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Lee AV, Nestler KA, Chiappinelli KB. Therapeutic targeting of DNA methylation alterations in cancer. Pharmacol Ther 2024; 258:108640. [PMID: 38570075 DOI: 10.1016/j.pharmthera.2024.108640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
DNA methylation is a critical component of gene regulation and plays an important role in the development of cancer. Hypermethylation of tumor suppressor genes and silencing of DNA repair pathways facilitate uncontrolled cell growth and synergize with oncogenic mutations to perpetuate cancer phenotypes. Additionally, aberrant DNA methylation hinders immune responses crucial for antitumor immunity. Thus, inhibiting dysregulated DNA methylation is a promising cancer therapy. Pharmacologic inhibition of DNA methylation reactivates silenced tumor suppressors and bolster immune responses through induction of viral mimicry. Now, with the advent of immunotherapies and discovery of the immune-modulatory effects of DNA methylation inhibitors, there is great interest in understanding how targeting DNA methylation in combination with other therapies can enhance antitumor immunity. Here, we describe the role of aberrant DNA methylation in cancer and mechanisms by which it promotes tumorigenesis and modulates immune responses. Finally, we review the initial discoveries and ongoing efforts to target DNA methylation as a cancer therapeutic.
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Affiliation(s)
- Abigail V Lee
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Kevin A Nestler
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.
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2
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Wang Q, Ma C, Wang N, Mao H. Effects of quercetin on the DNA methylation pattern in tumor therapy: an updated review. Food Funct 2024; 15:3897-3907. [PMID: 38535893 DOI: 10.1039/d3fo03831a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Quercetin is a unique bioactive flavonoid, and is an excellent antioxidant and has anti-tumor effects by regulating different tumor-related processes like proliferation, apoptosis, invasion, and spread. The latest investigations reveal that quercetin may have the capability to influence DNA methylation modification, one of the primary factors in the development of tumors. Despite the fact that quercetin has significant therapeutic properties, its use as an anti-tumor medicine is constrained by its poor solubility, short half-life, and ineffective tumor targeting. Here, we review the structure and properties of quercetin, its capacity for DNA methylation modification in tumors, and the possibility of nanoscale delivery of quercetin for future tumor treatment.
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Affiliation(s)
- Qin Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China.
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Chen Ma
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China.
| | - Nan Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China.
| | - Huixian Mao
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China.
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3
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Fackler MJ, Pleas M, Li Y, Soni A, Xing D, Cope L, Ali S, Van Le Q, Van Nguyen C, Pham HT, Duong LM, Vanden Berg E, Wadee R, Michelow P, Chen WC, Joffe M, Fjeldbo CS, Lyng H, Sukumar S. Discovery and technical validation of high-performance methylated DNA markers for the detection of cervical lesions at risk of malignant progression in low- and middle-income countries. Clin Epigenetics 2024; 16:56. [PMID: 38643219 PMCID: PMC11032610 DOI: 10.1186/s13148-024-01669-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/04/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Cervical cancer remains a leading cause of death, particularly in developing countries. WHO screening guidelines recommend human papilloma virus (HPV) detection as a means to identify women at risk of developing cervical cancer. While HPV testing identifies those at risk, it does not specifically distinguish individuals with neoplasia. We investigated whether a quantitative molecular test that measures methylated DNA markers could identify high-risk lesions in the cervix with accuracy. RESULTS Marker discovery was performed in TCGA-CESC Infinium Methylation 450 K Array database and verified in three other public datasets. The panel was technically validated using Quantitative Multiplex-Methylation-Specific PCR in tissue sections (N = 252) and cervical smears (N = 244) from the USA, South Africa, and Vietnam. The gene panel consisted of FMN2, EDNRB, ZNF671, TBXT, and MOS. Cervical tissue samples from all three countries showed highly significant differential methylation in squamous cell carcinoma (SCC) with a sensitivity of 100% [95% CI 74.12-100.00], and specificity of 91% [95% CI 62.26-99.53] to 96% [95% CI 79.01-99.78], and receiver operating characteristic area under the curve (ROC AUC) = 1.000 [95% CI 1.00-1.00] compared to benign cervical tissue, and cervical intraepithelial neoplasia 2/3 with sensitivity of 55% [95% CI 37.77-70.84] to 89% [95% CI 67.20-98.03], specificity of 93% [95% CI 84.07-97.38] to 96% [95% CI 79.01-99.78], and a ROC AUC ranging from 0.793 [95% CI 0.68-0.89] to 0.99 [95% CI 0.97-1.00] compared to CIN1. In cervical smears, the marker panel detected SCC with a sensitivity of 87% [95% CI 77.45-92.69], specificity 95% [95% CI 88.64-98.18], and ROC AUC = 0.925 [95% CI 0.878-0.974] compared to normal, and high-grade squamous intraepithelial lesion (HSIL) at a sensitivity of 70% (95% CI 58.11-80.44), specificity of 94% (95% CI 88.30-97.40), and ROC AUC = 0.884 (95% CI 0.822-0.945) compared to low-grade intraepithelial lesion (LSIL)/normal in an analysis of pooled data from the three countries. Similar to HPV-positive, HPV-negative cervical carcinomas were frequently hypermethylated for these markers. CONCLUSIONS This 5-marker panel detected SCC and HSIL in cervical smears with a high level of sensitivity and specificity. Molecular tests with the ability to rapidly detect high-risk HSIL will lead to timely treatment for those in need and prevent unnecessary procedures in women with low-risk lesions throughout the world. Validation of these markers in prospectively collected cervical smear cells followed by the development of a hypermethylated marker-based cervical cancer detection test is warranted.
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Affiliation(s)
- Mary Jo Fackler
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA
| | - Madison Pleas
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA
| | - Youran Li
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA
| | - Anushri Soni
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA
| | - Deyin Xing
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA
| | - Leslie Cope
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA
| | - Syed Ali
- Division of Cytopathology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Quang Van Le
- Hanoi Medical University, National Cancer Hospital, Hanoi, Vietnam
| | - Chu Van Nguyen
- Department of Quansu Pathology, National Cancer Hospital, Hanoi, Vietnam
| | - Han Thi Pham
- Department of Quansu Pathology, National Cancer Hospital, Hanoi, Vietnam
| | - Long Minh Duong
- Department of Quansu Pathology, National Cancer Hospital, Hanoi, Vietnam
| | - Eunice Vanden Berg
- Department of Anatomical Pathology, Faculty of Health Sciences, University of the Witwatersrand/National Health Laboratory Service, Johannesburg, South Africa
| | - Reubina Wadee
- Department of Anatomical Pathology, Faculty of Health Sciences, University of the Witwatersrand/National Health Laboratory Service, Johannesburg, South Africa
| | - Pamela Michelow
- Department of Anatomical Pathology, Faculty of Health Sciences, University of the Witwatersrand/National Health Laboratory Service, Johannesburg, South Africa
| | - Wenlong Carl Chen
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maureen Joffe
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Christina Saetan Fjeldbo
- Department of Radiation Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Heidi Lyng
- Department of Radiation Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Physics, University of Oslo, Oslo, Norway
| | - Saraswati Sukumar
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA.
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Ferro dos Santos MR, Giuili E, De Koker A, Everaert C, De Preter K. Computational deconvolution of DNA methylation data from mixed DNA samples. Brief Bioinform 2024; 25:bbae234. [PMID: 38762790 PMCID: PMC11102637 DOI: 10.1093/bib/bbae234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/30/2024] [Accepted: 04/30/2024] [Indexed: 05/20/2024] Open
Abstract
In this review, we provide a comprehensive overview of the different computational tools that have been published for the deconvolution of bulk DNA methylation (DNAm) data. Here, deconvolution refers to the estimation of cell-type proportions that constitute a mixed sample. The paper reviews and compares 25 deconvolution methods (supervised, unsupervised or hybrid) developed between 2012 and 2023 and compares the strengths and limitations of each approach. Moreover, in this study, we describe the impact of the platform used for the generation of methylation data (including microarrays and sequencing), the applied data pre-processing steps and the used reference dataset on the deconvolution performance. Next to reference-based methods, we also examine methods that require only partial reference datasets or require no reference set at all. In this review, we provide guidelines for the use of specific methods dependent on the DNA methylation data type and data availability.
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Affiliation(s)
- Maísa R Ferro dos Santos
- VIB-UGent Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Zwijnaarde, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Edoardo Giuili
- VIB-UGent Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Zwijnaarde, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Andries De Koker
- VIB-UGent Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Zwijnaarde, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Celine Everaert
- VIB-UGent Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Zwijnaarde, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Katleen De Preter
- VIB-UGent Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Zwijnaarde, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
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Wang M, Bissonnette N, Laterrière M, Dudemaine PL, Gagné D, Roy JP, Sirard MA, Ibeagha-Awemu EM. DNA methylation haplotype block signatures responding to Staphylococcus aureus subclinical mastitis and association with production and health traits. BMC Biol 2024; 22:65. [PMID: 38486242 PMCID: PMC10941392 DOI: 10.1186/s12915-024-01843-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND DNA methylation has been documented to play vital roles in diseases and biological processes. In bovine, little is known about the regulatory roles of DNA methylation alterations on production and health traits, including mastitis. RESULTS Here, we employed whole-genome DNA methylation sequencing to profile the DNA methylation patterns of milk somatic cells from sixteen cows with naturally occurring Staphylococcus aureus (S. aureus) subclinical mastitis and ten healthy control cows. We observed abundant DNA methylation alterations, including 3,356,456 differentially methylated cytosines and 153,783 differential methylation haplotype blocks (dMHBs). The DNA methylation in regulatory regions, including promoters, first exons and first introns, showed global significant negative correlations with gene expression status. We identified 6435 dMHBs located in the regulatory regions of differentially expressed genes and significantly correlated with their corresponding genes, revealing their potential effects on transcriptional activities. Genes harboring DNA methylation alterations were significantly enriched in multiple immune- and disease-related pathways, suggesting the involvement of DNA methylation in regulating host responses to S. aureus subclinical mastitis. In addition, we found nine discriminant signatures (differentiates cows with S. aureus subclinical mastitis from healthy cows) representing the majority of the DNA methylation variations related to S. aureus subclinical mastitis. Validation of seven dMHBs in 200 cows indicated significant associations with mammary gland health (SCC and SCS) and milk production performance (milk yield). CONCLUSIONS In conclusion, our findings revealed abundant DNA methylation alterations in milk somatic cells that may be involved in regulating mammary gland defense against S. aureus infection. Particularly noteworthy is the identification of seven dMHBs showing significant associations with mammary gland health, underscoring their potential as promising epigenetic biomarkers. Overall, our findings on DNA methylation alterations offer novel insights into the regulatory mechanisms of bovine subclinical mastitis, providing further avenues for the development of effective control measures.
