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Zhu L, Zhou Q. Aberrant epigenetic regulation of FZD3 by TET2 is involved in ovarian cancer cell resistance to cisplatin. J Chemother 2024; 36:143-155. [PMID: 37300277 DOI: 10.1080/1120009x.2023.2219920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/16/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
A major challenge in platinum-based cancer therapy, including cisplatin (DDP), is the clinical management of chemo-resistant tumours, which have unknown pathogenesis at the level of epigenetic mechanism. To identify potential resistance mechanisms, we integrated ovarian cancers (OC)-related GEO database retrieval and prognostic analyses. The results of bioinformatics prediction showed that frizzled class receptor 3 (FZD3) was a DDP-associated gene and closely related to the prognosis of OC. DDP resistance in OC inhibited FZD3 expression. FZD3 reduced DDP resistance in OC cells, increased the inhibitory effect of DDP on the growth and aggressiveness of DDP-resistant cells, and promoted apoptosis and DNA damage. TET2 was reduced in OC. TET2 promoted the transcription of FZD3 through DNA hydroxymethylation. TET2 sensitized the drug-resistant cells to DDP in vitro and in vivo, and the ameliorating effect of TET2 on drug resistance was significantly reversed after the inhibition of FZD3. Our findings reveal a previously unknown epigenetic axis TET2/FZD3 suppression as a potential resistance mechanism to DDP in OC.
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Affiliation(s)
- Li Zhu
- Department of Obstetrics and Gynecology, Gezhouba Central Hospital of Sinopharm, China Three Gorges University, Yichang, Hubei, P.R. China
| | - Qian Zhou
- Department of Obstetrics and Gynecology, The Third Clinical Medical College of China, Three Gorges University, Gezhouba Central Hospital of Sinopharm, Yichang, Hubei, P.R. China
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Skardžiūtė K, Kvederavičiūtė K, Pečiulienė I, Narmontė M, Gibas P, Ličytė J, Klimašauskas S, Kriukienė E. One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci. Cell Chem Biol 2024; 31:607-621.e9. [PMID: 38154461 PMCID: PMC10962225 DOI: 10.1016/j.chembiol.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023]
Abstract
We present a method, named Mx-TOP, for profiling of three epigenetic regulatory layers-chromatin accessibility, general DNA modification, and DNA hydroxymethylation-from a single library. The approach is based on chemo-enzymatic covalent tagging of unmodified CG sites and hydroxymethylated cytosine (5hmC) along with GC sites in chromatin, which are then mapped using tag-selective base-resolution TOP-seq sequencing. Our in-depth validation of the approach revealed its sensitivity and informativity in evaluating chromatin accessibility and DNA modification interactions that drive transcriptional regulation. We employed the technology in a study of chromatin and DNA demethylation dynamics during in vitro neuronal differentiation. The study highlighted the involvement of gene body 5hmC in modulating an extensive decoupling between promoter accessibility and transcription. The importance of 5hmC in chromatin remodeling was further demonstrated by the observed resistance of the developmentally acquired open loci to the global 5hmC erasure in neuronal progenitors.
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Affiliation(s)
- Kotryna Skardžiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Kotryna Kvederavičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Inga Pečiulienė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Milda Narmontė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Povilas Gibas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Janina Ličytė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania.
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Li KX, Li JR, Zuo SJ, Li X, Chen XT, Xiao PY, Li HT, Sun L, Qian T, Zhang HM, Zhu D, Yu XY, Chen G, Jiang XY. Identification of miR-20b-5p as an inhibitory regulator in cardiac differentiation via TET2 and DNA hydroxymethylation. Clin Epigenetics 2024; 16:42. [PMID: 38491513 PMCID: PMC10943922 DOI: 10.1186/s13148-024-01653-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is a prevalent congenital cardiac malformation, which lacks effective early biological diagnosis and intervention. MicroRNAs, as epigenetic regulators of cardiac development, provide potential biomarkers for the diagnosis and treatment of CHD. However, the mechanisms underlying miRNAs-mediated regulation of cardiac development and CHD malformation remain to be further elucidated. This study aimed to explore the function of microRNA-20b-5p (miR-20b-5p) in cardiac development and CHD pathogenesis. METHODS AND RESULTS miRNA expression profiling identified that miR-20b-5p was significantly downregulated during a 12-day cardiac differentiation of human embryonic stem cells (hESCs), whereas it was markedly upregulated in plasma samples of atrial septal defect (ASD) patients. Our results further revealed that miR-20b-5p suppressed hESCs-derived cardiac differentiation by targeting tet methylcytosine dioxygenase 2 (TET2) and 5-hydroxymethylcytosine, leading to a reduction in key cardiac transcription factors including GATA4, NKX2.5, TBX5, MYH6 and cTnT. Additionally, knockdown of TET2 significantly inhibited cardiac differentiation, which could be partially restored by miR-20b-5p inhibition. CONCLUSIONS Collectively, this study provides compelling evidence that miR-20b-5p functions as an inhibitory regulator in hESCs-derived cardiac differentiation by targeting TET2, highlighting its potential as a biomarker for ASD.
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Affiliation(s)
- Ke-Xin Li
- Affiliated Qingyuan Hospital, Qingyuan People's Hospital, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jia-Ru Li
- Affiliated Qingyuan Hospital, Qingyuan People's Hospital, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Sheng-Jia Zuo
- Peking University Cancer Hospital Yunnan, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Xudong Li
- Affiliated Qingyuan Hospital, Qingyuan People's Hospital, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Xian-Tong Chen
- Affiliated Qingyuan Hospital, Qingyuan People's Hospital, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Pei-Yi Xiao
- Affiliated Qingyuan Hospital, Qingyuan People's Hospital, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Hui-Tao Li
- Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, 518028, China
| | - Ling Sun
- Department of Cardiac Pediatrics, Guangdong Provincial Cardiovascular Institute, Guangdong Provincial People's Hospital, Southern Medical University, Guangzhou, 510280, China
| | - Tao Qian
- Affiliated Qingyuan Hospital, Qingyuan People's Hospital, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Hao-Min Zhang
- Affiliated Qingyuan Hospital, Qingyuan People's Hospital, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Dongxing Zhu
- Affiliated Qingyuan Hospital, Qingyuan People's Hospital, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Xi-Yong Yu
- Affiliated Qingyuan Hospital, Qingyuan People's Hospital, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Science, Guangzhou Medical University, Guangzhou, 511436, China.
| | - Guojun Chen
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Xue-Yan Jiang
- Affiliated Qingyuan Hospital, Qingyuan People's Hospital, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Science, Guangzhou Medical University, Guangzhou, 511436, China.
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Yi Y, Wang Y, Wu Y, Liu Y. Targeting SIRT4/TET2 Signaling Alleviates Human Keratinocyte Senescence by Reducing 5-hydroxymethylcytosine Loss. J Transl Med 2024; 104:100268. [PMID: 37898292 DOI: 10.1016/j.labinv.2023.100268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 10/07/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023] Open
Abstract
Skin aging is characterized by wrinkle formation and increased frailty and laxity, leading to the risk of age-related skin diseases. Keratinocyte is an important component of the epidermis in skin structure, and keratinocyte senescence has been identified as a pivotal factor in skin aging development. Because epigenetic pathways play a vital role in the regulation of skin aging, we evaluated human skin samples for DNA hydroxymethylation (5-hydroxymethylcytosine; 5-hmC) and SIRT4 expressions. Results found that both 5-hmC and SIRT4 showed a significant decrease in aged human skin samples. To test the results in vitro, human keratinocytes were cultured in H2O2, which modulates skin aging in vivo. However, H2O2-induced keratinocytes showed senescence-associated protein expression and significant downregulation of 5-hmC and SIRT4 expressions. Moreover, 5-hmC-converting enzymes ten eleven translocation 2 (TET2) showed a decrease and enhanced TET2 acetylation level in H2O2-induced keratinocytes. However, the overexpression of SIRT4 in keratinocytes alleviates the senescence phenotype, such as senescence-associated protein expression, decreases the TET2 acetylation, but increases TET2 and 5-hmC expressions. Our results provide a novel relevant mechanism whereby the epigenetic regulation of keratinocytes in skin aging may be correlated with SIRT4 expression and TET2 acetylation in 5-hmC alteration. Our study may provide a potential strategy for antiskin aging, which targets the SIRT4/TET2 axis involving epigenetic modification in keratinocyte senescence.
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Affiliation(s)
- Yi Yi
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Yuchang Wang
- Trauma Center/Department of Emergency and Traumatic Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yiping Wu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Yukun Liu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China.
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Ghaffarinia A, Póliska S, Ayaydin F, Goblos A, Parvaneh S, Manczinger M, Balogh F, Erdei L, Veréb Z, Szabó K, Bata-Csörgő Z, Kemény L. Unraveling Transcriptome Profile, Epigenetic Dynamics, and Morphological Changes in Psoriasis-like Keratinocytes: "Insights into Similarity with Psoriatic Lesional Epidermis". Cells 2023; 12:2825. [PMID: 38132145 PMCID: PMC10741855 DOI: 10.3390/cells12242825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
Keratinocytes are one of the primary cells affected by psoriasis inflammation. Our study aimed to delve deeper into their morphology, transcriptome, and epigenome changes in response to psoriasis-like inflammation. We created a novel cytokine mixture to mimic mild and severe psoriasis-like inflammatory conditions in cultured keratinocytes. Upon induction of inflammation, we observed that the keratinocytes exhibited a mesenchymal-like phenotype, further confirmed by increased VIM mRNA expression and results obtained from confocal microscopy. We performed RNA sequencing to achieve a more global view, revealing 858 and 6987 DEGs in mildly and severely inflamed keratinocytes, respectively. Surprisingly, we found that the transcriptome of mildly inflamed keratinocytes more closely mimicked that of the psoriatic epidermis transcriptome than the severely inflamed keratinocytes. Genes involved in the IL-17 pathway were a major contributor to the similarities of the transcriptomes between mildly inflamed KCs and psoriatic epidermis. Mild and severe inflammation led to the gene regulation of epigenetic modifiers such as HATs, HDACs, DNMTs, and TETs. Immunofluorescence staining revealed distinct 5-hmC patterns in inflamed versus control keratinocytes, and consistently low 5-mC intensity in both groups. However, the global DNA methylation assay detected a tendency of decreased 5-mC levels in inflamed keratinocytes versus controls. This study emphasizes how inflammation severity affects the transcriptomic similarity of keratinocytes to psoriatic epidermis and proves dynamic epigenetic regulation and adaptive morphological changes in inflamed keratinocytes.
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Affiliation(s)
- Ameneh Ghaffarinia
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary; (A.G.); (S.P.); (F.B.); (L.E.); (K.S.); (Z.B.-C.)
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary;
- Doctoral School of Clinical Medicine, University of Szeged, H-6720 Szeged, Hungary
| | - Szilárd Póliska
- Genomic Medicine and Bioinformatics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Ferhan Ayaydin
- HCEMM-USZ Functional Cell Biology and Immunology, Advanced Core Facility, H-6728 Szeged, Hungary;
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary
| | - Aniko Goblos
- Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, H-6720 Szeged, Hungary; (A.G.); (Z.V.)
| | - Shahram Parvaneh
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary; (A.G.); (S.P.); (F.B.); (L.E.); (K.S.); (Z.B.-C.)
- Doctoral School of Clinical Medicine, University of Szeged, H-6720 Szeged, Hungary
- Regenerative Medicine and Cellular Pharmacology Laboratory (HECRIN), Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary
| | - Máté Manczinger
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary;
- Systems Immunology Research Group, Institute of Biochemistry, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
- HCEMM-Systems Immunology Research Group, H-6726 Szeged, Hungary
| | - Fanni Balogh
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary; (A.G.); (S.P.); (F.B.); (L.E.); (K.S.); (Z.B.-C.)
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary;
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
| | - Lilla Erdei
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary; (A.G.); (S.P.); (F.B.); (L.E.); (K.S.); (Z.B.-C.)
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary;
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
| | - Zoltán Veréb
- Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, H-6720 Szeged, Hungary; (A.G.); (Z.V.)
- Regenerative Medicine and Cellular Pharmacology Laboratory (HECRIN), Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary
| | - Kornélia Szabó
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary; (A.G.); (S.P.); (F.B.); (L.E.); (K.S.); (Z.B.-C.)
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary;
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
| | - Zsuzsanna Bata-Csörgő
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary; (A.G.); (S.P.); (F.B.); (L.E.); (K.S.); (Z.B.-C.)
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary;
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
| | - Lajos Kemény
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary; (A.G.); (S.P.); (F.B.); (L.E.); (K.S.); (Z.B.-C.)
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary;
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
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Liu J, Sun T, Yin L. ZMIZ1 Upregulation of TET3-Mediated Hydroxymethylation Induces M2 Polarization of Kupffer Cells in Hepatocellular Carcinogenesis by Mediating Notch1/c-Myc Signaling. J Transl Med 2023; 103:100264. [PMID: 37839636 DOI: 10.1016/j.labinv.2023.100264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/05/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023] Open
Abstract
Hydroxymethylation of DNA, mediated by the ten-eleven translocation (TET) family of methylcytosine dioxygenases, represents a crucial epigenetic modification that manipulates gene expression in numerous biological processes. This study focuses on the effect of TET3 on the polarization of Kupffer cells (KCs) and its connection to the development of hepatocellular carcinoma (HCC). TET3 was found to be abundant in KCs, and its knockdown induced an M2-M1 phenotype shift, resulting in the suppression of viability, migration, and invasion of cocultured HCC cells. Additionally, the TET3 knockdown inhibited the tumorigenesis of HCC cells in nude mice. Downstream targets of TET3 were predicted using bioinformatics. TET3-mediated DNA hydroxymethylation of zinc finger MIZ-type containing 1 (ZMIZ1) promoter. The ZMIZ1 protein interacted with notch receptor 1 (Notch1) protein to activate the transcription of c-Myc. Silencing of ZMIZ1 in KCs similarly suppressed M2 polarization of KCs and malignant phenotype of cocultured HCC cells. However, these changes were counteracted by the overexpression of either Notch1 or c-Myc overexpression in KCs. In summary, this study demonstrates that TET3-mediated hydroxymethylation of ZMIZ1 enhances hepatocellular carcinogenesis by promoting M2 skewing of KCs through the Notch1/c-Myc axis.
