Blanco-Luquin I, Mendioroz M. Liquid Biopsy in Alzheimer's Disease Patients Reveals Epigenetic Changes in the PRLHR Gene. Cells 2023; 12:2679. [PMID: 38067107 PMCID: PMC10705731 DOI: 10.3390/cells12232679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
In recent years, new DNA methylation variants have been reported in genes biologically relevant to Alzheimer's disease (AD) in human brain tissue. However, this AD-specific epigenetic information remains brain-locked and unreachable during patients' lifetimes. In a previous methylome performed in the hippocampus of 26 AD patients and 12 controls, we found higher methylation levels in AD patients in the promoter region of PRLHR, a gene involved in energy balance regulation. Our aim was to further characterize PRLHR's role in AD and to evaluate if the liquid biopsy technique would provide life access to this brain information in a non-invasive way. First, we extended the methylation mapping of PRLHR and validated previous methylome results via bisulfite cloning sequencing. Next, we observed a positive correlation between PRLHR methylation levels and AD-related neuropathological changes and a decreased expression of PRLHR in AD hippocampus. Then, we managed to replicate the hippocampal methylation differences in plasma cfDNA from an additional cohort of 35 AD patients and 35 controls. The isolation of cfDNA from the plasma of AD patients may constitute a source of potential epigenetic biomarkers to aid AD clinical management.
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Affiliation(s)
- Mónica Macías
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Blanca Acha
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Jon Corroza
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
| | - Amaya Urdánoz-Casado
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Miren Roldan
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Maitane Robles
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Javier Sánchez-Ruiz de Gordoa
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
| | - María Elena Erro
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
| | - Ivonne Jericó
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
| | - Idoia Blanco-Luquin
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Maite Mendioroz
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
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