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Affiliation(s)
- Mengqi Wang
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Mario Laterrière
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Pier-Luc Dudemaine
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - David Gagné
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Jean-Philippe Roy
- Department of Clinical Sciences, Université de Montréal, St-Hyacinthe, QC, Canada
| | | | - Eveline M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada.
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Rashidiani S, Mamo G, Farkas B, Szabadi A, Farkas B, Uszkai V, Császár A, Brandt B, Kovács K, Pap M, Rauch TA. Integrative Epigenetic and Molecular Analysis Reveals a Novel Promoter for a New Isoform of the Transcription Factor TEAD4. Int J Mol Sci 2024; 25:2223. [PMID: 38396900 PMCID: PMC10888684 DOI: 10.3390/ijms25042223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
TEAD4 is a transcription factor that plays a crucial role in the Hippo pathway by regulating the expression of genes related to proliferation and apoptosis. It is also involved in the maintenance and differentiation of the trophectoderm during pre- and post-implantation embryonic development. An alternative promoter for the TEAD4 gene was identified through epigenetic profile analysis, and a new transcript from the intronic region of TEAD4 was discovered using the 5'RACE method. The transcript of the novel promoter encodes a TEAD4 isoform (TEAD4-ΔN) that lacks the DNA-binding domain but retains the C-terminal protein-protein interaction domain. Gene expression studies, including end-point PCR and Western blotting, showed that full-length TEAD4 was present in all investigated tissues. However, TEAD4-ΔN was only detectable in certain cell types. The TEAD4-ΔN promoter is conserved throughout evolution and demonstrates transcriptional activity in transient-expression experiments. Our study reveals that TEAD4 interacts with the alternative promoter and increases the expression of the truncated isoform. DNA methylation plays a crucial function in the restricted expression of the TEAD4-ΔN isoform in specific tissues, including the umbilical cord and the placenta. The data presented indicate that the DNA-methylation status of the TEAD4-ΔN promoter plays a critical role in regulating organ size, cancer development, and placenta differentiation.
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Affiliation(s)
- Shima Rashidiani
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary; (S.R.); (G.M.); (B.F.); (A.S.)
| | - Gizaw Mamo
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary; (S.R.); (G.M.); (B.F.); (A.S.)
| | - Benjámin Farkas
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary; (S.R.); (G.M.); (B.F.); (A.S.)
| | - András Szabadi
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary; (S.R.); (G.M.); (B.F.); (A.S.)
- Department of Dentistry, Oral and Maxillofacial Surgery, Medical School, University of Pécs, 7623 Pécs, Hungary
| | - Bálint Farkas
- Department of Obstetrics and Gynecology, Medical School, University of Pécs, 7624 Pécs, Hungary; (B.F.); (V.U.); (A.C.)
- National Laboratory of Human Reproduction, University of Pécs, 7624 Pécs, Hungary
| | - Veronika Uszkai
- Department of Obstetrics and Gynecology, Medical School, University of Pécs, 7624 Pécs, Hungary; (B.F.); (V.U.); (A.C.)
| | - András Császár
- Department of Obstetrics and Gynecology, Medical School, University of Pécs, 7624 Pécs, Hungary; (B.F.); (V.U.); (A.C.)
| | - Barbara Brandt
- Department of Medical Biology and Central Electron Microscope Laboratory, Medical School, University of Pécs, 7624 Pécs, Hungary (M.P.)
| | - Kálmán Kovács
- Department of Obstetrics and Gynecology, Medical School, University of Pécs, 7624 Pécs, Hungary; (B.F.); (V.U.); (A.C.)
- National Laboratory of Human Reproduction, University of Pécs, 7624 Pécs, Hungary
| | - Marianna Pap
- Department of Medical Biology and Central Electron Microscope Laboratory, Medical School, University of Pécs, 7624 Pécs, Hungary (M.P.)
| | - Tibor A. Rauch
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary; (S.R.); (G.M.); (B.F.); (A.S.)
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Song XQ, Chen BB, Jin YM, Wang CY. DNMT1-mediated epigenetic suppression of FBXO32 expression promoting cyclin dependent kinase 9 (CDK9) survival and esophageal cancer cell growth. Cell Cycle 2024; 23:262-278. [PMID: 38597826 PMCID: PMC11057636 DOI: 10.1080/15384101.2024.2309022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/25/2023] [Indexed: 04/11/2024] Open
Abstract
Esophageal cancer (EC) is a common and serious form of cancer, and while DNA methyltransferase-1 (DNMT1) promotes DNA methylation and carcinogenesis, the role of F-box protein 32 (FBXO32) in EC and its regulation by DNMT1-mediated methylation is still unclear. FBXO32 expression was examined in EC cells with high DNMT1 expression using GSE163735 dataset. RT-qPCR assessed FBXO32 expression in normal and EC cells, and impact of higher FBXO32 expression on cell proliferation, migration, and invasion was evaluated, along with EMT-related proteins. The xenograft model established by injecting EC cells transfected with FBXO32 was used to evaluate tumor growth, apoptosis, and tumor cells proliferation and metastasis. Chromatin immunoprecipitation (ChIP) assay was employed to study the interaction between DNMT1 and FBXO32. HitPredict, co-immunoprecipitation (Co-IP), and Glutathione-S-transferase (GST) pulldown assay analyzed the interaction between FBXO32 and cyclin dependent kinase 9 (CDK9). Finally, the ubiquitination assay identified CDK9 ubiquitination, and its half-life was measured using cycloheximide and confirmed through western blotting. DNMT1 negatively correlated with FBXO32 expression in esophageal cells. High FBXO32 expression was associated with better overall survival in patients. Knockdown of DNMT1 in EC cells increased FBXO32 expression and suppressed malignant phenotypes. FBXO32 repressed EC tumor growth and metastasis in mice. Enrichment of DNMT1 in FBXO32 promoter region led to increased DNA methylation and reduced transcription. Mechanistically, FBXO32 degraded CDK9 through promoting its ubiquitination.
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Affiliation(s)
- Xian-Qiang Song
- Department of Radiotherapy, Qinhuai Medical District, General Hospital of Eastern Theater Command, Nanjing, PR China
| | - Bin-Bin Chen
- Departments of Laboratory Medicine, Qinhuai Medical District, General Hospital of Eastern Theater Command, Nanjing, PR China
| | - Yong-Mei Jin
- Department of Cardiothoracic Surgery, Qinhuai Medical District, General Hospital of Eastern Theater Command, Nanjing, PR China
| | - Chang-Yong Wang
- Department of Cardiothoracic Surgery, Qinhuai Medical District, General Hospital of Eastern Theater Command, Nanjing, PR China
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Legault LM, Breton-Larrivée M, Langford-Avelar A, Lemieux A, McGraw S. Sex-based disparities in DNA methylation and gene expression in late-gestation mouse placentas. Biol Sex Differ 2024; 15:2. [PMID: 38183126 PMCID: PMC10770955 DOI: 10.1186/s13293-023-00577-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND The placenta is vital for fetal development and its contributions to various developmental issues, such as pregnancy complications, fetal growth restriction, and maternal exposure, have been extensively studied in mice. The placenta forms mainly from fetal tissue and therefore has the same biological sex as the fetus it supports. Extensive research has delved into the placenta's involvement in pregnancy complications and future offspring development, with a notable emphasis on exploring sex-specific disparities. However, despite these investigations, sex-based disparities in epigenetic (e.g., DNA methylation) and transcriptomic features of the late-gestation mouse placenta remain largely unknown. METHODS We collected male and female mouse placentas at late gestation (E18.5, n = 3/sex) and performed next-generation sequencing to identify genome-wide sex differences in transcription and DNA methylation. RESULTS Our comparison between male and female revealed 358 differentially expressed genes (DEGs) on autosomes, which were associated with signaling pathways involved in transmembrane transport and the responses to viruses and external stimuli. X chromosome DEGs (n = 39) were associated with different pathways, including those regulating chromatin modification and small GTPase-mediated signal transduction. Differentially methylated regions (DMRs) were more common on the X chromosomes (n = 3756) than on autosomes (n = 1705). Interestingly, while most X chromosome DMRs had higher DNA methylation levels in female placentas and tended to be included in CpG dinucleotide-rich regions, 73% of autosomal DMRs had higher methylation levels in male placentas and were distant from CpG-rich regions. Several DEGs were correlated with DMRs. A subset of the DMRs present in late-stage placentas were already established in mid-gestation (E10.5) placentas (n = 348 DMRs on X chromosome and 19 DMRs on autosomes), while others were acquired later in placental development. CONCLUSION Our study provides comprehensive lists of DEGs and DMRs between male and female that collectively cause profound differences in the DNA methylation and gene expression profiles of late-gestation mouse placentas. Our results demonstrate the importance of incorporating sex-specific analyses into epigenetic and transcription studies to enhance the accuracy and comprehensiveness of their conclusions and help address the significant knowledge gap regarding how sex differences influence placental function.
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Affiliation(s)
- Lisa-Marie Legault
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Mélanie Breton-Larrivée
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Alexandra Langford-Avelar
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Anthony Lemieux
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Serge McGraw
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada.
- Department of Obstetrics and Gynecology, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada.
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9
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Lin YZ, Liu WH, Wu YP, Cai H, Zheng QS, Wei Y, Xu N, Xue XY. Revealing the potential of solute carrier family 31 (copper transporters), member 1: Insights into its role in bladder cancer progression and therapeutic implications. Int J Immunopathol Pharmacol 2024; 38:3946320241240706. [PMID: 38712735 PMCID: PMC11080779 DOI: 10.1177/03946320241240706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/26/2024] [Indexed: 05/08/2024] Open
Abstract
Introduction: Bladder cancer represents a significant public health concern with diverse genetic alterations influencing disease onset, progression, and therapy response. In this study, we explore the multifaceted role of Solute Carrier Family 31 Member 1 (SLC31A1) in bladder cancer, a pivotal gene involved in copper homeostasis. Methods: Our research involved analyzing the SLC31A1 gene expression via RT-qPCR, promoter methylation via targeted bisulfite sequencing, and mutational status via Next Generation Sequencing (NGS) using the clinical samples sourced by the local bladder cancer patients. Later on, The Cancer Genome Atlas (TCGA) datasets were utilized for validation purposes. Moreover, prognostic significance, gene enrichment terms, and therapeutic drugs of SLC31A1 were also explored using KM Plotter, DAVID, and DrugBank databases. Results: We observed that SLC31A1 was significantly up-regulated at both the mRNA and protein levels in bladder cancer tissue samples, suggesting its potential involvement in bladder cancer development and progression. Furthermore, our investigation into the methylation status revealed that SLC31A1 was significantly hypomethylated in bladder cancer tissues, which may contribute to its overexpression. The ROC analysis of the SLC31A1 gene indicated promising diagnostic potential, emphasizing its relevance in distinguishing bladder cancer patients from normal individuals. However, it is crucial to consider other factors such as cancer stage, metastasis, and recurrence for a more accurate evaluation in the clinical context. Interestingly, mutational analysis of SLC31A1 demonstrated only benign mutations, indicating their unknown role in the SLC31A1 disruption. In addition to its diagnostic value, high SLC31A1 expression was associated with poorer overall survival (OS) in bladder cancer patients, shedding light on its prognostic relevance. Gene enrichment analysis indicated that SLC31A1 could influence metabolic and copper-related processes, further underscoring its role in bladder cancer. Lastly, we explored the DrugBank database to identify potential therapeutic agents capable of reducing SLC31A1 expression. Our findings unveiled six important drugs with the potential to target SLC31A1 as a treatment strategy. Conclusion: Our comprehensive investigation highlights SLC31A1 as a promising biomarker for bladder cancer development, progression, and therapy.