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Affiliation(s)
- Jia Liu
- Department of Interventional Radiology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, P.R. China
| | - Tingting Sun
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China
| | - Linan Yin
- Department of Interventional Radiology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, P.R. China.
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Stuckel AJ, Zeng S, Lyu Z, Zhang W, Zhang X, Dougherty U, Mustafi R, Khare T, Zhang Q, Joshi T, Bissonnette M, Khare S. Sprouty4 is epigenetically upregulated in human colorectal cancer. Epigenetics 2023; 18:2145068. [PMID: 36384366 PMCID: PMC9980603 DOI: 10.1080/15592294.2022.2145068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sprouty4 (SPRY4) has been frequently reported as a tumor suppressor and is therefore downregulated in various cancers. For the first time, we report that SPRY4 is epigenetically upregulated in colorectal cancer (CRC). In this study, we explored DNA methylation and hydroxymethylation levels of SPRY4 in CRC cells and patient samples and correlated these findings with mRNA and protein expression levels. Three loci within the promoter region of SPRY4 were evaluated for 5mC levels in CRC using the combined bisulfite restriction analysis. In addition, hydroxymethylation levels within SPRY4 were measured in CRC patients. Lastly, DNA methylation and mRNA expression data were extracted from CRC patients in multiple high-throughput data repositories like Gene Expression Omnibus and The Cancer Genome Atlas. Combined in vitro and in silico analysis of promoter methylation levels of SPRY4 clearly demonstrates that the distal promoter region undergoes hypomethylation in CRC patients and is associated with increased expression. Moreover, a decrease in gene body hydroxymethylation and an increase in gene body methylation within the coding region of SPRY4 were found in CRC patients and correlated with increased expression. SPRY4 is epigenetically upregulated in CRC by promoter hypomethylation and hypermethylation within the gene body that warrants future investigation of atypical roles of this established tumor suppressor.
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Affiliation(s)
- Alexei J. Stuckel
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA
| | - Shuai Zeng
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65201, USA,Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, 65201, USA
| | - Zhen Lyu
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65201, USA,Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, 65201, USA
| | - Wei Zhang
- Department of Preventive Medicine and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA
| | - Xu Zhang
- Department of Medicine, University of Illinois, Chicago, Illinois, 60607, USA
| | - Urszula Dougherty
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition; the University of Chicago, Chicago, Illinois, 60637, USA
| | - Reba Mustafi
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition; the University of Chicago, Chicago, Illinois, 60637, USA
| | - Tripti Khare
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA
| | - Qiong Zhang
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA
| | - Trupti Joshi
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65201, USA,Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, 65211, USA,Department of Health Management and Informatics; School of Medicine, University of Missouri, Columbia, Missouri, 65212, USA
| | - Marc Bissonnette
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition; the University of Chicago, Chicago, Illinois, 60637, USA
| | - Sharad Khare
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA,Harry S. Truman Memorial Veterans’ Hospital, Columbia, Missouri, 65201, USA,CONTACT Sharad Khare Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA
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Jiang J, Li D, Zhong Y, Zhang Y, Zhong M. TET2-mediated DNA hydroxymethylation of TGFB1 is related to selective intrauterine growth restriction in monochorionic twin pregnancies. Placenta 2023; 144:45-54. [PMID: 37992596 DOI: 10.1016/j.placenta.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/29/2023] [Accepted: 11/12/2023] [Indexed: 11/24/2023]
Abstract
INTRODUCTION Selective intrauterine growth restriction (sIUGR), which specifically occurs in monochorionic (MC) twins, usually has a poor prognosis and the underlying mechanisms are not well understood. It is an ideal model for exploring epigenetic-modified mechanisms for fetal development in MCDA twins due to eliminating the interference of different heritable backgrounds and intrauterine environments among individuals. METHODS The levels of ten-eleven translocation 2 (TET2) and its upstream and downstream targets miR-29b-3p and transforming growth factor beta 1 (TGFB1) were determined using RT‒qPCR, western blotting, and immunohistochemistry. Using TET2 overexpression and knockdown methods, we investigated the role of TET2 in trophoblast functions. The regulatory relationships among TET2, miR-29b-3p, and TGFB1 were explored by cell migration assay, invasion assay, apoptotic ratio assays, Western blot, hMeDIP-qPCR and dual-luciferase assay. RESULTS A consistent upregulation of TET2 and TGFB1 was observed in the smaller placental shares compared to the larger placental shares in sIUGR. Gain-of-function studies of TET2 in trophoblasts showed decreased cell invasion and increased apoptosis, whereas loss-of-function studies of TET2 rescued this effect. Mechanistic studies revealed that miR-29b-3p and TGFB1 were the upstream factor and downstream target of TET2, respectively. Furthermore, miR-29b-3p/TET2/TGFB1-smad was identified as a unique axis that regulates trophoblast invasion, migration, and apoptosis in a DNA hydroxymethylation-dependent manner. DISCUSSION We elucidated the functional roles of TET2 and DNA hydroxymethylation in trophoblasts and identified a novel DNA regulatory mechanism, providing a basis for further exploration of DNA epigenetic regulatory patterns in sIUGR.
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Affiliation(s)
- Jiayi Jiang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, China
| | - Dianjie Li
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, China
| | - Yixiang Zhong
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, China
| | - Yi Zhang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, China.
| | - Mei Zhong
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, China.
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Konstantinidis I, Sætrom P, Brieuc S, Jakobsen KS, Liedtke H, Pohlmann C, Tsoulia T, Fernandes JMO. DNA hydroxymethylation differences underlie phenotypic divergence of somatic growth in Nile tilapia reared in common garden. Epigenetics 2023; 18:2282323. [PMID: 38010265 PMCID: PMC10732659 DOI: 10.1080/15592294.2023.2282323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023] Open
Abstract
Phenotypic plasticity of metabolism and growth are essential for adaptation to new environmental conditions, such as those experienced during domestication. Epigenetic regulation plays a key role in this process but the underlying mechanisms are poorly understood, especially in the case of hydroxymethylation. Using reduced representation 5-hydroxymethylcytosine profiling, we compared the liver hydroxymethylomes in full-sib Nile tilapia with distinct growth rates (3.8-fold difference) and demonstrated that DNA hydroxymethylation is strongly associated with phenotypic divergence of somatic growth during the early stages of domestication. The 2677 differentially hydroxymethylated cytosines between fast- and slow-growing fish were enriched within gene bodies (79%), indicating a pertinent role in transcriptional regulation. Moreover, they were found in genes involved in biological processes related to skeletal system and muscle structure development, and there was a positive association between somatic growth and 5hmC levels in genes coding for growth factors, kinases and receptors linked to myogenesis. Single nucleotide polymorphism analysis revealed no genetic differentiation between fast- and slow-growing fish. In addition to unveiling a new link between DNA hydroxymethylation and epigenetic regulation of growth in fish during the initial stages of domestication, this study suggests that epimarkers may be applied in selective breeding programmes for superior phenotypes.
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Affiliation(s)
| | - Pål Sætrom
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Computer Science, Norwegian University of Science and Technology, Trondheim, Norway
- Bioinformatics core facility-BioCore, Norwegian University of Science and Technology, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - S.O. Brieuc
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S. Jakobsen
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Hannes Liedtke
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Caroline Pohlmann
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Thomais Tsoulia
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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10
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Rajasekar P, Hall RJ, Binaya KC, Mahapatra PS, Puppala SP, Thakker D, MacIsaac JL, Lin D, Kobor M, Bolton CE, Sayers I, Hall IP, Clifford RL. Nepalese indoor cookstove smoke extracts alter human airway epithelial gene expression, DNA methylation and hydroxymethylation. Environ Pollut 2023; 337:122561. [PMID: 37742862 DOI: 10.1016/j.envpol.2023.122561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/26/2023]
Abstract
Household air pollution caused by inefficient cooking practices causes 4 million deaths a year worldwide. In Nepal, 86% of the rural population use solid fuels for cooking. Over 25% of premature deaths associated with air pollution are respiratory in nature. Here we aimed to identify molecular signatures of different cookstove and fuel type exposures in human airway epithelial cells, to understand the mechanisms mediating cook stove smoke induced lung disease. Primary human airway epithelial cells in submerged culture were exposed to traditional cook stove (TCS), improved cook stove (ICS) and liquefied petroleum gas (LPG) stove smoke extracts. Changes to gene expression, DNA methylation and hydroxymethylation were measured by bulk RNA sequencing and HumanMethylationEPIC BeadChip following oxidative bisulphite conversion, respectively. TCS smoke extract alone reproducibly caused changes in the expression of 52 genes enriched for oxidative stress pathways. TCS, ICS and LPG smoke extract exposures were associated with distinct changes to DNA methylation and hydroxymethylation. A subset of TCS induced genes were associated with differentially methylated and/or hydroxymethylated CpGs sites, and enriched for the ferroptosis pathway and the upstream regulator NFE2L2. DNA methylation and hydroxymethylation changes not associated with a concurrent change in gene expression, were linked to biological processes and molecular pathways important to airway health, including neutrophil function, transforming growth factor beta signalling, GTPase activity, and cell junction organisation. Our data identified differential impacts of TCS, ICS and LPG cook stove smoke on the human airway epithelium transcriptome, DNA methylome and hydroxymethylome and provide further insight into the association between indoor air pollution exposure and chronic lung disease mechanisms.
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Affiliation(s)
- Poojitha Rajasekar
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - Robert J Hall
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - K C Binaya
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Water and Air Theme, Atmosphere Initiative, International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | - Parth S Mahapatra
- Water and Air Theme, Atmosphere Initiative, International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | - Siva P Puppala
- Water and Air Theme, Atmosphere Initiative, International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | - Dhruma Thakker
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - Julia L MacIsaac
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Lin
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael Kobor
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charlotte E Bolton
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK
| | - Ian Sayers
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - Ian P Hall
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - Rachel L Clifford
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK.
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11
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Wang Y, Halawani D, Estill M, Ramakrishnan A, Shen L, Friedel RH, Zou H. Aryl hydrocarbon receptor restricts axon regeneration of DRG neurons in response to injury. bioRxiv 2023:2023.11.04.565649. [PMID: 37961567 PMCID: PMC10635160 DOI: 10.1101/2023.11.04.565649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Injured neurons sense environmental cues to balance neural protection and axon regeneration, but the mechanisms are unclear. Here, we unveil aryl hydrocarbon receptor (AhR), a ligand-activated bHLH-PAS transcription factor, as molecular sensor and key regulator of acute stress response at the expense of axon regeneration. We demonstrate responsiveness of DRG sensory neurons to ligand-mediated AhR signaling, which functions to inhibit axon regeneration. Ahr deletion mimics the conditioning lesion in priming DRG to initiate axonogenesis gene programs; upon peripheral axotomy, Ahr ablation suppresses inflammation and stress signaling while augmenting pro-growth pathways. Moreover, comparative transcriptomics revealed signaling interactions between AhR and HIF-1α, two structurally related bHLH-PAS α units that share the dimerization partner Arnt/HIF-1β. Functional assays showed that the growth advantage of AhR-deficient DRG neurons requires HIF-1α; but in the absence of Arnt, DRG neurons can still mount a regenerative response. We further unveil a link between bHLH-PAS transcription factors and DNA hydroxymethylation in response to peripheral axotomy, while neuronal single cell RNA-seq analysis revealed a link of the AhR regulon to RNA polymerase III regulation and integrated stress response (ISR). Altogether, AhR activation favors stress coping and inflammation at the expense of axon regeneration; targeting AhR can enhance nerve repair.
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Affiliation(s)
- Yiqun Wang
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Current address: Sport Medicine Center, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Dalia Halawani
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Molly Estill
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Roland H. Friedel
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Hongyan Zou
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, USA
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12
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Cheng G, Wu J, Ji M, Hu W, Wu C, Jiang J. TET2 inhibits the proliferation and metastasis of lung adenocarcinoma cells via activation of the cGAS-STING signalling pathway. BMC Cancer 2023; 23:825. [PMID: 37667220 PMCID: PMC10478367 DOI: 10.1186/s12885-023-11343-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Effective identification and development of new molecular methods for the diagnosis, treatment and prognosis of lung adenocarcinoma (LUAD) remains an urgent clinical need. DNA methylation patterns at cytosine bases in the genome are closely related to gene expression, and abnormal DNA methylation is frequently observed in various cancers. The ten-eleven translocation (TET) enzymes oxidize 5-methylcytosine (5mC) and promote locus-specific DNA methylation reversal. This study aimed to explore the role of the TET2 protein and its downstream effector, 5-hmC/5-mC DNA modification, in LUAD progression. METHODS The expression of TET2 was analysed by real-time PCR, Western blotting and immunohistochemistry. The 5-hmC DNA content was determined by a colorimetric kit. Activation of the cGAS-STING signalling pathway was evaluated by Western blotting. CCK-8, wound healing and Transwell assays were performed to evaluate the effect of TET2 on cell proliferation, migration and invasion abilities. A xenograft model was used to analyse the effect of TET2 on the tumorigenic ability of A549 cells. RESULTS TET2 overexpression decreased proliferation and metastasis of A549 and H1975 cells in vitro and in vivo. However, TET2 knockdown dramatically enhanced the proliferation, migration and invasion of A549 and H1975 cells. Mechanistically, activation of the cGAS-STING signalling pathway is critical for the TET2-mediated suppression of LUAD cell tumorigenesis and metastasis. CONCLUSION In this study, we demonstrate a tumour suppressor role of TET2 in LUAD, providing new potential molecular therapeutic targets and clinical therapies for patients with non-small cell lung cancer.
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Affiliation(s)
- Gui Cheng
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, 185 Juqian Street, Changzhou, 213003, P.R. China
| | - Jun Wu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, 185 Juqian Street, Changzhou, 213003, P.R. China
| | - Mei Ji
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, 185 Juqian Street, Changzhou, 213003, P.R. China
| | - Wenwei Hu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, 185 Juqian Street, Changzhou, 213003, P.R. China
| | - Changping Wu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, 185 Juqian Street, Changzhou, 213003, P.R. China.
| | - Jingting Jiang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, 185 Juqian Street, Changzhou, 213003, P.R. China.
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13
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Petroff RL, Cavalcante RG, Colacino JA, Goodrich JM, Jones TR, Lalancette C, Morgan RK, Neier K, Perera BPU, Rygiel CA, Svoboda LK, Wang K, Sartor MA, Dolinoy DC. Developmental exposures to common environmental contaminants, DEHP and lead, alter adult brain and blood hydroxymethylation in mice. Front Cell Dev Biol 2023; 11:1198148. [PMID: 37384255 PMCID: PMC10294071 DOI: 10.3389/fcell.2023.1198148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/25/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction: The developing epigenome changes rapidly, potentially making it more sensitive to toxicant exposures. DNA modifications, including methylation and hydroxymethylation, are important parts of the epigenome that may be affected by environmental exposures. However, most studies do not differentiate between these two DNA modifications, possibly masking significant effects. Methods: To investigate the relationship between DNA hydroxymethylation and developmental exposure to common contaminants, a collaborative, NIEHS-sponsored consortium, TaRGET II, initiated longitudinal mouse studies of developmental exposure to human-relevant levels of the phthalate plasticizer di(2-ethylhexyl) phthalate (DEHP), and the metal lead (Pb). Exposures to 25 mg DEHP/kg of food (approximately 5 mg DEHP/kg body weight) or 32 ppm Pb-acetate in drinking water were administered to nulliparous adult female mice. Exposure began 2 weeks before breeding and continued throughout pregnancy and lactation, until offspring were 21 days old. At 5 months, perinatally exposed offspring blood and cortex tissue were collected, for a total of 25 male mice and 17 female mice (n = 5-7 per tissue and exposure). DNA was extracted and hydroxymethylation was measured using hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq). Differential peak and pathway analysis was conducted comparing across exposure groups, tissue types, and animal sex, using an FDR cutoff of 0.15. Results: DEHP-exposed females had two genomic regions with lower hydroxymethylation in blood and no differences in cortex hydroxymethylation. For DEHP-exposed males, ten regions in blood (six higher and four lower) and 246 regions (242 higher and four lower) and four pathways in cortex were identified. Pb-exposed females had no statistically significant differences in blood or cortex hydroxymethylation compared to controls. Pb-exposed males, however, had 385 regions (all higher) and six pathways altered in cortex, but no differential hydroxymethylation was identified in blood. Discussion: Overall, perinatal exposure to human-relevant levels of two common toxicants showed differences in adult DNA hydroxymethylation that was specific to sex, exposure type, and tissue, but male cortex was most susceptible to hydroxymethylation differences by exposure. Future assessments should focus on understanding if these findings indicate potential biomarkers of exposure or are related to functional long-term health effects.
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Affiliation(s)
- Rebekah L. Petroff
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Raymond G. Cavalcante
- Epigenomics Core, Biomedical Research Core Facilities, Michigan Medicine, Ann Arbor, MI, United States
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Tamara R. Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Claudia Lalancette
- Epigenomics Core, Biomedical Research Core Facilities, Michigan Medicine, Ann Arbor, MI, United States
| | - Rachel K. Morgan
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Kari Neier
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Bambarendage P. U. Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Christine A. Rygiel
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, Ann Arbor, MI, United States
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, Ann Arbor, MI, United States
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
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14
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Li Z, Ren Y, Li X, Wang W. KDM2A interacts with estrogen receptor α to promote bisphenol A and S-induced breast cancer cell proliferation by repressing TET2 expression. Ecotoxicol Environ Saf 2023; 262:115132. [PMID: 37315367 DOI: 10.1016/j.ecoenv.2023.115132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
As a recognized endocrine disruptor in the environment targeting estrogen receptors (ERs), Bisphenol A (BPA) and its bisphenol S (BPS) analogs are involved in the development of breast cancer. Epigenetic modifications are crucial in many biological processes, and DNA hydroxymethylation (DNAhm) coupled with histone methylation is implicated in epigenetic machinery covering cancer occurrence. Our previous study indicated that BPA/BPS induces breast cancer cell (BCC) proliferation with enhanced estrogenic transcriptional activity and causes the change of DNAhm depending on ten-eleven translocation 2 (TET2) dioxygenase. Herein, we investigated the interplay of KDM2A-mediated histone demethylation with ER-dependent estrogenic activity (EA) and identified their function in DNAhm catalyzed by TET2 for ER-positive (ER+) BCC proliferation induced by BPA/BPS. We found that BPA/BPS-treated ER+ BCCs presented increased KDM2A mRNA and protein levels but reduced TET2 and genomic DNAhm. Furthermore, KDM2A promoted H3K36me2 loss and suppressed TET2-dependent DNAhm by reducing its chromatin binding during BPA/BPS-induced cell proliferation. Results of Co-IP & ChIP assays suggested the direct interplay of KDM2A with ERα in multiple manners. KDM2A reduced the lysine methylation of ERα protein to increase its phosphorylated activation. On the other hand, ERα did not affect KDM2A expression, while KDM2A protein levels decreased after ERα deletion, indicating that ERα binding might maintain KDM2A protein stability. In conclusion, a potential feedback circuit of KDM2A/ERα-TET2-DNAhm was identified among ER+ BCCs with significant effects on regulating BPA/BPS-induced cell proliferation. These insights advanced the understanding of the relationship between histone methylation, DNAhm, and cancer cell proliferation with EA attributed to BPA/BPS exposure in the environment.
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Affiliation(s)
- Zhe Li
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China.
| | - Yun Ren
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Xuan Li
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Wenwen Wang
- Agilent Technologies (China) Co., Ltd, Beijing 100102, China
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15
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Li C, Pang M, Li Y, Han L, Fan Y, Xin X, Zhang X, Zhang N, Qin Y. Protective effect of vitamin C against tetrachlorobenzoquinone-induced 5-hydroxymethylation-dependent apoptosis in HepG2 cells mainly via the mitochondrial apoptosis pathway. Ecotoxicol Environ Saf 2023; 260:115097. [PMID: 37271103 DOI: 10.1016/j.ecoenv.2023.115097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
Tetrachlorobenzoquinone (TCBQ) is an active metabolite of pentachlorophenol, and stimulates the accumulation of ROS to trigger apoptosis. The preventive effect of vitamin C (Vc) against TCBQ-induced apoptosis in HepG2 cells is unknown. And there is little known about TCBQ-triggered 5-hydromethylcytosine (5hmC)-dependent apoptosis. Here, we confirmed that Vc alleviated TCBQ-induced apoptosis. Through investigating the underlying mechanism, we found TCBQ downregulated 5hmC levels of genomic DNA in a Tet-dependent manner, with a particularly pronounced decrease in the promoter region, using UHPLC-MS-MS analysis and hydroxymethylated DNA immunoprecipitation sequencing. Notably, TCBQ exposure resulted in alterations of 5hmC abundance to ∼91% of key genes at promoters in the mitochondrial apoptosis pathway, along with changes of mRNA expression in 87% of genes. By contrast, 5hmC abundance of genes only exhibited slight changes in the death receptor/ligand pathway. Interestingly, the pretreatment with Vc, a positive stimulator of 5hmC generation, restored 5hmC in the genomic DNA to near-normal levels. More notably, Vc pretreatment further counter-regulated TCBQ-induced alteration of 5hmC abundance in the promoter with 100% of genes, accompanying the reverse modulation of mRNA expressions in 89% of genes. These data from Vc pretreatment supported the relationship between TCBQ-induced apoptosis and the altered 5hmC abundance. Additionally, Vc also suppressed TCBQ-stimulated generation of ROS, and further increased the stability of mitochondria. Our study illuminates a new mechanism of TCBQ-induced 5hmC-dependent apoptosis, and the dual mechanisms of Vc against TCBQ-stimulated apoptosis via reversely regulating 5hmC levels and scavenging ROS. The work also provided a possible strategy for the detoxification of TCBQ.
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Affiliation(s)
- Cuiping Li
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China.
| | - Mengfan Pang
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Yaping Li
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China.
| | - Lirong Han
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Yajiao Fan
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Xuelian Xin
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Xian Zhang
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Ning Zhang
- College of Chemistry and Chemical Engineering, Dezhou University, Shandong 253023, PR China
| | - Yan Qin
- Central Laboratory, Affiliated Hospital of Hebei University, Baoding 071002, PR China
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16
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Dhat R, Mongad D, Raji S, Arkat S, Mahapatra NR, Singhal N, Sitasawad SL. Epigenetic modifier alpha-ketoglutarate modulates aberrant gene body methylation and hydroxymethylation marks in diabetic heart. Epigenetics Chromatin 2023; 16:12. [PMID: 37101286 PMCID: PMC10134649 DOI: 10.1186/s13072-023-00489-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/21/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Diabetic cardiomyopathy (DCM) is a leading cause of death in diabetic patients. Hyperglycemic myocardial microenvironment significantly alters chromatin architecture and the transcriptome, resulting in aberrant activation of signaling pathways in a diabetic heart. Epigenetic marks play vital roles in transcriptional reprogramming during the development of DCM. The current study is aimed to profile genome-wide DNA (hydroxy)methylation patterns in the hearts of control and streptozotocin (STZ)-induced diabetic rats and decipher the effect of modulation of DNA methylation by alpha-ketoglutarate (AKG), a TET enzyme cofactor, on the progression of DCM. METHODS Diabetes was induced in male adult Wistar rats with an intraperitoneal injection of STZ. Diabetic and vehicle control animals were randomly divided into groups with/without AKG treatment. Cardiac function was monitored by performing cardiac catheterization. Global methylation (5mC) and hydroxymethylation (5hmC) patterns were mapped in the Left ventricular tissue of control and diabetic rats with the help of an enrichment-based (h)MEDIP-sequencing technique by using antibodies specific for 5mC and 5hmC. Sequencing data were validated by performing (h)MEDIP-qPCR analysis at the gene-specific level, and gene expression was analyzed by qPCR. The mRNA and protein expression of enzymes involved in the DNA methylation and demethylation cycle were analyzed by qPCR and western blotting. Global 5mC and 5hmC levels were also assessed in high glucose-treated DNMT3B knockdown H9c2 cells. RESULTS We found the increased expression of DNMT3B, MBD2, and MeCP2 with a concomitant accumulation of 5mC and 5hmC, specifically in gene body regions of diabetic rat hearts compared to the control. Calcium signaling was the most significantly affected pathway by cytosine modifications in the diabetic heart. Additionally, hypermethylated gene body regions were associated with Rap1, apelin, and phosphatidyl inositol signaling, while metabolic pathways were most affected by hyperhydroxymethylation. AKG supplementation in diabetic rats reversed aberrant methylation patterns and restored cardiac function. Hyperglycemia also increased 5mC and 5hmC levels in H9c2 cells, which was normalized by DNMT3B knockdown or AKG supplementation. CONCLUSION This study demonstrates that reverting hyperglycemic damage to cardiac tissue might be possible by erasing adverse epigenetic signatures by supplementing epigenetic modulators such as AKG along with an existing antidiabetic treatment regimen.
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Affiliation(s)
- Rohini Dhat
- National Centre for Cell Science, NCCS Complex, S. P. Pune University, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Dattatray Mongad
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra, 411007, India
| | - Sivarupa Raji
- National Centre for Cell Science, NCCS Complex, S. P. Pune University, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Silpa Arkat
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Nitish R Mahapatra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Nishant Singhal
- National Centre for Cell Science, NCCS Complex, S. P. Pune University, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Sandhya L Sitasawad
- National Centre for Cell Science, NCCS Complex, S. P. Pune University, Ganeshkhind, Pune, Maharashtra, 411007, India.
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17
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Parsons E, Rifas-Shiman SL, Bozack AK, Baccarelli AA, DeMeo DL, Hivert MF, Godderis L, Duca RC, Oken E, Cardenas A. Prenatal trimester-specific intake of micronutrients: global DNA methylation and hydroxymethylation at birth and persistence in childhood. J Dev Orig Health Dis 2023; 14:311-318. [PMID: 36515010 PMCID: PMC9998337 DOI: 10.1017/s2040174422000642] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The prenatal environment may program health and disease susceptibility via epigenetic mechanisms. We evaluated associations of maternal trimester-specific intake of micronutrients with global DNA methylation (%5mC) and 5-hydroxymethylation (%5hmC) at birth in cord blood and tested for persistence into childhood. We quantified global %5mC and %5hmC in cord blood cells (n = 434) and in leukocytes collected in early (n = 108) and mid-childhood (n = 390) from children in Project Viva, a pre-birth cohort from Boston, MA. Validated food frequency questionnaires estimated maternal first- and second-trimester intakes of vitamin B2, vitamin B6, vitamin B12, folate, betaine, choline, methionine, iron, and zinc. Mean (SD) cord blood %5mC and %5hmC was 5.62% (2.04) and 0.25% (0.15), respectively. Each μg increase in first-trimester B12 intake was associated with 0.002 lower %5hmC in cord blood (95% CI: -0.005, -0.0003), and this association persisted in early childhood (β = -0.007; 95% CI: -0.01, -0.001) but not mid-childhood. Second-trimester iron (mg) was associated with 0.01 lower %5mC (95% CI: -0.02, -0.002) and 0.001 lower %5hmC (95% CI: -0.01, -0.00001) in cord blood only. Increased second-trimester zinc (mg) intake was associated with 0.003 greater %5hmC in early childhood (β = 0.003; 95% CI: 0.0004, 0.006). Second-trimester folate was positively associated with %5hmC in early childhood only (β = 0.08, 95% CI: 0.003, 0.16). Associations did not survive multiple testing adjustment; future replication is needed. Trimester-specific nutrients may impact various sensitive windows of epigenetic programming some with lasting effects in childhood. Further research is needed to understand the role of gene-specific epigenetic changes and how global DNA methylation measures relate to child health.