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Affiliation(s)
- Yun-Zhi Lin
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wei-hui Liu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yu-Peng Wu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Hai Cai
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Qing-Shui Zheng
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yong Wei
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ning Xu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xue-Yi Xue
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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10
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Kodosaki E, Daniels-Morgan A, Hassan N, Webb R, Morris K, Kelly CM. Development and characterisation of mgTHP-1, a novel in vitro model for neural macrophages with microglial characteristics. Neurol Res 2024; 46:1-13. [PMID: 37935114 DOI: 10.1080/01616412.2023.2257422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/23/2023] [Indexed: 11/09/2023]
Abstract
Neuroinflammation is primarily characterised by activation of the brain's resident macrophages - the microglia. However, other central nervous system (CNS) cells also contribute to this response, including the astrocytes and endothelial cells. In addition, there is infiltration into the CNS of peripherally derived immune cells. Together these cells mediate inflammation by the production of cytokines, chemokines, reactive oxygen species, and secondary messengers, and enacting of the appropriate response to those signals. However, deciphering the specific contributions of each cell type has been challenging. Studying CNS cell biology is often challenging, as the isolation of primary cells is not always feasible, and differentiation towards microglia-like cells is complex. Here, we demonstrate a novel method whereby THP-1 monocytic cells are differentiated into neural macrophage cells with microglia-like cell characteristics. The cells, designated mgTHP-1, show typical morphological and gene expression patterns of resident CNS macrophages and functionally respond to inflammatory stimuli by producing inflammatory cytokines. Furthermore, with the addition of Vicenin-2 (an anti-inflammatory flavonoid) such responses can be reversed. This novel cell model will allow further investigations, and hence insights, into the neuroinflammatory mechanisms associated with CNS diseases.
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Affiliation(s)
- E Kodosaki
- Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff, UK
| | - A Daniels-Morgan
- Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff, UK
| | - N Hassan
- Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff, UK
| | - R Webb
- Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff, UK
| | - K Morris
- Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff, UK
| | - C M Kelly
- Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff, UK
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11
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Yu Z, Wang G, Song S, Zhang Y, Wu Y, Zhang Y, Duan W, Liu X. Associations between the proliferation of palatal mesenchymal cells, Tgfβ2 promoter methylation, Meg3 expression, and Smad signaling in atRA-induced cleft palate. Reprod Toxicol 2023; 122:108486. [PMID: 37866657 DOI: 10.1016/j.reprotox.2023.108486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023]
Abstract
All-trans retinoic acid (atRA) is a teratogen that can induce cleft palate formation. During palatal development, murine embryonic palate mesenchymal (MEPM) cell proliferation is required for the appropriate development of the palatal frame, with Meg3 serving as a key regulator of the proliferative activity of these cells and the associated epithelial-mesenchymal transition process. DNA methylation and signaling via the TGFβ/Smad pathway are key in regulating embryonic development. Here, the impact of atRA on MEPM cell proliferation and associations between Tgfβ2 promoter methylation, Meg3, and signaling via the Smad pathway were explored using C57BL/6 N mice treated with atRA (100 mg/kg) to induce fetal cleft palate formation. Immunohistochemistry and BrdU assays were used to detect MEPM proliferation and DNA methylation assays were performed to detect Tgfβ2 promoter expression. These analyses revealed that atRA suppressed MEPM cell proliferation, promoted the upregulation of Meg3, and reduced the levels of Smad2 and Tgfβ2 expression phosphorylation, whereas Tgfβ2 promoter methylation was unaffected. RNA immunoprecipitation experiments indicated that the TgfβI receptor is directly targeted by Meg3, suggesting that the ability of atRA to induce cleft palate may be mediated through the Tgfβ/Smad signaling pathway.
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Affiliation(s)
- Zengli Yu
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China; School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Guoxu Wang
- School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuaixing Song
- School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yaxin Zhang
- School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yang Wu
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Yuwei Zhang
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Wenjing Duan
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Xiaozhuan Liu
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China.
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12
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Mozhui K, Kim H, Villani F, Haghani A, Sen S, Horvath S. Pleiotropic influence of DNA methylation QTLs on physiological and ageing traits. Epigenetics 2023; 18:2252631. [PMID: 37691384 PMCID: PMC10496549 DOI: 10.1080/15592294.2023.2252631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/31/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is influenced by genetic and non-genetic factors. Here, we chart quantitative trait loci (QTLs) that modulate levels of methylation at highly conserved CpGs using liver methylome data from mouse strains belonging to the BXD family. A regulatory hotspot on chromosome 5 had the highest density of trans-acting methylation QTLs (trans-meQTLs) associated with multiple distant CpGs. We refer to this locus as meQTL.5a. Trans-modulated CpGs showed age-dependent changes and were enriched in developmental genes, including several members of the MODY pathway (maturity onset diabetes of the young). The joint modulation by genotype and ageing resulted in a more 'aged methylome' for BXD strains that inherited the DBA/2J parental allele at meQTL.5a. Further, several gene expression traits, body weight, and lipid levels mapped to meQTL.5a, and there was a modest linkage with lifespan. DNA binding motif and protein-protein interaction enrichment analyses identified the hepatic nuclear factor, Hnf1a (MODY3 gene in humans), as a strong candidate. The pleiotropic effects of meQTL.5a could contribute to variations in body size and metabolic traits, and influence CpG methylation and epigenetic ageing that could have an impact on lifespan.
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Affiliation(s)
- Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hyeonju Kim
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
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13
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Zhang P, Lu Y, Li Y, Wang K, An H, Tan Y. Genome-wide DNA methylation analysis in schizophrenia with tardive dyskinesia: a preliminary study. Genes Genomics 2023; 45:1317-1328. [PMID: 37414911 DOI: 10.1007/s13258-023-01414-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Tardive dyskinesia (TD) develops in 20-30% of schizophrenia patients and up to 50% in patients > 50 years old. DNA methylation may play an important role in the development of TD. OBJECTIVE DNA methylation analyses in schizophrenia with TD. METHODS We conducted a genome-wide DNA methylation analysis in schizophrenia with TD using methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-Seq) in a Chinese sample including five schizophrenia patients with TD and five without TD (NTD), and five healthy controls. The results were expressed as the log2FC, fold change of normalized tags between two groups within the differentially methylated region (DMR). For validation, the pyrosequencing was used to quantify DNA methylation levels of several methylated genes in an independent sample (n = 30). RESULTS Through genome-wide MeDIP-Seq analysis, we identified 116 genes that were significantly differentially methylated in promotor regions in comparison of TD group with NTD group including 66 hypermethylated genes (top 4 genes are GABRR1, VANGL2, ZNF534, and ZNF746) and 50 hypomethylated genes (top 4 genes are DERL3, GSTA4, KNCN, and LRRK1). Part of these genes (such as DERL3, DLGAP2, GABRR1, KLRG2, LRRK1, VANGL2, and ZP3) were previously reported to be associated with methylation in schizophrenia. Gene Ontology enrichment and KEGG pathway analyses identified several pathways. So far, we have confirmed the methylation of 3 genes (ARMC6, WDR75, and ZP3) in schizophrenia with TD using pyrosequencing. CONCLUSIONS This study identified number of methylated genes and pathways for TD and will provide potential biomarkers for TD and serve as a resource for replication in other populations.
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Affiliation(s)
- Ping Zhang
- Beijing HuiLongGuan Hospital, Peking University HuiLongGuan Clinical Medical School, Beijing, 100096, China
| | - Yongke Lu
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, 25755, USA
| | - Yanli Li
- Beijing HuiLongGuan Hospital, Peking University HuiLongGuan Clinical Medical School, Beijing, 100096, China
| | - Kesheng Wang
- Department of Family and Community Health, School of Nursing, Health Sciences Center, West Virginia University, Office 6419, Post Office Box 9600, Morgantown, WV, 26506, USA.
| | - Huimei An
- Beijing HuiLongGuan Hospital, Peking University HuiLongGuan Clinical Medical School, Beijing, 100096, China
| | - Yunlong Tan
- Beijing HuiLongGuan Hospital, Peking University HuiLongGuan Clinical Medical School, Beijing, 100096, China.
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14
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Fang H, Peng Z, Tan B, Peng N, Li B, He D, Xu M, Yang Z. The involvement of PDIA2 gene in the progression of renal cell carcinoma is potentially through regulation of JNK signaling pathway. Clin Transl Oncol 2023; 25:2938-2949. [PMID: 37017923 DOI: 10.1007/s12094-023-03158-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/16/2023] [Indexed: 04/06/2023]
Abstract
Renal cell carcinoma (RCC) with poor prognosis and high incidence rate is a common malignant disease. Current therapies could bring little benefit for the patients with advanced-stage RCC. PDIA2 is an isomerase responsible for protein folding and its role in cancer including RCC is under investigation. In this study, we found that PDIA2 was expressed much higher in RCC tissues than the control but the methylation level of PDIA2 promoter was lower based on the TCGA data. Patients with higher PDIA2 expression exerted worse survival. In clinical specimen, PDIA2 expression was correlated to patients' clinical factors such as TNM stage (I/II vs III/IV, p = 0.025) and tumor size (≤ 7 cm vs > 7 cm, p = 0.004). Moreover, K-M analysis showed that PDIA2 was associated with patients' survival in RCC. PDIA2 was expressed much higher in cancer cells A498 than 786-O than that in 293 T cells. After PDIA2 was knocked down, cell proliferation, migration and invasion was potently inhibited. But cell apoptotic rate increased reversely. Furthermore, the efficacy of Sunitinib on RCC cells was strengthened after PDIA2 knockdown. In addition, knockdown of PDIA2 gene leaded to downregulation of levels of JNK1/2, phosphorylated JNK1/2, c-JUN, and Stat3. But this inhibition was partially released when JNK1/2 was overexpressed. In consistent, cell proliferation was also partially recovered. In summary, PDIA2 plays important role in progression of RCC and JNK signaling pathway might be regulated by PDIA2. This study suggests PDIA2 as a candidate target for therapy of RCC.