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Affiliation(s)
- Ella Parsons
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Sheryl L. Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Anne K. Bozack
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lode Godderis
- Centre for Environment & Health, Department of Public Health & Primary Care, University of Leuven (KU Leuven), Belgium
- IDEWE, External service for prevention and protection at work, Heverlee, Belgium
| | - Radu-Corneliu Duca
- Centre for Environment & Health, Department of Public Health & Primary Care, University of Leuven (KU Leuven), Belgium
- Environmantal Hygiene and Biological Surveillance at the National Health Laboratory (LNS), Luxembourg
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
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18
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Zhao T, Piao LH, Li DP, Xu SH, Wang SY, Yuan HB, Zhang CX. BDNF gene hydroxymethylation in hippocampus related to neuroinflammation-induced depression-like behaviors in mice. J Affect Disord 2023; 323:723-730. [PMID: 36529411 DOI: 10.1016/j.jad.2022.12.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 10/31/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Neuroinflammation is a multifactorial condition related to glial cells and neurons activation, and it is implicated in CNS disorders including depression. BDNF is a crucial molecule that related to the pathology of depression, and it is the target of DNA methylation. DNA hydroxymethylation, an active demethylation process can convert 5-mC to 5-hmC by Tets catalyzation to regulate gene transcription. The regulatory function for BDNF gene in response to neuroinflammation remains poorly understood. METHODS Neuroinflammation and depressive-like behaviors were induced by lipopolysaccharide (LPS) administration in mice. The microglial activation and cellular 5-hmC localization in the hippocampus were confirmed by immunostaining. The transcripts of Tets and BDNF were examined by qPCR method. The global 5-hmC levels and enrichment of 5-hmC in BDNF gene in the hippocampus were analyzed using dot bolt and hMeDIP-sequencing analysis. RESULTS LPS administration induced a spectrum of depression-like behaviors (including behavioral despair and anhedonia) and increased expression of Iba-1, a marker for microglia activation, in hippocampus, demonstrating that LPS treatment cloud provide stable model of neuroinflammation with depressive-like behaviors as expected. Our results showed that Tet1, Tet2 and Tet3 mRNA expressions and consequent global 5-hmC levels were significantly decreased in the hippocampus of LPS group compared to saline group. We also demonstrated that 5-hmC fluorescence in the hippocampus located in excitatory neurons identified by CaMK II immunostaining. Furthermore, we demonstrated that the enrichment of 5-hmC in BDNF gene was decreased and corresponding BDNF mRNA was down-regulated in the hippocampus in LPS group compared to saline group. CONCLUSION Neuroinflammation-triggered aberrant BDNF gene hydroxymethylation in the hippocampus is an important epigenetic element that relates with depression-like behaviors.
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Affiliation(s)
- Te Zhao
- Department of Physiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Lian-Hua Piao
- Department of Physiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Dan-Ping Li
- Department of Physiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Shi-Han Xu
- Department of Physiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Shu-Yi Wang
- The Second Bethune Clinical Medical College of Jilin University, Changchun, Jilin 130021, China
| | - Hai-Bo Yuan
- Department of Respiratory Medicine & Sleep Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China.
| | - Chun-Xiao Zhang
- Department of Physiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China.
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19
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Li J, Hong T, Wei Y, Guo L, Lee M, Yang H, Class C, Yang Y, Wang X, He H, Siwko S, You MJ, Zhou Y, Garcia-Manero G, Huang Y. Aberrant DNA hydroxymethylation reshapes transcription factor binding in myeloid neoplasms. Clin Epigenetics 2022; 14:81. [PMID: 35765052 PMCID: PMC9241241 DOI: 10.1186/s13148-022-01297-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/05/2022] [Indexed: 11/17/2022] Open
Abstract
Epigenetic abnormalities in DNA hydroxymethylation (5hmC) have been detected in patients with myeloid neoplasms, suggesting that 5hmC might act as a valuable epigenetic mark to reflect the disease status of myeloid neoplasms. Here, we report systematic genome-wide mapping of the DNA hydroxymethylomes in over 70 patients with myeloid neoplasms. Our integrative analysis leads to the identification of distinct 5hmC signatures that can sensitively discriminate patients from healthy individuals. At the molecular level, we unveiled dynamic 5hmC changes within key transcription factor (e.g., the CEBP family) binding motifs that are essential for hematopoiesis and myeloid lineage specification. 5hmC redistribution was found to alter the genome-wide binding of CEBP-α, thereby reprogramming transcriptional outputs to affect leukemia cell survival and stemness. Taken together, we provide a comprehensive 5hmC atlas representative of myeloid neoplasms, which sets the stage for future exploration on the epigenetic etiology of hematological malignancies. Mechanistically, our study further furnishes important insights into how abnormal 5hmC distribution in patients directly interrupts the binding of transcription factors to reshape transcriptional landscapes and aggravate leukemogenesis.
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Affiliation(s)
- Jia Li
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Room 404, 2121. W. Holcombe Blvd, Houston, TX, 77030, USA.
| | - Tingting Hong
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Room 404, 2121. W. Holcombe Blvd, Houston, TX, 77030, USA
| | - Yue Wei
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lei Guo
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Room 404, 2121. W. Holcombe Blvd, Houston, TX, 77030, USA
| | - Minjung Lee
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Room 404, 2121. W. Holcombe Blvd, Houston, TX, 77030, USA
| | - Hui Yang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Caleb Class
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Yaling Yang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiaoqiong Wang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hua He
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Stefan Siwko
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - M James You
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Guillermo Garcia-Manero
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Room 404, 2121. W. Holcombe Blvd, Houston, TX, 77030, USA.
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20
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Tan H, Tong X, Gao Z, Xu Y, Tan L, Zhang W, Xiang R, Xu Y. The hMeDIP-Seq identified INPP4A as a novel biomarker for eosinophilic chronic rhinosinusitis with nasal polyps. Epigenomics 2022; 14:757-775. [PMID: 35765979 DOI: 10.2217/epi-2022-0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: Eosinophilic chronic rhinosinusitis with nasal polyps (ECRSwNP) is an endotype of chronic rhinosinusitis with nasal polyps characterized by more severe symptoms, a stronger association with asthma and a greater recurrence risk. It is unknown whether DNA hydroxymethylation could influence ECRSwNP. Methods: Hydroxymethylated DNA immunoprecipitation sequencing was carried out in three distinct groups (control, ECRSwNP and NECRSwNP). Additional qRT-PCR, immunohistochemistry and analysis of the receiver operating characteristic curve were performed. Results: Between ECRSwNP and NECRSwNP, 26 genes exhibited differential DNA hydroxymethylation. Consistent with their hydroxymethylation level, GNAL, INPP4A and IRF4 expression levels were significantly different between ECRSwNP and the other two groups. The receiver operating characteristic curve revealed that INPP4A mRNA has a high predictive accuracy for ECRSwNP. Conclusion: DNA hydroxymethylation regulates the expression of multiple genes in ECRSwNP. INPP4A mRNA was markedly decreased in ECRSwNP polyps and can predict ECRSwNP.
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Affiliation(s)
- Hanyu Tan
- Department of Otolaryngology - Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xiaoting Tong
- Department of Otolaryngology - Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Ziang Gao
- Department of Otolaryngology - Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yingying Xu
- Department of Otolaryngology - Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Lu Tan
- Department of Otolaryngology - Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Wei Zhang
- Department of Otolaryngology - Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Rong Xiang
- Department of Otolaryngology - Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yu Xu
- Department of Otolaryngology - Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
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21
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Song YP, Lv JW, Zhao Y, Chen X, Zhang ZC, Fan YJ, Zhang C, Gao L, Huang Y, Wang H, Xu DX. DNA hydroxymethylation reprogramming of β-oxidation genes mediates early-life arsenic-evoked hepatic lipid accumulation in adult mice. J Hazard Mater 2022; 430:128511. [PMID: 35739688 DOI: 10.1016/j.jhazmat.2022.128511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 06/15/2023]
Abstract
The metabolic disorders are becoming an epidemic disease endangering public health in countries. Environmental factors are mainly reason for the growth of metabolic disorders. Previous research suggests that DNA methylation is a potential mechanism. Recently, it has been reported that DNA hydroxymethylation is also a stable marker of epigenetic reprogramming. Hence, the study aims to investigate whether DNA hydroxymehylation mediates early-life environmental stress-evoked metabolic disorder in adulthood. Mice were orally administered with arsenic (As), an environmental stressor, throughout pregnancy. We show that early-life As exposure induces glucose intolerance and hepatic lipid accumulation in adulthood. Early-life As exposure alters epigenetic reprogramming and expression of lipid metabolism-related genes including β-oxidation-specific genes in adulthood. Of interest, early-life As exposure alters epigenetic reprogramming of hepatic lipid metabolism partially through reducing DNA hydroxymethylation modification of β-oxidation-related genes in developing liver. Mechanistically, early-life As exposure suppresses ten-eleven translocation (TET) activity through downregulating isocitrate dehydrogenases (Idh) and reducing alpha-ketoglutarate (α-KG) content in the developing liver. In addition, early-life As exposure inhibits TET1 binding to CpG-rich fragments of β-oxidation-related genes in developing liver. This study provide novel evidence that early-life environmental stress leads to later life metabolic disorders by altering hepatic DNA hydroxymethylation reprogramming.
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Affiliation(s)
- Ya-Ping Song
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Jin-Wei Lv
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Ying Zhao
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Xu Chen
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Zhi-Cheng Zhang
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Yi-Jun Fan
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Cheng Zhang
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Lan Gao
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Yichao Huang
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Hua Wang
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - De-Xiang Xu
- Department of Toxicology, Anhui Medical University, Hefei 230032, China.
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22
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Lejart A, Zentout S, Chapuis C, D'Augustin O, Smith R, Salbert G, Huet S. The N-terminal domain of TET1 promotes the formation of dense chromatin regions refractory to transcription. Chromosoma 2022; 131:47-58. [PMID: 35235010 DOI: 10.1007/s00412-022-00769-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/03/2022]
Abstract
TET (ten-eleven translocation) enzymes initiate active cytosine demethylation via the oxidation of 5-methylcytosine. TET1 is composed of a C-terminal domain, which bears the catalytic activity of the enzyme, and a N-terminal region that is less well characterized except for the CXXC domain responsible for the targeting to CpG islands. While cytosine demethylation induced by TET1 promotes transcription, this protein also interacts with chromatin-regulating factors that rather silence this process, the coordination between these two opposite functions of TET1 being unclear. In the present work, we uncover a new function of the N-terminal part of the TET1 protein in the regulation of the chromatin architecture. This domain of the protein promotes the establishment of a compact chromatin architecture displaying reduced exchange rate of core histones and partial dissociation of the histone linker. This chromatin reorganization process, which does not rely on the CXXC domain, is associated with a global shutdown of transcription and an increase in heterochromatin-associated histone epigenetic marks. Based on these findings, we propose that the dense chromatin organization generated by the N-terminal domain of TET1 could contribute to restraining the transcription enhancement induced by the DNA demethylation activity of this enzyme.
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Affiliation(s)
- Audrey Lejart
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Siham Zentout
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Catherine Chapuis
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Ostiane D'Augustin
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
- Institut de Biologie François Jacob, Institute of Cellular and Molecular Radiobiology, Université Paris-Saclay, Université de Paris, CEA, 92265, Fontenay-aux-Roses, France
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Gilles Salbert
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France.
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France.
- Institut Universitaire de France, Paris, France.
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23
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Domingo-Relloso A, Bozack A, Kiihl S, Rodriguez-Hernandez Z, Rentero-Garrido P, Casasnovas JA, Leon-Latre M, Garcia-Barrera T, Gomez-Ariza JL, Moreno B, Cenarro A, de Marco G, Parvez F, Siddique AB, Shahriar H, Uddin MN, Islam T, Navas-Acien A, Gamble M, Tellez-Plaza M. Arsenic exposure and human blood DNA methylation and hydroxymethylation profiles in two diverse populations from Bangladesh and Spain. Environ Res 2022; 204:112021. [PMID: 34516978 PMCID: PMC8734953 DOI: 10.1016/j.envres.2021.112021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/31/2021] [Accepted: 09/04/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Associations of arsenic (As) with the sum of 5-mC and 5-hmC levels have been reported; however, As exposure-related differences of the separated 5-mC and 5-hmC markers have rarely been studied. METHODS In this study, we evaluated the association of arsenic exposure biomarkers and 5-mC and 5-hmC in 30 healthy men (43-55 years) from the Aragon Workers Health Study (AWHS) (Spain) and 31 healthy men (31-50 years) from the Folic Acid and Creatinine Trial (FACT) (Bangladesh). We conducted 5-mC and 5-hmC profiling using Infinium MethylationEPIC arrays, on paired standard and modified (ox-BS in AWHS and TAB in FACT) bisulfite converted blood DNA samples. RESULTS The median for the sum of urine inorganic and methylated As species (ΣAs) (μg/L) was 12.5 for AWHS and 89.6 for FACT. The median of blood As (μg/L) was 8.8 for AWHS and 10.2 for FACT. At a statistical significance p-value cut-off of 0.01, the differentially methylated (DMP) and hydroxymethylated (DHP) positions were mostly located in different genomic sites. Several DMPs and DHPs were consistently found in AWHS and FACT both for urine ΣAs and blood models, being of special interest those attributed to the DIP2C gene. Three DMPs (annotated to CLEC12A) for AWHS and one DHP (annotated to NPLOC4) for FACT remained statistically significant after false discovery rate (FDR) correction. Pathways related to chronic diseases including cardiovascular, cancer and neurological were enriched. CONCLUSIONS While we identified common 5-hmC and 5-mC signatures in two populations exposed to varying levels of inorganic As, differences in As-related epigenetic sites across the study populations may additionally reflect low and high As-specific associations. This work contributes a deeper understanding of potential epigenetic dysregulations of As. However, further research is needed to confirm biological consequences associated with DIP2C epigenetic regulation and to investigate the role of 5-hmC and 5-mC separately in As-induced health disorders at different exposure levels.
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Affiliation(s)
- Arce Domingo-Relloso
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, Madrid, Spain; Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA; Department of Statistics and Operations Research, University of Valencia, Spain
| | - Anne Bozack
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA; Department of Environmental Health Sciences, School of Public Health, University of California, Berkeley, USA
| | - Samara Kiihl
- Department of Statistics, State University of Campinas, Brazil
| | - Zulema Rodriguez-Hernandez
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Pilar Rentero-Garrido
- Precision Medicine Unit, Biomedical Research Institute Hospital Clinic de Valencia INCLIVA, Valencia, Spain
| | - J Antonio Casasnovas
- CIBERCV, And Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain; Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain
| | - Montserrat Leon-Latre
- CIBERCV, And Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain; Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain
| | - Tamara Garcia-Barrera
- Research Center on Natural Resources, Health and the Environment, Department of Chemistry, University of Huelva, Huelva, Spain
| | - J Luis Gomez-Ariza
- Research Center on Natural Resources, Health and the Environment, Department of Chemistry, University of Huelva, Huelva, Spain
| | - Belen Moreno
- Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain; Department of Microbiology, Pediatrics, Radiology and Public Health, University of Zaragoza, Zaragoza, Spain
| | - Ana Cenarro
- CIBERCV, And Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain; Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain
| | - Griselda de Marco
- Genomics Area, Foundation for the Promotion of Health and Biomedical Research of the Valencian Region (FISABIO), Valencia, Spain
| | - Faruque Parvez
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Abu B Siddique
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Hasan Shahriar
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Mohammad N Uddin
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Tariqul Islam
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
| | - Mary Gamble
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
| | - Maria Tellez-Plaza
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, Madrid, Spain.
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24
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Wang Q, Wang W, Sun B, Zhang A. Genomic DNA hydroxymethylation reveals potential role in identification of lung injury in coal-burning arsenicosis populations. Environ Res 2022; 204:112053. [PMID: 34536373 DOI: 10.1016/j.envres.2021.112053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/11/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Arsenic (As) is a toxic metalloid element that causes lung cancer and multiple non-malignant respiratory diseases. The toxicity of arsenic is mediated in part by epigenetic mechanisms, such as alterations in DNA methylation. While increasing studies have highlighted the potential importance of arsenic exposure to DNA methylation patterns and the subsequent risks for arsenic toxicity, there has been little focus on DNA hydroxymethylation-a negative regulation mechanism of DNA methylation. Therefore, this study aimed to investigate the relationship between genomic DNA methylation/hydroxymethylation and lung injury in arsenicosis populations. First, an increased risk of lung injury and exacerbation of lung function impairment in the arsenicosis population was confirmed. Levels of 5-methylcytosine/deoxycytidine (5 mC/dC), 5-hydroxymethylcytosine/deoxycytidine (5 hmC/dC) and 5 hmC/5 mC in genomic DNA of peripheral blood were decreased in the arsenicosis population compared to in the control. Additionally, multivariate logistic regression models showed an increased risk of chest digital radiography (DR) abnormalities when 5 hmC/dC and 5 hmC/5 mC levels were lower (OR = 3.12 and 3.96, all P < 0.001). For 3 years follow-up, regression analysis showed that a decline in 5 hmC/dC was significantly associated with the decline of lung function parameters [forced vital capacity (FVC), forced expiratory volume in 1 s (FEV1) and maximal mid-expiratory flow (MMEF); β = 0.167, 0.122 and 0.073, respectively; all P < 0.05]. Using the receiver operating characteristic (ROC) curve, a combination of 5 hmC/5 dC and 5 hmC/5 mC obtained the highest value for distinguishing lung injury in all subjects (AUC = 0.82, P < 0.01). In contrast, in arsenicosis subjects, 5 hmC/dC was better at distinguishing lung injury (AUC = 0.84, P < 0.01). Together, the results revealed that a decrease in genomic DNA hydroxymethylation markers was associated with lung injury in coal-burning arsenicosis populations. Genomic DNA hydroxymethylation could be a novel biomarker for identifying the risk of lung injury caused by coal-burning arsenicosis.
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Affiliation(s)
- Qingling Wang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, PR China
| | - Wenjuan Wang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, PR China
| | - Baofei Sun
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, PR China
| | - Aihau Zhang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, PR China.
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Zhang Z, Lee MK, Perreard L, Kelsey KT, Christensen BC, Salas LA. Navigating the hydroxymethylome: experimental biases and quality control tools for the tandem bisulfite and oxidative bisulfite Illumina microarrays. Epigenomics 2022; 14:139-152. [PMID: 35029129 PMCID: PMC8914583 DOI: 10.2217/epi-2021-0490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Aim: Tandem bisulfite (BS) and oxidative bisulfite (oxBS) conversion on DNA followed by hybridization to Infinium HumanMethylation BeadChips allows nucleotide resolution of 5-hydroxymethylcytosine genome-wide. Here, the authors compared data quality acquired from BS-treated and oxBS-treated samples. Materials & methods: Raw BeadArray data from 417 pairs of samples across 12 independent datasets were included in the study. Probe call rates were compared between paired BS and oxBS treatments controlling for technical variables. Results: oxBS-treated samples had a significantly lower call rate. Among technical variables, DNA-specific extraction kits performed better with higher call rates after oxBS conversion. Conclusion: The authors emphasize the importance of quality control during oxBS conversion to minimize information loss and recommend using a DNA-specific extraction kit for DNA extraction and an oxBSQC package for data preprocessing.
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Affiliation(s)
- Ze Zhang
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA
| | - Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA
| | - Laurent Perreard
- Department of Molecular & Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA
| | - Karl T Kelsey
- Department of Epidemiology, Department of Pathology & Laboratory Medicine, Brown University School of Public Health, Providence, 02912 RI, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA,Department of Molecular & Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA,Department of Molecular & Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA,Author for correspondence: Tel.: 603 646 5496;
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Xie Y, Tan J, Qin Y, Cao Y, Wang Y, Li A, Wang Z, Qiao Z, Yan Z. MiR-3571 modulates the proliferation and migration of vascular smooth muscle cells by targeting claudin 1. Int J Med Sci 2022; 19:511-524. [PMID: 35370461 PMCID: PMC8964332 DOI: 10.7150/ijms.64639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 02/09/2022] [Indexed: 11/22/2022] Open
Abstract
Background and aims: The miRNA-based post-transcription modification has been extensively studied in hypertension. It however remains elusive how miRNA expression is regulated in this pathological process. We hypothesize that hydroxymethylation in the promoter regions tightly controls the levels of key miRNAs, which in turn affects the development of hypertension. Methods: The levels of hydroxymethylation in the promoter regions from thoracic aortic tissues were compared between spontaneously hypertensive rats (SHRs) and normotensive Wistar-Kyoto rats (WKYs), using hydroxymethylcytosine DNA immunoprecipitation (hMeDIP) sequencing. The altered hydroxymethylation level of miR-3571 was confirmed by glucosylation-coupled hydroxymethylation-sensitive qPCR. We further identified claudin 1(CLDN1) as a key target of miR-3571 via bioinformatic prediction (targetscan) and dual-luciferase activity assays. Finally, we analyzed the contribution of miR-3571/CLDN1 axis in the proliferation and migration of vascular smooth muscle cells (VSMCs). Results: The hydroxymethylation level of miR-3571 promoter region in thoracic aortic tissue from spontaneously hypertensive rats was lower than that from normotensive Wistar-Kyoto rats. Accordingly, the expression of miR-3571 was lower during hypertension, with up-regulated CLDN1 protein levels. More importantly, we found that miR3571 overexpression led to phenotypic changes of VSMCs, and inhibited the proliferation and migration of muscle cells via suppressing CLDN1 as well. Our findings further suggested that CLDN1 up-regulation increase the activity of ERK1/2 in VSMCs. Conclusions: Our study suggested that hydroxymethylation in the promoter regions controlled the level of miR-3571 and revealed the important roles of miR-3571 and CLDN1 in VSMCs during the development of hypertension. In addition, our results also indicated that miR-3571/CLDN1 axis regulated the functions of VSMCs via the ERK1/2 pathway. Taken together, our findings support miR-3571 as a novel biomarker for the diagnosis and prevention of hypertension.
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Affiliation(s)
- Yilin Xie
- Shanghai Jiao Tong University - Minhang Campus, School of Life Science and Biotechnology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai, China
| | - Juanjuan Tan
- Shanghai Jiao Tong University - Minhang Campus, School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composite Materials and Shanghai Key Lab of Electrical Insulation and Thermal Ageing, Shanghai, China
| | - Yingchun Qin
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yong Cao
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology, Shanghai, China
| | - Yicheng Wang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology, Shanghai, China
| | - Aihua Li
- Anhui University of Science and Technology, Huainan, Anhui, China
| | - Zhaoxia Wang
- Shanghai Jiao Tong University Laboratory Animal Center, Shanghai, China
| | - Zhongdong Qiao
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology, Shanghai, China
| | - Zhiqiang Yan
- Shanghai Jiao Tong University affiliated sixth people's hospital south campus, Central Laboratory, Shanghai, China
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Lv JW, Song YP, Zhang ZC, Fan YJ, Xu FX, Gao L, Zhang XY, Zhang C, Wang H, Xu DX. Gestational arsenic exposure induces anxiety-like behaviors in adult offspring by reducing DNA hydroxymethylation in the developing brain. Ecotoxicol Environ Saf 2021; 227:112901. [PMID: 34673408 DOI: 10.1016/j.ecoenv.2021.112901] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/28/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Several studies found that reduction of 5-hydroxymethylcytosine (5hmC), a marker of DNA hydroxymethylation highly enriched in developing brain, is associated with anxiety-like behaviors. This study aimed to investigate whether gestational arsenic (As) exposure induces anxiety-like behaviors in adult offspring by reducing DNA hydroxymethylation in the developing brain. The dams drank ultrapure water containing NaAsO2 (15 mg/L) throughout pregnancy. Anxiety-like behaviors were evaluated and developing brain 5hmC was detected. Results showed that anxiety-like behaviors were observed in As-exposed adult offspring. In addition, 5hmC content was reduced in As-exposed fetal brain. Despite no difference on Tet1, Tet2 and Tet3 expression, TET activity was suppressed in As-exposed fetal brain. Mechanistically, alpha-ketoglutarate (α-KG), a cofactor for TET dioxygenases, was reduced and Idh2, a key enzymatic gene for mitochondrial α-KG synthesis, was downregulated in As-exposed fetal brain. Of interest, ascorbic acid, a cofactor for TET dioxygenases, reversed As-induced suppression of TET activity. Moreover, ascorbic acid attenuated As-induced reduction of 5hmC in fetal brain. In addition, ascorbic acid alleviated As-induced anxiety-like behaviors in adult offspring. Taken together, these results suggest that gestational As exposure induces anxiety-like behaviors in adult offspring, possibly at part, by inhibiting DNA hydroxymethylation in developing brain.
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Affiliation(s)
- Jin-Wei Lv
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Ya-Ping Song
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Zhi-Cheng Zhang
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Yi-Jun Fan
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Fei-Xiang Xu
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Lan Gao
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Xiao-Yi Zhang
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Cheng Zhang
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - Hua Wang
- Department of Toxicology, Anhui Medical University, Hefei 230032, China
| | - De-Xiang Xu
- Department of Toxicology, Anhui Medical University, Hefei 230032, China.
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Liu X, Cui H. The palliative effects of folic acid on retinal microvessels in diabetic retinopathy via regulating the metabolism of DNA methylation and hydroxymethylation. Bioengineered 2021; 12:10766-10774. [PMID: 34874218 PMCID: PMC8809984 DOI: 10.1080/21655979.2021.2003924] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Diabetic retinopathy (DR) is one of the severe microvascular complications of diabetes. The protective effects of FA on retinal vascular endothelial cells against high glucose levels involve in multiple aspects in DR; however, the underlying mechanism is not fully elucidated. In present study, we investigated the transcriptome as well as genome-wide DNA methylation and hydroxymethylation signature in human retinal microvascular endothelial ACBRI 181 cells cultured within high glucose (HG) medium supplemented with or without FA by RNA-seq, MeDIP-seq, and hMeDIP-seq. Total 3308 differential expressed genes (DEGs) were involved in multiple biological processes and molecular functions containing angiogenesis, inflammation, S-adenosyl methionine metabolism, and hypoxia response. Moreover, the global DNA methylation and hydroxymethylation in ACBRI 181 cells with FA treatment were both compromised compared to HG. Combined with transcriptome data, four subclusters of DEGs with hyper- or hypomethylated promoters were further verified. Unexpectedly, promoters of these 487 genes all displayed a pattern of increased DNA hydroxymethylation. Furthermore, hyperglycemia rat model was established and administered with FA. The DNA methylation and hydroxymethylation changes of selected target genes COL1A1, ITGA7, MMP-14, and VEGFB confirmed by MeDIP-qPCR were consistent with the results in human ACBRI 181 cells. Finally, the presence of activated DNMT1 and TET2 induced by FA was determined in ACBRI 181 cells and hyperglycemia rat. Taken together, this research provided a resource of expression and epigenetic profiles in retinal microvascular endothelial cell, emphasizing a pharmacological mechanism of FA on DNA methylation and hydroxymethylation regulation in retinal microvessel cells of DR.