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Affiliation(s)
- Huilong Fang
- School of Basic Medical Sciences, Xiangnan University, Street Chenzhou No. 889, Chenzhou, 423000, China
| | - Zhonglu Peng
- School of Basic Medical Sciences, Xiangnan University, Street Chenzhou No. 889, Chenzhou, 423000, China
| | - Bin Tan
- School of Basic Medical Sciences, Xiangnan University, Street Chenzhou No. 889, Chenzhou, 423000, China
| | - Nan Peng
- School of Basic Medical Sciences, Xiangnan University, Street Chenzhou No. 889, Chenzhou, 423000, China
| | - Biao Li
- School of Basic Medical Sciences, Xiangnan University, Street Chenzhou No. 889, Chenzhou, 423000, China
| | - Dongyang He
- School of Basic Medical Sciences, Xiangnan University, Street Chenzhou No. 889, Chenzhou, 423000, China.
| | - Mingjie Xu
- Medical Research and Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong First Medical University and Shandong Academy of Medical Sciences, 105 Jiefang Road, Jinan, Shandong, 250013, People's Republic of China.
| | - Zhiying Yang
- School of Basic Medical Sciences, Xiangnan University, Street Chenzhou No. 889, Chenzhou, 423000, China.
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15
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Bogan SN, Strader ME, Hofmann GE. Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity. BMC Biol 2023; 21:149. [PMID: 37365578 DOI: 10.1186/s12915-023-01645-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Epigenetic processes are proposed to be a mechanism regulating gene expression during phenotypic plasticity. However, environmentally induced changes in DNA methylation exhibit little-to-no association with differential gene expression in metazoans at a transcriptome-wide level. It remains unexplored whether associations between environmentally induced differential methylation and expression are contingent upon other epigenomic processes such as chromatin accessibility. We quantified methylation and gene expression in larvae of the purple sea urchin Strongylocentrotus purpuratus exposed to different ecologically relevant conditions during gametogenesis (maternal conditioning) and modeled changes in gene expression and splicing resulting from maternal conditioning as functions of differential methylation, incorporating covariates for genomic features and chromatin accessibility. We detected significant interactions between differential methylation, chromatin accessibility, and genic feature type associated with differential expression and splicing. RESULTS Differential gene body methylation had significantly stronger effects on expression among genes with poorly accessible transcriptional start sites while baseline transcript abundance influenced the direction of this effect. Transcriptional responses to maternal conditioning were 4-13 × more likely when accounting for interactions between methylation and chromatin accessibility, demonstrating that the relationship between differential methylation and gene regulation is partially explained by chromatin state. CONCLUSIONS DNA methylation likely possesses multiple associations with gene regulation during transgenerational plasticity in S. purpuratus and potentially other metazoans, but its effects are dependent on chromatin accessibility and underlying genic features.
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Affiliation(s)
- Samuel N Bogan
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA.
| | - Marie E Strader
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA
- Department of Biology, Texas A&M University, College Station, USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA
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16
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Okano LM, Fonseca LMMD, Erthal ID, Malta TM. Epigenomic integrative analysis pinpoint master regulator transcription factors associated with tumorigenesis in squamous cell carcinoma of oral tongue. Genet Mol Biol 2023; 46:e20220358. [PMID: 37338302 DOI: 10.1590/1678-4685-gmb-2022-0358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/04/2023] [Indexed: 06/21/2023] Open
Abstract
Head and Neck Cancer (HNC) is a heterogeneous group of cancers, which includes cancers arising in the oral cavity, nasopharynx, oropharynx, hypopharynx, and larynx. Epidemiological studies have revealed that several factors such as tobacco and alcohol use, exposure to environmental pollutants, viral infection, and genetic factors are risk factors for developing HNC. The squamous cell carcinoma of oral tongue (SCCOT), which is significantly more aggressive than the other forms of oral squamous cell carcinoma, presents a propensity for rapid local invasion and spread, and a high recurrence rate. Dysregulation in the epigenetic machinery of cancer cells might help uncover the mechanisms of SCOOT tumorigenesis. Here, we used DNA methylation changes to identify cancer-specific enhancers that were enriched for specific transcription factor binding sites (TFBS), and potential master regulator transcription factors (MRTF) associated with SCCOT. We identified the activation of MRTFs associated with increased invasiveness, metastasis, epithelial-to-mesenchymal transition, poor prognosis, and stemness. On the other hand, we found the downregulation of MRTFs associated with tumor suppression. The identified MRTFs should be further investigated to clarify their role in oral cancer tumorigenesis and for their potential use as biological markers.
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Affiliation(s)
- Larissa Miyuki Okano
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | - Isabela Dias Erthal
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Tathiane Maistro Malta
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Ribeirão Preto, SP, Brazil
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17
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Uribe-Etxebarria V, Pineda JR, García-Gallastegi P, Agliano A, Unda F, Ibarretxe G. Notch and Wnt Signaling Modulation to Enhance DPSC Stemness and Therapeutic Potential. Int J Mol Sci 2023; 24:ijms24087389. [PMID: 37108549 PMCID: PMC10138690 DOI: 10.3390/ijms24087389] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/16/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
The Dental Pulp of permanent human teeth is home to stem cells with remarkable multilineage differentiation ability: human Dental Pulp Stem Cells (DPSCs). These cells display a very notorious expression of pluripotency core factors, and the ability to give rise to mature cell lineages belonging to the three embryonic layers. For these reasons, several researchers in the field have long considered human DPSCs as pluripotent-like cells. Notably, some signaling pathways such as Notch and Wnt contribute to maintaining the stemness of these cells through a complex network involving metabolic and epigenetic regulatory mechanisms. The use of recombinant proteins and selective pharmacological modulators of Notch and Wnt pathways, together with serum-free media and appropriate scaffolds that allow the maintenance of the non-differentiated state of hDPSC cultures could be an interesting approach to optimize the potency of these stem cells, without a need for genetic modification. In this review, we describe and integrate findings that shed light on the mechanisms responsible for stemness maintenance of hDPSCs, and how these are regulated by Notch/Wnt activation, drawing some interesting parallelisms with pluripotent stem cells. We summarize previous work on the stem cell field that includes interactions between epigenetics, metabolic regulations, and pluripotency core factor expression in hDPSCs and other stem cell types.
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Affiliation(s)
| | - Jose Ramon Pineda
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Achucarro Basque Center for Neuroscience Fundazioa Leioa, Sede Building, 3rd Floor, 48940 Leioa, Spain
| | - Patricia García-Gallastegi
- Physiology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Alice Agliano
- Division of Radiotherapy and Imaging, Cancer Research UK Cancer Imaging Centre, The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, London SW7 3RP, UK
- Department of Materials and Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Fernando Unda
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Gaskon Ibarretxe
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
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18
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Zhang F, Niu L, Zhong R, Li S, Le W. Chronic Sleep Disturbances Alters Sleep Structure and Tau Phosphorylation in AβPP/PS1 AD Mice and Their Wild-Type Littermates. J Alzheimers Dis 2023; 92:1341-1355. [PMID: 37038814 DOI: 10.3233/jad-221048] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Background: Emerging evidence indicates that sleep disorders are the common non-cognitive symptoms of Alzheimer’s disease (AD), and they may contribute to the pathogenesis of this disease. Objective: In this study, we aim to investigate the effect of chronic sleep deprivation (CSD) on AD-related pathologies with a focus on tau phosphorylation and the underlying DNA methylation regulation. Methods: AβPPswe/PS1ΔE9 AD mice and their wild-type (WT) littermates were subjected to a two-month CSD followed by electroencephalography and electromyography recording. The mice were examined for learning and memory evaluation, then pathological, biochemical, and epigenetic assessments including western blotting, immunofluorescence, dot blotting, and bisulfite sequencing. Results: The results show that CSD caused sleep disorders shown as sleep pattern change, poor sleep maintenance, and increased sleep fragmentation. CSD increased tau phosphorylation at different sites and increased the level of tau kinases in AD and WT mice. The increased expression of cyclin-dependent kinase 5 (CDK5) may result from decreased DNA methylation of CpG sites in the promoter region of CDK5 gene, which might be associated with the downregulation of DNA methyltransferase 3A and 3B. Conclusion: CSD altered AD-related tau phosphorylation through epigenetic modification of tau kinase gene. The findings in this study may give insights into the mechanisms underlying the effects of sleep disorders on AD pathology and provide new therapeutic targets for the treatment of this disease.
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Affiliation(s)
- Feng Zhang
- Center for Clinical and Translational Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, China
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Long Niu
- Center for Clinical Research on Neurological Diseases, the First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Rujia Zhong
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Song Li
- Center for Clinical Research on Neurological Diseases, the First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Weidong Le
- Center for Clinical and Translational Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, China
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Center for Clinical Research on Neurological Diseases, the First Affiliated Hospital, Dalian Medical University, Dalian, China
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Szukiewicz D. Aberrant epigenetic regulation of estrogen and progesterone signaling at the level of endometrial/endometriotic tissue in the pathomechanism of endometriosis. VITAMINS AND HORMONES 2023; 122:193-235. [PMID: 36863794 DOI: 10.1016/bs.vh.2022.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Endometriosis is a term referring to a condition whereby the endometrial tissue is found outside the uterine cavity. This progressive and debilitating condition affects up to 15% of women of reproductive age. Due to the fact that endometriosis cells may express estrogen receptors (ERα, Erβ, GPER) and progesterone (P4) receptors (PR-A, PR-B), their growth, cyclic proliferation, and breakdown are similar to the processes occurring in the endometrium. The underlying etiology and pathogenesis of endometriosis are still not fully explained. The retrograde transport of viable menstrual endometrial cells with the retained ability to attach within the pelvic cavity, proliferate, differentiate and invade into the surrounding tissue explains the most widely accepted implantation theory. Endometrial stromal cells (EnSCs) with clonogenic potential constitute the most abundant population of cells within endometrium that resemble the properties of mesenchymal stem cells (MSCs). Accordingly, formation of the endometriotic foci in endometriosis may be due to a kind of EnSCs dysfunction. Increasing evidence indicates the underestimated role of epigenetic mechanisms in the pathogenesis of endometriosis. Hormone-mediated epigenetic modifications of the genome in EnSCs or even MSCs were attributed an important role in the etiopathogenesis of endometriosis. The roles of excess estrogen exposure and P4 resistance were also found to be crucial in the development of epigenetic homeostasis failure. Therefore, the aim of this review was to consolidate the current knowledge regarding the epigenetic background of EnSCs and MSCs and the changed properties due to estrogen/P4 imbalances in the context of the etiopathogenesis of endometriosis.