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Affiliation(s)
- Xianli Liu
- Department of Ophthalmology, Zibo Municipal Hospital, Zibo, Shandong, China
| | - Hongbao Cui
- Department of Ophthalmology, Zibo Kangming AIER Ophthalmology Hospital, Shandong, China
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Shen Y, Zhao H, Zhang L, Hu Y, Cai L, Li J, Zhou S. The roles of DNA methylation and hydroxymethylation at short interspersed nuclear elements in the hypothalamic arcuate nucleus during puberty. Mol Ther Nucleic Acids 2021; 26:242-52. [PMID: 34513307 DOI: 10.1016/j.omtn.2021.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/13/2021] [Indexed: 12/26/2022]
Abstract
Puberty is the gateway to adult reproductive competence, encompassing a suite of complex, integrative, and coordinated changes in neuroendocrine functions. However, the regulatory mechanisms of transcriptional reprogramming in the arcuate nucleus (ARC) during onset of puberty are still not fully understood. To understand the role of epigenetics in regulating gene expression, mouse hypothalamic ARCs were isolated at 4 and 8 weeks, and the transcriptome, DNA hydroxymethylation, DNA methylation, and chromatin accessibility were assessed via RNA sequencing (RNA-seq), reduced representation bisulfite sequencing (RRBS-seq), reduced representation hydroxymethylation profiling (RRHP)-seq, and assay for transposase-accessible chromatin (ATAC-seq), respectively. The overall DNA hydroxymethylation and DNA methylation changes in retroelements (REs) were associated with gene expression modeling for puberty in the ARC. We focused on analyzing DNA hydroxymethylation and DNA methylation at two short interspersed nuclear elements (SINEs) located on the promoter of the 5-hydroxytryptamine receptor 6 (Htr6) gene and the enhancer of the KISS-1 metastasis suppressor (Kiss1) gene and investigated their regulatory roles in gene expression. Our data uncovered a novel epigenetic mechanism by which SINEs regulate gene expression during puberty.
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Angeles AK, Janke F, Bauer S, Christopoulos P, Riediger AL, Sültmann H. Liquid Biopsies beyond Mutation Calling: Genomic and Epigenomic Features of Cell-Free DNA in Cancer. Cancers (Basel) 2021; 13:5615. [PMID: 34830770 PMCID: PMC8616179 DOI: 10.3390/cancers13225615] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 01/12/2023] Open
Abstract
Cell-free DNA (cfDNA) analysis using liquid biopsies is a non-invasive method to gain insights into the biology, therapy response, mechanisms of acquired resistance and therapy escape of various tumors. While it is well established that individual cancer treatment options can be adjusted by panel next-generation sequencing (NGS)-based evaluation of driver mutations in cfDNA, emerging research additionally explores the value of deep characterization of tumor cfDNA genomics and fragmentomics as well as nucleosome modifications (chromatin structure), and methylation patterns (epigenomics) for comprehensive and multi-modal assessment of cfDNA. These tools have the potential to improve disease monitoring, increase the sensitivity of minimal residual disease identification, and detection of cancers at earlier stages. Recent progress in emerging technologies of cfDNA analysis is summarized, the added potential clinical value is highlighted, strengths and limitations are identified and compared with conventional targeted NGS analysis, and current challenges and future directions are discussed.
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Affiliation(s)
- Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Simone Bauer
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Petros Christopoulos
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
- Department of Oncology, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Anja Lisa Riediger
- Helmholtz Young Investigator Group, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- Department of Urology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
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Wanner N, Larsen PA, McLain A, Faulk C. The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing. BMC Genomics 2021; 22:726. [PMID: 34620074 PMCID: PMC8499546 DOI: 10.1186/s12864-021-08046-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/29/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The golden lion tamarin (Leontopithecus rosalia) is an endangered Platyrrhine primate endemic to the Atlantic coastal forests of Brazil. Despite ongoing conservation efforts, genetic data on this species remains scarce. Complicating factors include limitations on sample collection and a lack of high-quality reference sequences. Here, we used nanopore adaptive sampling to resequence the L. rosalia mitogenome from feces, a sample which can be collected non-invasively. RESULTS Adaptive sampling doubled the fraction of both host-derived and mitochondrial sequences compared to sequencing without enrichment. 258x coverage of the L. rosalia mitogenome was achieved in a single flow cell by targeting the unfinished genome of the distantly related emperor tamarin (Saguinus imperator) and the mitogenome of the closely related black lion tamarin (Leontopithecus chrysopygus). The L. rosalia mitogenome has a length of 16,597 bp, sharing 99.68% sequence identity with the L. chrysopygus mitogenome. A total of 38 SNPs between them were identified, with the majority being found in the non-coding D-loop region. DNA methylation and hydroxymethylation were directly detected using a neural network model applied to the raw signal from the MinION sequencer. In contrast to prior reports, DNA methylation was negligible in mitochondria in both CpG and non-CpG contexts. Surprisingly, a quarter of the 642 CpG sites exhibited DNA hydroxymethylation greater than 1% and 44 sites were above 5%, with concentration in the 3' side of several coding regions. CONCLUSIONS Overall, we report a robust new mitogenome assembly for L. rosalia and direct detection of cytosine base modifications in all contexts.
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Affiliation(s)
- Nicole Wanner
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, 1988 Fitch Ave., Saint Paul, MN 55108 USA
| | - Peter A. Larsen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN USA
| | - Adam McLain
- Department of Biology and Chemistry, College of Arts and Sciences, SUNY Polytechnic Institute, Utica, NY USA
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, 1988 Fitch Ave., Saint Paul, MN 55108 USA
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Luo K, Wang L, Shen Y, She S, Cui Y, Liu K. TET3-mediated accumulation of DNA hydroxymethylation contributes to the activity-dependent gene expression of Rab3a in post-mitotic neurons. J Integr Neurosci 2021; 20:529-539. [PMID: 34645086 DOI: 10.31083/j.jin2003057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/28/2021] [Accepted: 07/23/2021] [Indexed: 11/06/2022] Open
Abstract
Rab3a, a subtype protein in the Rab3 family amongst the small G proteins, is closely associated with the learning and memory formation process. Various neuronal stimuli can induce the expression of Rab3a; however, how DNA modification is involved in regulating its expression is not fully understood. Ten-eleven translocation (TET) proteins can oxidate methylcytosine to hydroxymethylcytosine, which can further activate gene expression. Previous studies reported that TET-mediated regulation of 5hmC induced by learning is involved in neuronal activation. However, whether Tet protein regulates Rab3a is unknown. To understand the role of TET-mediated 5hmC on Rab3a in neuronal activation, we adopted a KCl-induced depolarization protocol in cultured primary cortical neurons to mimic neuronal activity in vitro. After KCl treatment, Rab3a and Tet3 mRNA expression were induced. Moreover, we observed a decrease in the methylation level and an increase of hydroxymethylation level surrounding the CpG island near the transcription start site of Rab3a. Furthermore, recently, Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) has proven powerful in identifying open chromatin in the genome of various eukaryotes. Using FAIRE-qPCR, we observed a euchromatin state and the increased occupancy of Tet3, H3K4me3, and H3K27ac at the promoter region of Rab3a after KCl treatment. Finally, by using shRNA to knockdown Tet3 prior KCl treatment, all changes mentioned above vanished. Thus, our findings elucidated that the neuronal activity-induced accumulation of hydroxymethylation, which Tet3 mediates, can introduce an active and permissive chromatin structure at Rab3a promoter and lead to the induction of Rab3a mRNA expression.
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Affiliation(s)
- Kun Luo
- The First People's Hospital of Huaihua, Affiliated to University of South China, 418008 Huaihua, Hunan, China
| | - Lesheng Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, Hubei, China
| | - Yulong Shen
- The First People's Hospital of Huaihua, Affiliated to University of South China, 418008 Huaihua, Hunan, China
| | - Shuhua She
- The First People's Hospital of Huaihua, Affiliated to University of South China, 418008 Huaihua, Hunan, China
| | - Yong Cui
- Department of Neurosurgery, Third Affiliated Hospital of Naval Medical University, 200438 Shanghai, China
| | - Kui Liu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, Hubei, China
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Konstantinidis I, Anastasiadi D, Sætrom P, Nedoluzhko AV, Mjelle R, Podgorniak T, Piferrer F, Fernandes JMO. Epigenetic mapping of the somatotropic axis in Nile tilapia reveals differential DNA hydroxymethylation marks associated with growth. Genomics 2021; 113:2953-64. [PMID: 34214627 DOI: 10.1016/j.ygeno.2021.06.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/02/2021] [Accepted: 06/25/2021] [Indexed: 12/29/2022]
Abstract
In vertebrates, the somatotropic axis comprising the pituitary gland, liver and muscle plays a major role in myogenesis. Its output in terms of muscle growth is highly affected by nutritional and environmental cues, and thus likely epigenetically regulated. Hydroxymethylation is emerging as a DNA modification that modulates gene expression but a holistic characterization of the hydroxymethylome of the somatotropic axis has not been investigated to date. Using reduced representation 5-hydroxymethylcytosine profiling we demonstrate tissue-specific localization of 5-hydroxymethylcytosines at single nucleotide resolution. Their abundance within gene bodies and promoters of several growth-related genes supports their pertinent role in gene regulation. We propose that cytosine hydroxymethylation may contribute to the phenotypic plasticity of growth through epigenetic regulation of the somatotropic axis.
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Tiedemann RL, Eden HE, Huang Z, Robertson KD, Rothbart SB. Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays. Methods Mol Biol 2021; 2272:97-140. [PMID: 34009611 DOI: 10.1007/978-1-0716-1294-1_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The 5-carbon positions on cytosine nucleotides preceding guanines in genomic DNA (CpG) are common targets for DNA methylation (5mC). DNA methylation removal can occur through both active and passive mechanisms. Ten-eleven translocation enzymes (TETs) oxidize 5mC in a stepwise manner to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5mC can also be removed passively through sequential cell divisions in the absence of DNA methylation maintenance. In this chapter, we describe approaches that couple TET-assisted bisulfite (TAB) and oxidative bisulfite (OxBS) conversion to the Illumina MethylationEPIC BeadChIP (EPIC array) and show how these technologies can be used to distinguish active versus passive DNA demethylation. We also describe integrative bioinformatics pipelines to facilitate this analysis.
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Affiliation(s)
| | - Hope E Eden
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Zhijun Huang
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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Zupkovitz G, Kabiljo J, Kothmayer M, Schlick K, Schöfer C, Lagger S, Pusch O. Analysis of Methylation Dynamics Reveals a Tissue-Specific, Age-Dependent Decline in 5-Methylcytosine Within the Genome of the Vertebrate Aging Model Nothobranchius furzeri. Front Mol Biosci 2021; 8:627143. [PMID: 34222326 PMCID: PMC8242171 DOI: 10.3389/fmolb.2021.627143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
Erosion of the epigenetic DNA methylation landscape is a widely recognized hallmark of aging. Emerging advances in high throughput sequencing techniques, in particular DNA methylation data analysis, have resulted in the establishment of precise human and murine age prediction tools. In vertebrates, methylation of cytosine at the C5 position of CpG dinucleotides is executed by DNA methyltransferases (DNMTs) whereas the process of enzymatic demethylation is highly dependent on the activity of the ten-eleven translocation methylcytosine dioxygenase (TET) family of enzymes. Here, we report the identification of the key players constituting the DNA methylation machinery in the short-lived teleost aging model Nothobranchius furzeri. We present a comprehensive spatio-temporal expression profile of the methylation-associated enzymes from embryogenesis into late adulthood, thereby covering the complete killifish life cycle. Data mining of the N. furzeri genome produced five dnmt gene family orthologues corresponding to the mammalian DNMTs (DNMT1, 2, 3A, and 3B). Comparable to other teleost species, N. furzeri harbors multiple genomic copies of the de novo DNA methylation subfamily. A related search for the DNMT1 recruitment factor UHRF1 and TET family members resulted in the identification of N. furzeri uhrf1, tet1, tet2, and tet3. Phylogenetic analysis revealed high cross-species similarity on the amino acid level of all individual dnmts, tets, and uhrf1, emphasizing a high degree of functional conservation. During early killifish development all analyzed dnmts and tets showed a similar expression profile characterized by a strong increase in transcript levels after fertilization, peaking either at embryonic day 6 or at the black eye stage of embryonic development. In adult N. furzeri, DNA methylation regulating enzymes showed a ubiquitous tissue distribution. Specifically, we observed an age-dependent downregulation of dnmts, and to some extent uhrf1, which correlated with a significant decrease in global DNA methylation levels in the aging killifish liver and muscle. The age-dependent DNA methylation profile and spatio-temporal expression characteristics of its enzymatic machinery reported here may serve as an essential platform for the identification of an epigenetic aging clock in the new vertebrate model system N. furzeri.
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Affiliation(s)
- Gordin Zupkovitz
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria.,Department of Life Science Engineering, University of Applied Sciences Technikum Wien, Vienna, Austria.,City of Vienna Competence Team Aging Tissue, Vienna, Austria
| | - Julijan Kabiljo
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria.,Department of General Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Michael Kothmayer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Katharina Schlick
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Christian Schöfer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Sabine Lagger
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Oliver Pusch
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
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Chen HQ, Chen DJ, Li Y, Han F, Jiang X, Cao J, Liu JY, Liu WB. DNA methylation and hydroxymethylation associated with gene expression regulatory network during 3-methylcholanthrene induced lung cell malignant transformation. Sci Total Environ 2021; 771:144839. [PMID: 33545462 DOI: 10.1016/j.scitotenv.2020.144839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 12/05/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
3-methylcholanthrene (3-MCA) is a typical representative PAH. It has strong toxicity and is a typical chemical carcinogen. However, the epigenetic mechanisms underlying 3-MCA-induced tumourigenesis are largely unknown. In this study, a model of the 3-MCA-induced malignant transformation of human bronchial epithelial (HBE) cells was established successfully. The profiles of gene expression and DNA methylation and hydroxymethylation were obtained and analysed with an Illumina HiSeq 4000. A total of 707 genes were found to be significantly up-regulated, and 686 genes were found to be significantly down-regulated. Compared to control cells, 8545 mRNA-associated differentially methylated regions and 15,121 mRNA-associated differentially hydroxymethylated regions in promoters were found to be significantly altered in transformed cells. By using mRNA expression and DNA methylation and hydroxymethylation interaction analysis, 99 differentially expressed genes were identified. Among them, CA9 and EGLN3 were verified to be significantly down-regulated, and CARD6 and LCP1 were shown to be significantly up-regulated, and these genes mainly participated in cell growth, migration and invasion, indicating that these genes were key genes involved in the 3-MCA-induced malignant transformation of HBE cells. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that a large number of differentially expressed genes (DEGs) were involved mainly in RNA polymerase II transcription factor activity, chemical carcinogenesis, base-excision repair (BER), cytokine-cytokine receptor interactions, glycerolipid metabolism, steroid hormone biosynthesis, cAMP signalling pathways and other signalling pathways. Our study suggested that characteristic gene alterations associated with DNA methylation and hydroxymethylation could play important roles in environmental 3-MCA-induced lung carcinogenesis.
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Affiliation(s)
- Hong-Qiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Dong-Jiao Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, PR China; College of Public Health and Management, Ningxia Medical University, Yinchuan 750004, PR China
| | - Yan Li
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, PR China; Department of Emergency, Yun Qiao Hospital, Kunming 650224, China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Xiao Jiang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, PR China
| | - Jin-Yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, PR China.
| | - Wen-Bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, PR China.
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Abstract
The persistence of the addiction phenotype in methamphetamine use disorder (MUD) suggests the potential presence of epigenetic changes and potential structural adaptations that may drive the manifestations of MUD in humans. In the present review, we discuss the evidence that documents the fact that methamphetamine exposure can cause changes in epigenetic modifications, including histone acetylation and methylation, as well as DNA methylation and hydroxymethylation in a complex manner that need to be fully dissected. Nevertheless, our work has demonstrated the existence of correlations between behavioral changes and epigenetic alterations during methamphetamine self-administration. We found that prolonged methamphetamine self-administration and contingent footshocks resulted in rats with compulsive drug-taking and abstinent phenotypes. In addition, rats that reduce their methamphetamine intake in the presence of punishment showed increased DNA hydroxymethylation in genes encoding potassium channels in their nucleus accumbens. Moreover, altered DNA hydroxymethylation in those genes led to an increase in their mRNA expression. Additional studies revealed decreased mRNA expression of histone deacetylases associated with increased histone acetylation and induced gene expression in the dorsal striatum. These changes were associated with a reduction in methamphetamine intake in response to contingent footshocks. More research is necessary in order to further dissect how pharmacological or genetic manipulations of identified epigenetic alterations and expression of potassium channels can impact methamphetamine-taking behaviors or relapse to methamphetamine-taking after long periods of abstinence. Investigations that use discovery approaches, such as whole-genome sequencing after chromatin immunoprecipitation, should accelerate our efforts to develop epigenetic therapeutic approaches against MUD.
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Affiliation(s)
- Jean Lud Cadet
- Molecular Neuropsychiatry Research Branch Molecular Neuropsychiatry Section NIH/NIDA Intramural Research Program National Institutes of Health; Baltimore, MD , United States
| | - Subramaniam Jayanthi
- Molecular Neuropsychiatry Research Branch Molecular Neuropsychiatry Section NIH/NIDA Intramural Research Program National Institutes of Health; Baltimore, MD , United States
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38
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Abstract
Substance use disorders are complex biopsychosocial disorders that have substantial negative neurocognitive impact in various patient populations. These diseases involve the compulsive use of licit or illicit substances despite adverse medicolegal consequences and appear to be secondary to long-lasting epigenetic and transcriptional adaptations in brain reward and non-reward circuits. The accumulated evidence supports the notion that repeated drug use causes changes in post-translational histone modifications and in DNA methylation/hydroxymethylation processes in several brain regions. This review provides an overview of epigenetic changes reported in models of cocaine, methamphetamine, and opioid use disorders. The accumulated data suggest that future therapeutic interventions should focus on the development of epigenetic drugs against addictive diseases.
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De Dieuleveult M, Bizet M, Colin L, Calonne E, Bachman M, Li C, Stancheva I, Miotto B, Fuks F, Deplus R. The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome. Epigenetics 2021; 17:422-443. [PMID: 33960278 DOI: 10.1080/15592294.2021.1917152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ten-Eleven Translocation (TET) proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) leading to a dynamic epigenetic state of DNA that can influence transcription and chromatin organization. While TET proteins interact with complexes involved in transcriptional repression and activation, the overall understanding of the molecular mechanisms involved in TET-mediated regulation of gene expression still remains limited. Here, we show that TET proteins interact with the chromatin remodelling protein lymphoid-specific helicase (LSH/HELLS) in vivo and in vitro. In mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESCs) knock out of Lsh leads to a significant reduction of 5-hydroxymethylation amount in the DNA. Whole genome sequencing of 5hmC in wild-type versus Lsh knock-out MEFs and ESCs showed that in absence of Lsh, some regions of the genome gain 5hmC while others lose it, with mild correlation with gene expression changes. We further show that differentially hydroxymethylated regions did not completely overlap with differentially methylated regions indicating that changes in 5hmC distribution upon Lsh knock-out are not a direct consequence of 5mC decrease. Altogether, our results suggest that LSH, which interacts with TET proteins, contributes to the regulation of 5hmC levels and distribution in MEFs and ESCs.
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Affiliation(s)
- Maud De Dieuleveult
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium.,Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Laurence Colin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Martin Bachman
- Medicines Discovery Catapult, Alderley Park, Macclesfield, UK
| | - Chao Li
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Irina Stancheva
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Benoit Miotto
- Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
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Caniçais C, Vasconcelos S, Ramalho C, Marques CJ, Dória S. Deregulation of imprinted genes expression and epigenetic regulators in placental tissue from intrauterine growth restriction. J Assist Reprod Genet 2021; 38:791-801. [PMID: 33389447 PMCID: PMC8079450 DOI: 10.1007/s10815-020-02047-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Intrauterine growth restriction (IUGR) is a fetal growth complication that can be caused by ineffective nutrient transfer from the mother to the fetus via the placenta. Abnormal placental development and function have been correlated with abnormal expression of imprinted genes, which are regulated by epigenetic modifications at imprinting control regions (ICRs). In this study, we analyzed the expression of imprinted genes known to be involved in fetal growth and epigenetic regulators involved in DNA methylation, as well as DNA methylation at the KvDMR1 imprinting control region and global levels of DNA hydroxymethylation, in IUGR cases. METHODS Expression levels of imprinted genes and epigenetic regulators were analyzed in term placental samples from 21 IUGR cases and 9 non-IUGR (control) samples, by RT-qPCR. Additionally, KvDMR1 methylation was analyzed by bisulfite sequencing and combined bisulfite restriction analysis (COBRA) techniques. Moreover, global DNA methylation and hydroxymethylation levels were also measured. RESULTS We observed increased expression of PHLDA2, CDKN1C, and PEG10 imprinted genes and of DNMT1, DNMT3A, DNMT3B, and TET3 epigenetic regulators in IUGR placentas. No differences in methylation levels at the KvDMR1 were observed between the IUGR and control groups; similarly, no differences in global DNA methylation and hydromethylation were detected. CONCLUSION Our study shows that deregulation of epigenetic mechanisms, namely increased expression of imprinted genes and epigenetic regulators, might be associated with IUGR etiology. Therefore, this study adds knowledge to the molecular mechanisms underlying IUGR, which may contribute to novel prediction tools and future therapeutic options for the management of IUGR pregnancies.
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Affiliation(s)
- Carla Caniçais
- Department of Genetics, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal
| | - Sara Vasconcelos
- Department of Genetics, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal
| | - Carla Ramalho
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal
- Department of Obstetrics and Gynecology, Faculty of Medicine, Hospital São João, Porto, Portugal
| | - C Joana Marques
- Department of Genetics, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal.
| | - Sofia Dória
- Department of Genetics, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal.
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41
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Pulczinski JC, Shang Y, Dao T, Limjunyawong N, Sun Q, Mitzner W, Cheng RY, Tang WY. Multigenerational Epigenetic Regulation of Allergic Diseases: Utilizing an Experimental Dust Mite-Induced Asthma Model. Front Genet 2021; 12:624561. [PMID: 33868365 PMCID: PMC8047068 DOI: 10.3389/fgene.2021.624561] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/20/2021] [Indexed: 11/13/2022] Open
Abstract
Environmental exposures have been linked to increased asthma risk, particularly during pregnancy and in early life. Here we use a mouse model of allergic lung disease to examine the effects of pre- and perinatal house dust mite (HDM) allergen exposure on offspring phenotypic and transcriptional outcomes in three generations. We show that maternal HDM exposure (F0) acts synergistically with adult HDM exposure, leading to enhanced airway hyperresponsiveness (AHR) and lung inflammation when compared to mice exposed solely in adulthood. Additionally, a subset of F1 males were not challenged in adulthood, and used to generate F2 progeny, which was then used to generate F3 progeny. Upon adult challenge to HDM, F2, and F3 males generated from the maternal HDM (F0) exposure lineage displayed increased airway reactivity and inflammation when compared to mice exposed solely in adulthood. These findings indicate that maternal allergen exposure is capable of enhancing either susceptibly to or severity of allergic airway disease. To examine the role of epigenetic inheritance of asthma susceptibility induced by maternal HDM exposure, we utilized a genome-wide MeDIP-seq and hMeDIP-seq analysis to identify genes differentially methylated (DMG) and hydroxymethylated (DHG), and their association with the enhanced AHR. In addition, we validated the relationship between DNA methylation and mRNA expression of the DMGs and DHGs in the male sub-generations (F1-F3). We found the expression of Kchn1, Nron, and Spag17 to be differentially hydroxymethylated and upregulated in the F1 exposed to HDM both in early life and in adulthood when compared to F1 mice exposed solely in adulthood. Kcnh1 remained upregulated in the F2 and F3 from the maternal HDM (F0) exposure lineage, when compared to F1 mice exposed solely in adulthood. In summary, we demonstrated that maternal HDM exposure in early life can alter the gene expression and phenotype of offspring upon adult HDM exposure, resulting in more severe disease. These effects persist at least two generations past the initial insult, transmitted along the paternal line.
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Affiliation(s)
- Jairus C Pulczinski
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Yan Shang
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Tyna Dao
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Nathachit Limjunyawong
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Qinying Sun
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Wayne Mitzner
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Robert Ys Cheng
- Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Wan-Yee Tang
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States
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42
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Nikolac Perkovic M, Videtic Paska A, Konjevod M, Kouter K, Svob Strac D, Nedic Erjavec G, Pivac N. Epigenetics of Alzheimer's Disease. Biomolecules 2021; 11:biom11020195. [PMID: 33573255 PMCID: PMC7911414 DOI: 10.3390/biom11020195] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 02/07/2023] Open
Abstract
There are currently no validated biomarkers which can be used to accurately diagnose Alzheimer’s disease (AD) or to distinguish it from other dementia-causing neuropathologies. Moreover, to date, only symptomatic treatments exist for this progressive neurodegenerative disorder. In the search for new, more reliable biomarkers and potential therapeutic options, epigenetic modifications have emerged as important players in the pathogenesis of AD. The aim of the article was to provide a brief overview of the current knowledge regarding the role of epigenetics (including mitoepigenetics) in AD, and the possibility of applying these advances for future AD therapy. Extensive research has suggested an important role of DNA methylation and hydroxymethylation, histone posttranslational modifications, and non-coding RNA regulation (with the emphasis on microRNAs) in the course and development of AD. Recent studies also indicated mitochondrial DNA (mtDNA) as an interesting biomarker of AD, since dysfunctions in the mitochondria and lower mtDNA copy number have been associated with AD pathophysiology. The current evidence suggests that epigenetic changes can be successfully detected, not only in the central nervous system, but also in the cerebrospinal fluid and on the periphery, contributing further to their potential as both biomarkers and therapeutic targets in AD.
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Affiliation(s)
- Matea Nikolac Perkovic
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
| | - Alja Videtic Paska
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.V.P.); (K.K.)
| | - Marcela Konjevod
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
| | - Katarina Kouter
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.V.P.); (K.K.)
| | - Dubravka Svob Strac
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
| | - Gordana Nedic Erjavec
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
| | - Nela Pivac
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
- Correspondence: ; Tel.: +38-514-571-207
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Pomerleau J, Weidmann C, Coutant K, Lowry CM, Veilleux MP, Bérubé J, Wagner JR, Landreville S. Experimental eye research / short communication format characterization of DNA hydroxymethylation in the ocular choroid. Exp Eye Res 2021; 205:108473. [PMID: 33524365 DOI: 10.1016/j.exer.2021.108473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/05/2021] [Accepted: 01/21/2021] [Indexed: 12/11/2022]
Abstract
DNA methylation and hydroxymethylation represent important epigenetic modifications involved in cell differentiation. DNA hydroxymethylation can be used to classify independent biological samples by tissue type. Relatively little is known regarding the genomic abundance and function of 5-hydroxymethylcytosine (5-hmC) in ocular tissues. The choroid supplies oxygen and nutrients to the outer retina through its dense network of blood vessels. This connective tissue is mainly composed of pigmented melanocytes, and stromal fibroblasts. Since DNA hydroxymethylation level is relatively high in cutaneous melanocytes, we investigated the presence of 5-hmC in choroidal melanocytes, as well as the expression of ten-eleven translocation methylcytosine dioxygenases (TETs) and isocitrate dehydrogenases (IDHs) implicated in this DNA demethylation pathway. Immunofluorescence, DNA slot blots and liquid chromatography coupled to tandem mass spectrometry performed with choroidal tissues and melanocytes within these tissues revealed that they have a relatively high level of 5-hmC. We also examined the expression of TET1/2 and IDH1/2 in choroidal melanocytes by gene expression profiling, qPCR and Western blotting. In addition, we detected decreased levels of 5-hmC when choroidal melanocytes were exposed to a lower concentration of oxygen. Our study therefore demonstrates that DNA hydroxymethylation is present in choroidal melanocytes, and that the abundance of this epigenetic mark is impacted by hypoxia.