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Affiliation(s)
- Dariusz Szukiewicz
- Department of Biophysics, Physiology & Pathophysiology, Faculty of Health Sciences, Medical University of Warsaw, Warsaw, Poland.
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20
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Luzna P, Weiser Drozdkova D, Flodrova P, Ondruskova K, Uberall I, Minarik J, Kolar Z, Smesny Trtkova K. Global DNA methylation and increased DNMT3A expression in multiple myeloma patients. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2023; 167:43-49. [PMID: 35173353 DOI: 10.5507/bp.2022.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
AIMS The aim of this study was to compare the expression profile of selected DNA methyltransferases and global DNA methylation status in patients with different phases of multiple myeloma (MM) . For the analysis, different cellular populations including unsorted myeloma cells and a set of plasma cells purified by relevant antibodies were used. Consequently, laboratory data were compared to patients' clinical data. PATIENTS AND METHODS For the analysis, unsorted bone marrow cell population of 44 MM patients (30 newly diagnosed, 9 relapsed and 5 patients in remission) and a set of 8 patients' samples of sorted plasma cells were used. We used commercially available RNA isolated from BM of 3 healthy individuals as control samples. Expression analysis of three DNA methyltransferases - DNMT1, DNMT3A, and DNMT3B was performed by quantitative RT-PCR and the patient global DNA methylation profiles were detected by colorimetric assay. RESULTS Unchanged DNMT1 expression was detected in the selected cohort of patients. Normalized DNMT3A gene expression was globally higher in comparison with controls in unsorted and sorted cell populations. Low (0.08-1.81%) global DNA methylation status in unsorted samples of multiple myeloma patients did not correlate either with expression profiles of monitored DNA methyltransferases or with the stages of MM based on Durie-Salmon and International Staging System. CONCLUSION This is the first comparative study between DNA methyltransferases expression profiles and global DNA methylation status in different phases of multiple myeloma patients. No significant correlation between the level of global methylation and the clinical stage of the unsorted cell population of patients with multiple myeloma was registered. Overexpression of the DNMT3A gene occurred in both sorted and unsorted cell populations of patients with multiple myeloma. This fact highlights the DNMT3A as a potential marker of multiple myeloma tumor progression. Moreover, we demonstrated comparable results in the expression of DNA methyltransferases in both sorted and unsorted cell populations. This is a promising result from the methodical point of view because when compared to samples of unsorted multiple myeloma cells, samples of sorted cells bring reduction of the number of possible analyses performed.
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Affiliation(s)
- Petra Luzna
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Denisa Weiser Drozdkova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Pavla Flodrova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Katarina Ondruskova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Ivo Uberall
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Jiri Minarik
- Department of Hemato-Oncology, University Hospital Olomouc, Czech Republic.,Department of Hemato-Oncology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Zdenek Kolar
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Katerina Smesny Trtkova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic.,Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
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21
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Wei J, Zheng H, Li G, Chen Z, Fang G, Yan J. Involvement of oxytocin receptor deficiency in psychiatric disorders and behavioral abnormalities. Front Cell Neurosci 2023; 17:1164796. [PMID: 37153633 PMCID: PMC10159063 DOI: 10.3389/fncel.2023.1164796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/24/2023] [Indexed: 05/10/2023] Open
Abstract
Oxytocin and its target receptor (oxytocin receptor, OXTR) exert important roles in the regulation of complex social behaviors and cognition. The oxytocin/OXTR system in the brain could activate and transduce several intracellular signaling pathways to affect neuronal functions or responses and then mediate physiological activities. The persistence and outcome of the oxytocin activity in the brain are closely linked to the regulation, state, and expression of OXTR. Increasing evidence has shown that genetic variations, epigenetic modification states, and the expression of OXTR have been implicated in psychiatric disorders characterized by social deficits, especially in autism. Among these variations and modifications, OXTR gene methylation and polymorphism have been found in many patients with psychiatric disorders and have been considered to be associated with those psychiatric disorders, behavioral abnormalities, and individual differences in response to social stimuli or others. Given the significance of these new findings, in this review, we focus on the progress of OXTR's functions, intrinsic mechanisms, and its correlations with psychiatric disorders or deficits in behaviors. We hope that this review can provide a deep insight into the study of OXTR-involved psychiatric disorders.
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Affiliation(s)
- Jinbao Wei
- Department of Pharmacy, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- Department of Pharmacy, Ningde Municipal Hospital Affiliated to Ningde Normal University, Ningde, Fujian, China
| | - Huanrui Zheng
- Department of Pharmacy, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Guokai Li
- Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Zichun Chen
- Department of Pharmacy, Ningde Municipal Hospital Affiliated to Ningde Normal University, Ningde, Fujian, China
| | - Gengjing Fang
- Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujia, China
- Gengjing Fang
| | - Jianying Yan
- Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
- Department of Obstetrics, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Jianying Yan
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22
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Yohannes YB, Nakayama SM, Yabe J, Toyomaki H, Kataba A, Nakata H, Muzandu K, Miyashita C, Ikenaka Y, Choongo K, Ishizuka M. Methylation profiles of global LINE-1 DNA and the GSTP1 promoter region in children exposed to lead (Pb). Epigenetics 2022; 17:2377-2388. [PMID: 36131534 PMCID: PMC9665151 DOI: 10.1080/15592294.2022.2123924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/12/2022] [Accepted: 09/05/2022] [Indexed: 11/03/2022] Open
Abstract
Lead (Pb) exposure has adverse health effects and altered DNA methylation may contribute to Pb toxicity. LINE-1 is an interspersed repeated DNA that is used as a surrogate marker for estimating genomic DNA methylation levels, and GSTP1 is an isozyme that detoxifies xenobiotics like Pb, and its expression is inhibited by methylation. Thus, to assess the effects of Pb exposure on global hypomethylation and gene-specific promoter hypermethylation, we examined DNA methylation at LINE-1 repetitive elements and the GSTP1 promoter region. Blood samples were obtained from children (N = 123) living in Pb-polluted areas (as exposed children) and children (N = 63) living in Pb-unpolluted areas (as control children) in Kabwe, Zambia. ICP-MS was used to determine blood lead levels (BLLs), and pyrosequencing and a fluorescence-based polymerase chain reaction assay were used to determine levels of LINE-1 methylation and GSTP1 promoter methylation, respectively. Inverse association was found between BLLs and LINE-1 methylation (β = - 0.046, p = 0.006). The highest quartile of BLL had significant hypomethylation of LINE-1 (p for trend = 0.03), suggesting the higher the BLL, the lower LINE-1 methylation. GSTP1 methylation levels did not differ significantly between the two areas (p = 0.504), nor was it associated with Pb poisoning risk (OR = 1.03, p = 0.476), indicating GSTP1 methylation may not be a reliable biomarker of Pb exposure in healthy people. Therefore, Pb-related health problems could result from global DNA methylation changes due to high BLLs.
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Affiliation(s)
- Yared Beyene Yohannes
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Department of Chemistry, College of Natural and Computational Science, University of Gondar, Gondar, Ethiopia
| | - Shouta M.M. Nakayama
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - John Yabe
- School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
- Department of Veterinary Para-Clinical Studies, School of Veterinary Medicine, University of Namibia, Windhoek, Namibia
| | - Haruya Toyomaki
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Andrew Kataba
- School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Hokuto Nakata
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Kaampwe Muzandu
- School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Chihiro Miyashita
- Center for Environmental and Health Sciences, Hokkaido University, Sapporo, Japan
| | - Yoshinori Ikenaka
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Water Research Group, Unit for Environmental Sciences and Management, Potchefstroom Campus, North-West University, Potchefstroom, South Africa
- Translational Research Unit, Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Kennedy Choongo
- School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
- College of Agriculture, Fisheries & Forestry, School of Animal and Veterinary Sciences, Fiji National University, Koronivia Campus, Suva, Fiji
| | - Mayumi Ishizuka
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
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23
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Murphy MD, Heller EA. Convergent actions of stress and stimulants via epigenetic regulation of neural circuitry. Trends Neurosci 2022; 45:955-967. [PMID: 36280459 PMCID: PMC9671852 DOI: 10.1016/j.tins.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/21/2022] [Accepted: 10/01/2022] [Indexed: 11/17/2022]
Abstract
The dorsal striatum integrates prior and current information to guide appropriate decision-making. Chronic stress and stimulant exposure interferes with decision-making, and can confer similar cognitive and behavioral inflexibilities. This review examines the literature on acute and chronic regulation of the epigenome by stress and stimulants. Recent evidence suggests that exposures to stress and stimulants share similarities in the manners in which they regulate the dorsal striatum epigenome through DNA methylation, transposable element activity, and histone post-translational modifications. These findings suggest that chronic stress and stimulant exposure leads to the accumulation of epigenetic modifications that impair immediate and future neuron function and activity. Such epigenetic mechanisms represent potential therapeutic targets for ameliorating convergent symptoms of stress and addiction.
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Affiliation(s)
- Michael D Murphy
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, 19104, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elizabeth A Heller
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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24
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Murray KO, Brant JO, Kladde MP, Clanton TL. Long-term epigenetic and metabolomic changes in the mouse ventricular myocardium after exertional heat stroke. Physiol Genomics 2022; 54:486-500. [PMID: 36215393 PMCID: PMC9705024 DOI: 10.1152/physiolgenomics.00147.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 12/15/2022] Open
Abstract
Evidence from human epidemiological studies suggests that exertional heat stroke (EHS) results in an elevated risk of long-term cardiovascular and systemic disease. Previous results using a preclinical mouse model of EHS demonstrated severe metabolic imbalances in ventricular myocardium developing at 9-14 days of recovery. Whether this resolves over time is unknown. We hypothesized that the long-term effects of EHS on the heart reflect retained maladaptive epigenetic responses. In this study, we evaluated genome-wide DNA methylation, RNA-Seq, and metabolomic profiles of the left ventricular myocardium in female C57BL/6 mice, 30 days after EHS (exercise in 37.5°C; n = 7-8), compared with exercise controls. EHS mice ran to loss of consciousness, reaching core temperatures of 42.4 ± 0.2°C. All mice recovered quickly. After 30 days, the left ventricles were rapidly frozen for DNA methyl sequencing, RNA-Seq, and untargeted metabolomics. Ventricular DNA from EHS mice revealed >13,000 differentially methylated cytosines (DMCs) and >900 differentially methylated regions (DMRs; ≥5 DMCs with ≤300 bp between each CpG). Pathway analysis using DMRs revealed alterations in genes regulating basic cell functions, DNA binding, transcription, and metabolism. Metabolomics and mRNA expression revealed modest changes that are consistent with a return to homeostasis. Methylation status did not predict RNA expression or metabolic state at 30 days. We conclude that EHS induces a sustained DNA methylation memory lasting over 30 days of recovery, but ventricular gene expression and metabolism return to a relative homeostasis at rest. Such long-lasting alterations to the DNA methylation landscape could alter responsiveness to environmental or clinical challenges later in life.
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Affiliation(s)
- Kevin O Murray
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, Florida
| | - Jason O Brant
- Department of Biostatistics, University of Florida, Gainesville, Florida
- University of Florida Health Cancer Center, University of Florida, Gainesville, Florida
| | - Michael P Kladde
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida
- University of Florida Health Cancer Center, University of Florida, Gainesville, Florida
| | - Thomas L Clanton
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, Florida
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25
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Godoy-Tena G, Barmada A, Morante-Palacios O, de la Calle-Fabregat C, Martins-Ferreira R, Ferreté-Bonastre AG, Ciudad L, Ruiz-Sanmartín A, Martínez-Gallo M, Ferrer R, Ruiz-Rodriguez JC, Rodríguez-Ubreva J, Vento-Tormo R, Ballestar E. Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines. Genome Med 2022; 14:134. [PMID: 36443794 PMCID: PMC9706884 DOI: 10.1186/s13073-022-01137-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND COVID-19 manifests with a wide spectrum of clinical phenotypes, ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by marked changes in the myeloid compartment, especially monocytes. However, little is known about the epigenetic alterations that occur in these cells during hyperinflammatory responses in severe COVID-19 patients. METHODS In this study, we obtained the DNA methylome and transcriptome of peripheral blood monocytes from severe COVID-19 patients. DNA samples extracted from CD14 + CD15- monocytes of 48 severe COVID-19 patients and 11 healthy controls were hybridized on MethylationEPIC BeadChip arrays. In parallel, single-cell transcriptomics of 10 severe COVID-19 patients were generated. CellPhoneDB was used to infer changes in the crosstalk between monocytes and other immune cell types. RESULTS We observed DNA methylation changes in CpG sites associated with interferon-related genes and genes associated with antigen presentation, concordant with gene expression changes. These changes significantly overlapped with those occurring in bacterial sepsis, although specific DNA methylation alterations in genes specific to viral infection were also identified. We also found these alterations to comprise some of the DNA methylation changes occurring during myeloid differentiation and under the influence of inflammatory cytokines. A progression of DNA methylation alterations in relation to the Sequential Organ Failure Assessment (SOFA) score was found to be related to interferon-related genes and T-helper 1 cell cytokine production. CellPhoneDB analysis of the single-cell transcriptomes of other immune cell types suggested the existence of altered crosstalk between monocytes and other cell types like NK cells and regulatory T cells. CONCLUSION Our findings show the occurrence of an epigenetic and transcriptional reprogramming of peripheral blood monocytes, which could be associated with the release of aberrant immature monocytes, increased systemic levels of pro-inflammatory cytokines, and changes in immune cell crosstalk in these patients.
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Affiliation(s)
- Gerard Godoy-Tena
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Anis Barmada
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1RQ, UK
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Octavio Morante-Palacios
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Carlos de la Calle-Fabregat
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Ricardo Martins-Ferreira
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Anna G Ferreté-Bonastre
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Adolfo Ruiz-Sanmartín
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Mónica Martínez-Gallo
- Immunology Division, Vall d'Hebron University Hospital and Diagnostic Immunology Research Group, Vall d'Hebron Research Institute (VHIR), 08035, Barcelona, Spain
| | - Ricard Ferrer
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Juan Carlos Ruiz-Rodriguez
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1RQ, UK
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain.
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, 200241, China.
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26
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Hirayama T, Kadooka Y, Tarusawa E, Saitoh S, Nakayama H, Hoshino N, Nakama S, Fukuishi T, Kawanishi Y, Umeshima H, Tomita K, Yoshimura Y, Galjart N, Hashimoto K, Ohno N, Yagi T. CTCF loss induces giant lamellar bodies in Purkinje cell dendrites. Acta Neuropathol Commun 2022; 10:172. [PMID: 36447271 PMCID: PMC9706876 DOI: 10.1186/s40478-022-01478-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
CCCTC-binding factor (CTCF) has a key role in higher-order chromatin architecture that is important for establishing and maintaining cell identity by controlling gene expression. In the mature cerebellum, CTCF is highly expressed in Purkinje cells (PCs) as compared with other cerebellar neurons. The cerebellum plays an important role in motor function by regulating PCs, which are the sole output neurons, and defects in PCs cause motor dysfunction. However, the role of CTCF in PCs has not yet been explored. Here we found that the absence of CTCF in mouse PCs led to progressive motor dysfunction and abnormal dendritic morphology in those cells, which included dendritic self-avoidance defects and a proximal shift in the climbing fibre innervation territory on PC dendrites. Furthermore, we found the peculiar lamellar structures known as "giant lamellar bodies" (GLBs), which have been reported in PCs of patients with Werdnig-Hoffman disease, 13q deletion syndrome, and Krabbe disease. GLBs are localized to PC dendrites and are assumed to be associated with neurodegeneration. They have been noted, however, only in case reports following autopsy, and reports of their existence have been very limited. Here we show that GLBs were reproducibly formed in PC dendrites of a mouse model in which CTCF was deleted. GLBs were not noted in PC dendrites at infancy but instead developed over time. In conjunction with GLB development in PC dendrites, the endoplasmic reticulum was almost absent around the nuclei, the mitochondria were markedly swollen and their cristae had decreased drastically, and almost all PCs eventually disappeared as severe motor deficits manifested. Our results revealed the important role of CTCF during normal development and in maintaining PCs and provide new insights into the molecular mechanism of GLB formation during neurodegenerative disease.
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Affiliation(s)
- Teruyoshi Hirayama
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan ,grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Yuuki Kadooka
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
| | - Etsuko Tarusawa
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
| | - Sei Saitoh
- grid.467811.d0000 0001 2272 1771Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, 444-8787 Japan ,grid.256115.40000 0004 1761 798XDepartment of Anatomy II and Cell Biology, Fujita Health University School of Medicine, 1-98 Dengakubo, Kutsukake-cho, Toyoake, 470-1192 Japan
| | - Hisako Nakayama
- grid.410818.40000 0001 0720 6587Department of Physiology, Division of Neurophysiology, School of Medicine, Tokyo Women’s Medical University, Tokyo, 162-8666 Japan ,grid.257022.00000 0000 8711 3200Department of Neurophysiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551 Japan
| | - Natsumi Hoshino
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
| | - Soichiro Nakama
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Takahiro Fukuishi
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Yudai Kawanishi
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Hiroki Umeshima
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Koichi Tomita
- grid.267335.60000 0001 1092 3579Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8503 Japan
| | - Yumiko Yoshimura
- grid.467811.d0000 0001 2272 1771Section of Visual Information Processing, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585 Japan ,grid.275033.00000 0004 1763 208XDepartment of Physiological Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585 Japan
| | - Niels Galjart
- grid.5645.2000000040459992XDepartment of Cell Biology, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Kouichi Hashimoto
- grid.257022.00000 0000 8711 3200Department of Neurophysiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551 Japan
| | - Nobuhiko Ohno
- grid.467811.d0000 0001 2272 1771Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, 444-8585 Japan ,grid.410804.90000000123090000Department of Anatomy, Division of Histology and Cell Biology, Jichi Medical University, Shimotsuke, 329-0498 Japan
| | - Takeshi Yagi
- grid.136593.b0000 0004 0373 3971KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871 Japan
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Barciszewska AM, Belter A, Gawrońska I, Giel-Pietraszuk M, Naskręt-Barciszewska MZ. Cross-reactivity between histone demethylase inhibitor valproic acid and DNA methylation in glioblastoma cell lines. Front Oncol 2022; 12:1033035. [PMID: 36465345 PMCID: PMC9709419 DOI: 10.3389/fonc.2022.1033035] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/24/2022] [Indexed: 08/22/2023] Open
Abstract
Currently, valproic acid (VPA) is known as an inhibitor of histone deacetylase (epigenetic drug) and is used for the clinical treatment of epileptic events in the course of glioblastoma multiforme (GBM). Which improves the clinical outcome of those patients. We analyzed the level of 5-methylcytosine, a DNA epigenetic modulator, and 8-oxodeoxyguanosine, an cellular oxidative damage marker, affected with VPA administration, alone and in combination with temozolomide (TMZ), of glioma (T98G, U118, U138), other cancer (HeLa), and normal (HaCaT) cell lines. We observed the VPA dose-dependent changes in the total DNA methylation in neoplastic cell lines and the lack of such an effect in a normal cell line. VPA at high concentrations (250-500 μM) induced hypermethylation of DNA in a short time frame. However, the exposition of GBM cells to the combination of VPA and TMZ resulted in DNA hypomethylation. At the same time, we observed an increase of genomic 8-oxo-dG, which as a hydroxyl radical reaction product with guanosine residue in DNA suggests a red-ox imbalance in the cancer cells and radical damage of DNA. Our data show that VPA as an HDAC inhibitor does not induce changes only in histone acetylation, but also changes in the state of DNA modification. It shows cross-reactivity between chromatin remodeling due to histone acetylation and DNA methylation. Finally, total DNA cytosine methylation and guanosine oxidation changes in glioma cell lines under VPA treatment suggest a new epigenetic mechanism of that drug action.