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Affiliation(s)
- Jade Pomerleau
- Axe Médecine Régénératrice and Centre Universitaire d'Ophtalmologie (CUO)-Recherche, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC, Canada; Département d'Ophtalmologie et ORL-CCF, Faculté de Médecine, Université Laval, Quebec City, QC, Canada; Centre de Recherche en Organogénése Expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
| | - Cindy Weidmann
- Axe Médecine Régénératrice and Centre Universitaire d'Ophtalmologie (CUO)-Recherche, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC, Canada; Département d'Ophtalmologie et ORL-CCF, Faculté de Médecine, Université Laval, Quebec City, QC, Canada; Centre de Recherche en Organogénése Expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Quebec City, QC, Canada
| | - Kelly Coutant
- Axe Médecine Régénératrice and Centre Universitaire d'Ophtalmologie (CUO)-Recherche, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC, Canada; Département d'Ophtalmologie et ORL-CCF, Faculté de Médecine, Université Laval, Quebec City, QC, Canada; Centre de Recherche en Organogénése Expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Quebec City, QC, Canada
| | - Carolyne-Mary Lowry
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Marie-Pier Veilleux
- Axe Médecine Régénératrice and Centre Universitaire d'Ophtalmologie (CUO)-Recherche, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC, Canada; Département d'Ophtalmologie et ORL-CCF, Faculté de Médecine, Université Laval, Quebec City, QC, Canada; Centre de Recherche en Organogénése Expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Quebec City, QC, Canada
| | - Julie Bérubé
- Axe Médecine Régénératrice and Centre Universitaire d'Ophtalmologie (CUO)-Recherche, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC, Canada; Centre de Recherche en Organogénése Expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Quebec City, QC, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Solange Landreville
- Axe Médecine Régénératrice and Centre Universitaire d'Ophtalmologie (CUO)-Recherche, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC, Canada; Département d'Ophtalmologie et ORL-CCF, Faculté de Médecine, Université Laval, Quebec City, QC, Canada; Centre de Recherche en Organogénése Expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Quebec City, QC, Canada.
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Abstract
Simultaneous measurement of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) at the single-nucleotide level can be obtained by combining data from DNA processing methods including traditional bisulfite (BS), oxidative bisulfite (oxBS), or Tet-assisted (TAB) bisulfite conversion. Array-based technologies have been widely used in this task, due to their time and cost efficiency. For methylation studies using BS data, many protocols and related packages have been suggested in the literature to deal with limitations and confounders that arise from array data. In this chapter, we illustrate how the reader can make small adjustments to these protocols to obtain estimates of methylation and hydroxymethylation proportions.
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Abstract
5-Methylcytosine (5mC) is one of the most abundant and well-studied chemical DNA modifications of vertebrate genomes. 5mC plays an essential role in genome regulation including: silencing of retroelements, X chromosome inactivation, and heterochromatin stability. Furthermore, 5mC shapes the activity of cis-regulatory elements crucial for cell fate determination. TET enzymes can oxidize 5mC to form 5-hydroxymethylcytosine (5hmC), thereby adding an additional layer of complexity to the DNA methylation landscape dynamics. The advent of techniques enabling genome-wide 5hmC profiling provided critical insights into its genomic distribution, scope, and function. These methods include immunoprecipitation, chemical labeling and capture-based approaches, as well as single-nucleotide 5hmC profiling techniques such as TET-assisted bisulfite sequencing (TAB-seq) and APOBEC-coupled epigenetic sequencing (ACE-seq). Here we provide a detailed protocol for computational analysis required for the genomic alignment of TAB-seq and ACE-seq data, 5hmC calling, and statistical analysis.
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Shen Y, Zhou S, Zhao X, Li H, Sun J. Characterization of Genome-Wide DNA Methylation and Hydroxymethylation in Mouse Arcuate Nucleus of Hypothalamus During Puberty Process. Front Genet 2021; 11:626536. [PMID: 33381157 PMCID: PMC7768033 DOI: 10.3389/fgene.2020.626536] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Pulsatile pituitary gonadotropin secretion governed by hypothalamic gonadotropin-releasing hormone (GnRH) is essential for the pubertal onset. The epigenetic mechanism underlying the activation of GnRH-dependent regulatory axis in hypothalamus remains elusive. This study aims to explore the potential correlation between the signature of DNA (hydroxyl)methylation and pubertal process. Methods: Hypothalamic arcuate nucleus (ARC) of mouse at early (4-weeks) and late pubertal (8-weeks) stages underwent RNA-, RRBS-, and RRHP-seq to investigate the genome-wide profiles of transcriptome, differential DNA methylation and hydroxymethylation. Results: A series of differential expressed genes (DEGs) involved in sexual development could be separated into three subgroups with the significant difference of DNA methylation or hydroxymethylation or both in promoter regions. Compared to DNA methylation, DNA hydroxymethylation partook in more signaling pathways including synapse morphology, channel activity and glial development, which could enhance transsynaptic change and glia-to-neuron communication to faciliate GnRH release. The correlation between transcription and these epigenetic modifications indicated that DNA hydroxymethylation impacted with gene transcription independently of DNA methylation spanning puberty. Conclusion: Our results characterized the hydroxymethylation pattern and provided an insight into the novel epigenetic regulation on gene expression during pubertal process.
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Affiliation(s)
- Yihang Shen
- Shanghai Center for Systems Biomedicine, Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shasha Zhou
- Department of Endocrinology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaodong Zhao
- Shanghai Center for Systems Biomedicine, Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jielin Sun
- Shanghai Center for Systems Biomedicine, Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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Chen HQ, Chen DJ, Li Y, Yuan WB, Fan J, Zhang Z, Han F, Jiang X, Chen JP, Wang DD, Cao J, Liu JY, Liu WB. Epigenetic silencing of TET1 mediated hydroxymethylation of base excision repair pathway during lung carcinogenesis. Environ Pollut 2021; 268:115860. [PMID: 33120142 DOI: 10.1016/j.envpol.2020.115860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/26/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
The methylcytosine dioxygenase Ten-eleven translocation 1 (TET1) is an important regulator for the balance of DNA methylation and hydroxymethylation through various pathways. Increasing evidence has suggested that TET1 probably involved in DNA methylation and demethylation dysregulation during chemical carcinogenesis. However, the role and mechanism of TET1 during lung cancer remains unclear. In this study, we found that TET1 expression was significantly down-regulated and the methylation level was significantly up-regulated in 3-methylcholanthrene (3-MCA) induced cell malignant transformation model, rat chemical carcinogenesis model, and human lung cancer tissues. Demethylation experiment further confirmed that DNA methylation negatively regulated TET1 gene expression. TET1 overexpression inhibited cell proliferation, migration and invasion in vitro and in vivo, while knockdown of TET1 resulted in an opposite phenotype. DNA hydroxymethylation level in the promoter region of base excision repair (BER) pathway key genes XRCC1, OGG1, APEX1 significantly decreased and the degree of methylation gradually increased in malignant transformed cells. After differential expression of TET1, the level of hydroxymethylation, methylation and expression of these genes also changed significantly. Furthermore, TET1 binds to XRCC1, OGG1, and APEX1 to maintain them hydroxymethylated. Blockade of BER pathway key gene alone or in combination significantly diminished the effect of TET1. Our study demonstrated for the first time that TET1 expression is regulated by DNA methylation and TET1-mediated hydroxymethylation regulates BER pathway to inhibit the proliferation, migration and invasion during 3-MCA-induced lung carcinogenesis. These results suggested that TET1 gene can be a potential biomarker and therapy target for lung cancer.
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Affiliation(s)
- Hong-Qiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Dong-Jiao Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; College of Public Health and Management, Ningxia Medical University, Yinchuan, 750004, PR China
| | - Yan Li
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; Department of Emergency, Yun Qiao Hospital, Kunming, 650224, PR China
| | - Wen-Bo Yuan
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; School of Public Health, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Jun Fan
- Department of Breast and Thyroid Surgery, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, PR China
| | - Zhe Zhang
- Department of Breast and Thyroid Surgery, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, PR China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Xiao Jiang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jian-Ping Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Dan-Dan Wang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jin-Yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Wen-Bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.
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Tobias IC, Kao MMC, Parmentier T, Hunter H, LaMarre J, Betts DH. Targeted expression profiling reveals distinct stages of early canine fibroblast reprogramming are regulated by 2-oxoglutarate hydroxylases. Stem Cell Res Ther 2020; 11:528. [PMID: 33298190 PMCID: PMC7725121 DOI: 10.1186/s13287-020-02047-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Background Ectopic expression of a defined set of transcription factors allows the reprogramming of mammalian somatic cells to pluripotency. Despite continuous progress in primate and rodent reprogramming, limited attention has been paid to cell reprogramming in domestic and companion species. Previous studies attempting to reprogram canine cells have mostly assessed a small number of presumptive canine induced pluripotent stem cell (iPSC) lines for generic pluripotency attributes. However, why canine cell reprogramming remains extremely inefficient is poorly understood. Methods To better characterize the initial steps of pluripotency induction in canine somatic cells, we optimized an experimental system where canine fetal fibroblasts (cFFs) are transduced with the Yamanaka reprogramming factors by Sendai virus vectors. We use quantitative PCR arrays to measure the expression of 80 target genes at various stages of canine cell reprogramming. We ask how cFF reprogramming is influenced by small molecules affecting the epigenomic modification 5-hydroxymethylcytosine, specifically L-ascorbic acid and retinoic acid (AA/RA). Results We found that the expression and catalytic output of a class of 2-oxoglutarate-dependent (2-OG) hydroxylases, known as ten-eleven translocation (TET) enzymes, can be modulated in canine cells treated with AA/RA. We further show that AA/RA treatment induces TET1 expression and facilitates early canine reprogramming, evidenced by upregulation of epithelial and pluripotency markers. Using a chemical inhibitor of 2-OG hydroxylases, we demonstrate that 2-OG hydroxylase activity regulates the expression of a subset of genes involved in mesenchymal-to-epithelial transition (MET) and pluripotency in early canine reprogramming. We identify a set of transcription factors depleted in maturing reprogramming intermediates compared to pluripotent canine embryonic stem cells. Conclusions Our findings highlight 2-OG hydroxylases have evolutionarily conserved and divergent functions regulating the early reprogramming of canine somatic cells and show reprogramming conditions can be rationally optimized for the generation of maturing canine iPSC.
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Affiliation(s)
- Ian C Tobias
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, Dental Sciences Building, Room DSB 2022, London, Ontario, N6A 5C1, Canada.,Present Affiliation: Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Mian-Mian C Kao
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, Dental Sciences Building, Room DSB 2022, London, Ontario, N6A 5C1, Canada
| | - Thomas Parmentier
- Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Hailey Hunter
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, Dental Sciences Building, Room DSB 2022, London, Ontario, N6A 5C1, Canada
| | - Jonathan LaMarre
- Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Dean H Betts
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, Dental Sciences Building, Room DSB 2022, London, Ontario, N6A 5C1, Canada. .,Children's Health Research Institute, Lawson Health Research Institute, London, Ontario, Canada.
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Feng C, Huang X, Li X, Mao J. The Roles of Base Modifications in Kidney Cancer. Front Oncol 2020; 10:580018. [PMID: 33282735 PMCID: PMC7691527 DOI: 10.3389/fonc.2020.580018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/19/2020] [Indexed: 11/26/2022] Open
Abstract
Epigenetic modifications including histone modifications and DNA and RNA modifications are involved in multiple biological processes and human diseases. One disease, kidney cancer, includes a common type of tumor, accounts for about 2% of all cancers, and usually has poor prognosis. The molecular mechanisms and therapeutic strategy of kidney cancer are still under intensive study. Understanding the roles of epigenetic modifications and underlying mechanisms in kidney cancer is critical to its diagnosis and clinical therapy. Recently, the function of DNA and RNA modifications has been uncovered in kidney tumor. In the present review, we summarize recent findings about the roles of epigenetic modifications (particularly DNA and RNA modifications) in the incidence, progression, and metastasis of kidney cancer, especially the renal cell carcinomas.
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Affiliation(s)
- Chunyue Feng
- The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiaoli Huang
- The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China
| | - Xuekun Li
- The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China.,Institute of Translational Medicine of Zhejiang University School of Medicine, Hangzhou, China
| | - Jianhua Mao
- The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China
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Abstract
Objective: This review summarizes recent findings on the epigenetics of Alzheimer's disease (AD) and provides therapeutic strategies for AD. Methods: We searched the following keywords: “genetics,” “epigenetics,” “Alzheimer's disease,” “DNA methylation,” “DNA hydroxymethylation,” “histone modifications,” “non-coding RNAs,” and “therapeutic strategies” in PubMed. Results: In this review, we summarizes recent studies of epigenetics in AD, including DNA methylation/hydroxymethylation, histone modifications, and non-coding RNAs. There are no consistent results of global DNA methylation/hydroxymethylation in AD. Epigenetic genome-wide association studies show that many differentially methylated sites exist in AD. Several studies investigate the role of histone modifications in AD; for example, histone acetylation decreases, whereas H3 phosphorylation increases significantly in AD. In addition, non-coding RNAs, such as microRNA-16 and BACE1-antisense transcript (BACE1-AS), are associated with the pathology of AD. These epigenetic changes provide us with novel insights into the pathogenesis of AD and may be potential therapeutic strategies for AD. Conclusion: Epigenetics is associated with the pathogenesis of AD, including DNA methylation/hydroxymethylation, histone modifications, and non-coding RNAs, which provide potential therapeutic strategies for AD.
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Affiliation(s)
- Xuewen Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xixi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
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