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Affiliation(s)
- Anna-Maria Barciszewska
- Intraoperative Imaging Unit, Chair and Department of Neurosurgery and Neurotraumatology, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
- Department of Neurosurgery and Neurotraumatology, Heliodor Swiecicki Clinical Hospital, Poznan, Poland
| | - Agnieszka Belter
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Iwona Gawrońska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Fadaei S, Zarepour F, Parvaresh M, Motamedzadeh A, Tamehri Zadeh SS, Sheida A, Shabani M, Hamblin MR, Rezaee M, Zarei M, Mirzaei H. Epigenetic regulation in myocardial infarction: Non-coding RNAs and exosomal non-coding RNAs. Front Cardiovasc Med 2022; 9:1014961. [PMID: 36440025 PMCID: PMC9685618 DOI: 10.3389/fcvm.2022.1014961] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/17/2022] [Indexed: 08/13/2023] Open
Abstract
Myocardial infarction (MI) is one of the leading causes of deaths globally. The early diagnosis of MI lowers the rate of subsequent complications and maximizes the benefits of cardiovascular interventions. Many efforts have been made to explore new therapeutic targets for MI, and the therapeutic potential of non-coding RNAs (ncRNAs) is one good example. NcRNAs are a group of RNAs with many different subgroups, but they are not translated into proteins. MicroRNAs (miRNAs) are the most studied type of ncRNAs, and have been found to regulate several pathological processes in MI, including cardiomyocyte inflammation, apoptosis, angiogenesis, and fibrosis. These processes can also be modulated by circular RNAs and long ncRNAs via different mechanisms. However, the regulatory role of ncRNAs and their underlying mechanisms in MI are underexplored. Exosomes play a crucial role in communication between cells, and can affect both homeostasis and disease conditions. Exosomal ncRNAs have been shown to affect many biological functions. Tissue-specific changes in exosomal ncRNAs contribute to aging, tissue dysfunction, and human diseases. Here we provide a comprehensive review of recent findings on epigenetic changes in cardiovascular diseases as well as the role of ncRNAs and exosomal ncRNAs in MI, focusing on their function, diagnostic and prognostic significance.
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Affiliation(s)
- Sara Fadaei
- Department of Internal Medicine and Endocrinology, Shohadae Tajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Zarepour
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Mehrnoosh Parvaresh
- Department of Physical Medicine and Rehabilitation, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Alireza Motamedzadeh
- Department of Internal Medicine, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Amirhossein Sheida
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammad Shabani
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
- Department of Anesthesiology, School of Allied Medical Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Mehdi Rezaee
- Department of Anesthesiology, School of Medicine, Shahid Madani Hospital, Alborz University of Medical Sciences, Karaj, Iran
| | - Maryam Zarei
- Tehran Heart Center, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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Huang Y, Liao J, Wu S, Ye Y, Zeng H, Liang F, Yin X, Jiang Y, Ouyang N, Han P, Huang X. Upregulated YTHDF1 associates with tumor immune microenvironment in head and neck squamous cell carcinomas. Transl Cancer Res 2022; 11:3986-3999. [PMID: 36523307 PMCID: PMC9745380 DOI: 10.21037/tcr-22-503] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/25/2022] [Indexed: 02/19/2024]
Abstract
BACKGROUND The nature of the tumor immune microenvironment (TME) is essential for the head and neck squamous cell carcinomas (HNSCC) initiation, prognosis, and response to immunotherapy. However, its gene regulatory network remains to be elucidated. METHODS To identify N6-methyladenosine (m6A) regulators that are involved in regulating the HNSCC TME, a computational screen was applied to The Cancer Genome Atlas (TCGA) HNSCC patient samples. The effects of mutation, copy number variation (CNV), and transcriptional regulation on YTHDF1 expression were analyzed. We analyzed the TME infiltration, cancer-immunity cycle activities, and YTHDF1-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. RESULTS Among the 24 m6A regulators, 3 factors (YTHDF1, ELAVL1, and METTL3) were highly correlated with TME infiltration. As the top candidate, YTHDF1 was up-regulated and amplified in HNSCC. YTHDF1 promoter gains active histone marks and high chromatin accessibility, which might be transcriptionally activated by SOX2 and TP63. Moreover, YTHDF1 expression significantly associates with tumor malignant phenotype in HNSCC, which has a positive correlation with CD4+ T cells and a negative correlation with CD8+ T cells infiltration. Specifically, YTHDF1 expression is negatively associated with the cancer-immunity cycle and immune checkpoint inhibitors. In terms of the underlying biological mechanisms, YTHDF1 may interact with YTHDF2/3 to regulate several vital immune-related pathways. CONCLUSIONS We identify YTHDF1 associated with TME and elucidate an underlying mechanism of immune escape in HNSCC, which might be used as a predictive marker in guiding immunotherapy.
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Affiliation(s)
- Yongsheng Huang
- Department of Otolaryngology-Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianwei Liao
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sangqing Wu
- Department of Otolaryngology-Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuchu Ye
- Department of Otolaryngology-Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haicang Zeng
- Department of Otolaryngology-Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Faya Liang
- Department of Otolaryngology-Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinke Yin
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuanling Jiang
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Nengtai Ouyang
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ping Han
- Department of Otolaryngology-Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoming Huang
- Department of Otolaryngology-Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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Murray KO, Clanton TL, Horowitz M. Epigenetic responses to heat: From adaptation to maladaptation. Exp Physiol 2022; 107:1144-1158. [PMID: 35413138 PMCID: PMC9529784 DOI: 10.1113/ep090143] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/25/2022] [Indexed: 11/08/2022]
Abstract
NEW FINDINGS What is the topic of this review? This review outlines the history of research on epigenetic adaptations to heat exposure. The perspective taken is that adaptations reflect properties of hormesis, whereby low, repeated doses of heat induce adaptation (acclimation/acclimatization); whereas brief, life-threatening exposures can induce maladaptive responses. What advances does it highlight? The epigenetic mechanisms underlying acclimation/acclimatization comprise specific molecular programmes on histones that regulate heat shock proteins transcriptionally and protect the organism from subsequent heat exposures, even after long delays. The epigenetic signalling underlying maladaptive responses might rely, in part, on extensive changes in DNA methylation that are sustained over time and might contribute to later health challenges. ABSTRACT Epigenetics plays a strong role in molecular adaptations to heat by producing a molecular memory of past environmental exposures. Moderate heat, over long periods of time, induces an 'adaptive' epigenetic memory, resulting in a condition of 'resilience' to future heat exposures or cross-tolerance to other forms of toxic stress. In contrast, intense, life-threatening heat exposures, such as severe heat stroke, can result in a 'maladaptive' epigenetic memory that can place an organism at risk of later health complications. These cellular memories are coded by post-translational modifications of histones on the nucleosomes and/or by changes in DNA methylation. They operate by inducing changes in the level of gene transcription and therefore phenotype. The adaptive response to heat acclimation functions, in part, by facilitating transcription of essential heat shock proteins and exhibits a biphasic short programme (maintaining DNA integrity, followed by a long-term consolidation). The latter accelerates acclimation responses after de-acclimation. Although less studied, the maladaptive responses to heat stroke appear to be coded in long-lasting changes in DNA methylation near the promoter region of genes involved with basic cell function. Whether these memories are also encoded in histone modifications is not yet known. There is considerable evidence that both adaptive and maladaptive epigenetic responses to heat can be inherited, although most evidence comes from lower organisms. Future challenges include understanding the signalling mechanisms responsible and discovering new ways to promote adaptive responses while suppressing maladaptive responses to heat, as all life forms adapt to life on a warming planet.
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Affiliation(s)
- Kevin O. Murray
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Thomas L. Clanton
- Department of Applied Physiology and Kinesiology, University of Florida, Gainesville, FL, USA
| | - Michal Horowitz
- Laboratory of Environmental Physiology, Faculty of Dentistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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31
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Yang CH, Fagnocchi L, Apostle S, Wegert V, Casaní-Galdón S, Landgraf K, Panzeri I, Dror E, Heyne S, Wörpel T, Chandler DP, Lu D, Yang T, Gibbons E, Guerreiro R, Bras J, Thomasen M, Grunnet LG, Vaag AA, Gillberg L, Grundberg E, Conesa A, Körner A, Pospisilik JA. Independent phenotypic plasticity axes define distinct obesity sub-types. Nat Metab 2022; 4:1150-1165. [PMID: 36097183 PMCID: PMC9499872 DOI: 10.1038/s42255-022-00629-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/29/2022] [Indexed: 01/04/2023]
Abstract
Studies in genetically 'identical' individuals indicate that as much as 50% of complex trait variation cannot be traced to genetics or to the environment. The mechanisms that generate this 'unexplained' phenotypic variation (UPV) remain largely unknown. Here, we identify neuronatin (NNAT) as a conserved factor that buffers against UPV. We find that Nnat deficiency in isogenic mice triggers the emergence of a bi-stable polyphenism, where littermates emerge into adulthood either 'normal' or 'overgrown'. Mechanistically, this is mediated by an insulin-dependent overgrowth that arises from histone deacetylase (HDAC)-dependent β-cell hyperproliferation. A multi-dimensional analysis of monozygotic twin discordance reveals the existence of two patterns of human UPV, one of which (Type B) phenocopies the NNAT-buffered polyphenism identified in mice. Specifically, Type-B monozygotic co-twins exhibit coordinated increases in fat and lean mass across the body; decreased NNAT expression; increased HDAC-responsive gene signatures; and clinical outcomes linked to insulinemia. Critically, the Type-B UPV signature stratifies both childhood and adult cohorts into four metabolic states, including two phenotypically and molecularly distinct types of obesity.
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Affiliation(s)
- Chih-Hsiang Yang
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | | | - Vanessa Wegert
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Kathrin Landgraf
- Medical Faculty, University of Leipzig, University Hospital for Children & Adolescents, Center for Pediatric Research Leipzig, Leipzig, Germany
| | - Ilaria Panzeri
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Erez Dror
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Roche Diagnostics Deutschland, Mannheim, Germany
| | - Till Wörpel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Di Lu
- Van Andel Institute, Grand Rapids, MI, USA
| | - Tao Yang
- Van Andel Institute, Grand Rapids, MI, USA
| | - Elizabeth Gibbons
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Martin Thomasen
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Louise G Grunnet
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Allan A Vaag
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Herlev, Denmark
- Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Linn Gillberg
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, MO, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, USA
| | - Antje Körner
- Medical Faculty, University of Leipzig, University Hospital for Children & Adolescents, Center for Pediatric Research Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - J Andrew Pospisilik
- Van Andel Institute, Grand Rapids, MI, USA.
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Alpoim-Moreira J, Fernandes C, Pimenta J, Bliebernicht M, Rebordão MR, Castelo-Branco P, Szóstek-Mioduchowska A, Skarzynski DJ, Ferreira-Dias G. Metallopeptidades 2 and 9 genes epigenetically modulate equine endometrial fibrosis. Front Vet Sci 2022; 9:970003. [PMID: 36032279 PMCID: PMC9412240 DOI: 10.3389/fvets.2022.970003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/22/2022] [Indexed: 12/13/2022] Open
Abstract
Endometrium type I (COL1) and III (COL3) collagen accumulation, periglandular fibrosis and mare infertility characterize endometrosis. Metalloproteinase-2 (MMP-2), MMP-9 and tissue inhibitors of metalloproteinases (TIMP-1 and TIMP-2) are involved in collagen turnover. Since epigenetic changes may control fibroproliferative diseases, we hypothesized that epigenetic mechanisms could modulate equine endometrosis. Epigenetic changes can be reversed and therefore extremely promising for therapeutic use. Methylation pattern analysis of a particular gene zone is used to detect epigenetic changes. DNA methylation commonly mediates gene repression. Thus, this study aimed to evaluate if the transcription of some genes involved in equine endometrosis was altered with endometrial fibrosis, and if the observed changes were epigenetically modulated, through DNA methylation analysis. Endometrial biopsies collected from cyclic mares were histologically classified (Kenney and Doig category I, n = 6; category IIA, n = 6; category IIB, n = 6 and category III, n = 6). Transcription of COL1A1, COL1A2, COL3A1, MMP2, MMP9, TIMP1, and TIMP2 genes and DNA methylation pattern by pyrosequencing of COL1A1, MMP2, MMP9, TIMP1 genes were evaluated. Both MMP2 and MMP9 transcripts decreased with fibrosis, when compared with healthy endometrium (category I) (P < 0.05). TIMP1 transcripts were higher in category III, when compared to category I endometrium (P < 0.05). No differences were found for COL1A1, COL1A2, COL3A1 and TIMP2 transcripts between endometrial categories. There were higher methylation levels of (i) COL1A1 in category IIB (P < 0.05) and III (P < 0.01), when compared to category I; (ii) MMP2 in category III, when compared to category I (P < 0.001) and IIA (P < 0.05); and (iii) MMP9 in category III, when compared to category I and IIA (P < 0.05). No differences in TIMP1 methylation levels were observed between endometrial categories. The hypermethylation of MMP2 and MMP9, but not of COL1A1 genes, occurred simultaneously with a decrease in their mRNA levels, with endometrial fibrosis, suggesting that this hypermethylation is responsible for repressing their transcription. Our results show that endometrosis is epigenetically modulated by anti-fibrotic genes (MMP2 and MMP9) inhibition, rather than fibrotic genes activation and therefore, might be promising targets for therapeutic use.
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Affiliation(s)
- Joana Alpoim-Moreira
- CIISA - Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Lisbon, Portugal
| | - Carina Fernandes
- CIISA - Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Lisbon, Portugal
| | - Jorge Pimenta
- CIISA - Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos (UEISBR), Instituto Nacional de Investigação Agrária e Veterinária, I. P. (INIAV), Vairão, Portugal
| | | | - Maria Rosa Rebordão
- CIISA - Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Lisbon, Portugal
- Polytechnic of Coimbra, Coimbra Agriculture School, Coimbra, Portugal
| | - Pedro Castelo-Branco
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Faro, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal
| | | | | | - Graça Ferreira-Dias
- CIISA - Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Lisbon, Portugal
- *Correspondence: Graça Ferreira-Dias
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Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. Nat Neurosci 2022; 25:1049-1058. [PMID: 35915179 PMCID: PMC9343253 DOI: 10.1038/s41593-022-01123-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/16/2022] [Indexed: 11/08/2022]
Abstract
Mammalian neocortical neurons span one of the most diverse cell type spectra of any tissue. Cortical neurons are born during embryonic development, and their maturation extends into postnatal life. The regulatory strategies underlying progressive neuronal development and maturation remain unclear. Here we present an integrated single-cell epigenomic and transcriptional analysis of individual mouse and marmoset cortical neuron classes, spanning both early postmitotic stages of identity acquisition and later stages of neuronal plasticity and circuit integration. We found that, in both species, the regulatory strategies controlling early and late stages of pan-neuronal development diverge. Early postmitotic neurons use more widely shared and evolutionarily conserved molecular regulatory programs. In contrast, programs active during later neuronal maturation are more brain- and neuron-specific and more evolutionarily divergent. Our work uncovers a temporal shift in regulatory choices during neuronal diversification and maturation in both mice and marmosets, which likely reflects unique evolutionary constraints on distinct events of neuronal development in the neocortex.
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Pathania AS, Prathipati P, Pandey MK, Byrareddy SN, Coulter DW, Gupta SC, Challagundla KB. The emerging role of non-coding RNAs in the epigenetic regulation of pediatric cancers. Semin Cancer Biol 2022; 83:227-241. [PMID: 33910063 DOI: 10.1016/j.semcancer.2021.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/09/2023]
Abstract
Epigenetics is a process that involves the regulation of gene expression without altering the sequence of DNA. Numerous studies have documented that epigenetic mechanisms play a critical role in cell growth, differentiation, and cancer over the past decade. The well-known epigenetic modifications are either on DNA or at the histone proteins. Although several studies have focused on regulating gene expression by non-coding RNAs, the current understanding of their biological functions in various human diseases, particularly in cancers, is inadequate. Only about two percent of DNA is involved in coding the protein-coding genes, and leaving the rest 98 percent is non-coding and the scientific community regarded as junk or noise with no known purpose. Most non-coding RNAs are derived from such junk DNA and are known to be involved in various signaling pathways involving cancer initiation, progression, and the development of therapy resistance in many human cancer types. Recent studies have suggested that non-coding RNAs, especially microRNAs, piwi-interactingRNAs, and long non-coding RNAs, play a significant role in controlling epigenetic mechanism(s), indicating the potential effect of epigenetic modulation of non-coding RNAs on cancer progression. In this review article, we briefly presented epigenetic marks' characteristics, crosstalk between epigenetic modifications and microRNAs, piwi-interactingRNAs, and long non-coding RNAs to uncover the effect on the phenotype of pediatric cancers. Further, current knowledge on understanding the RNA epigenetics will help design novel therapeutics that target epigenetic regulatory networks to benefit cancer patients in the clinic.
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Affiliation(s)
- Anup S Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Philip Prathipati
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Manoj K Pandey
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Siddappa N Byrareddy
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Don W Coulter
- Department of Pediatrics, Division of Hematology/Oncology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Subash C Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Kishore B Challagundla
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; The Children's Health Research Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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35
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Chen Y, Wu Y, Yang H, Wang J, Kong J, Yu L, Ni M, Deng Y, Xu S, Yu H, Shuai Z, Pan F. DNA Methylation and mRNA Expression of B7-H3 Gene in Ankylosing Spondylitis: A Case-Control Study. Immunol Invest 2022; 51:2025-2034. [PMID: 35786112 DOI: 10.1080/08820139.2022.2095285] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Ankylosing spondylitis (AS) is a common inflammatory arthritis, with a high prevalence in patients in their mid-20s. Its pathogenesis is not well understood; however, genetic factors likely play a critical role. Epigenetic DNA changes may be involved in the pathogenesis of AS. In this study, we explored the methylation and transcription levels of the B7-H3 gene and its association with AS in an eastern Chinese Han population. METHODS Peripheral blood of AS patients and healthy controls was used to extract genomic DNA and B7-H3 methylation levels were analyzed using sodium bisulfite followed by multiplex polymerase chain reaction. SPSS software was used to determine the statistical significance of the results. RESULTS Hypomethylation of the promoter of the B7-H3 gene was observed in AS patients, whereas the B7-H3 gene expression was significantly enhanced in AS patients. CONCLUSION Epigenetic modifications of B7-H3 were associated with susceptibility to AS. Hypomethylation of the B7-H3 promoter, which leads to B7-H3 overexpression, may be involved in the pathogenesis of AS.
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Affiliation(s)
- Yuting Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Ye Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Hui Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Jinian Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Jiangping Kong
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Lingxiang Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Man Ni
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Yujie Deng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Shengqian Xu
- Department of Rheumatism and Immunity, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Haiyang Yu
- Department of Orthopedics, Fuyang People's Hospital, Fuyang, Anhui, China
| | - Zongwen Shuai
- Department of Rheumatism and Immunity, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Faming Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China
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Oxytocin receptor genes moderate BDNF epigenetic methylation by childhood trauma. J Affect Disord 2022; 306:167-173. [PMID: 35314247 DOI: 10.1016/j.jad.2022.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/24/2021] [Accepted: 03/10/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVES Gene-Environment (G × E) interaction is of increasing importance in understanding the pathophysiology of posttraumatic stress disorder (PTSD). This study investigated the interaction effect of childhood traumatic experience and epigenetic methylation of brain-derived neurotrophic factor (BDNF) and a possible moderating effect of oxytocin receptor (OXTR) gene rs53576. METHODS Ninety-nine patients with PTSD and 81 healthy controls (HCs) were recruited. Clinical assessments, including the childhood trauma questionnaire (CTQ) and posttraumatic stress disorder Checklist (PCL) were performed. BDNF methylation and OXTR genotyping (A vs. G allele) were conducted through blood sampling. A two-way multivariate analysis and a moderated regression analysis were conducted to investigate the moderating effect of the OXTR gene on the relationship between CTQ and BDNF methylation. RESULTS As for the HC group, the interaction effect of the CTQ and OXTR genotype was significant on BDNF methylation, and the moderation model showed that CTQ and OXTR group are significant predictors of BDNF methylation. In the G-OXTR type, the high CTQ group showed a greater BDNF methylation level. As for the PTSD group, no interaction or moderation effects were found. LIMITATIONS The present study did not control the dosage, duration of medications, and different trauma types and the assessment of childhood trauma was based on self-report. CONCLUSIONS These results suggested that childhood traumatic experience showed a significant impact on BDNF methylation, and OXTR genes have a moderating effect on this epigenetic mechanism in people who have experienced the childhood traumatic episodes.
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Grant OA, Wang Y, Kumari M, Zabet NR, Schalkwyk L. Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array. Clin Epigenetics 2022; 14:62. [PMID: 35568878 PMCID: PMC9107695 DOI: 10.1186/s13148-022-01279-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/18/2022] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Sex differences are known to play a role in disease aetiology, progression and outcome. Previous studies have revealed autosomal epigenetic differences between males and females in some tissues, including differences in DNA methylation patterns. Here, we report for the first time an analysis of autosomal sex differences in DNAme using the Illumina EPIC array in human whole blood by performing a discovery (n = 1171) and validation (n = 2471) analysis. RESULTS We identified and validated 396 sex-associated differentially methylated CpG sites (saDMPs) with the majority found to be female-biased CpGs (74%). These saDMP's are enriched in CpG islands and CpG shores and located preferentially at 5'UTRs, 3'UTRs and enhancers. Additionally, we identified 266 significant sex-associated differentially methylated regions overlapping genes, which have previously been shown to exhibit epigenetic sex differences, and novel genes. Transcription factor binding site enrichment revealed enrichment of transcription factors related to critical developmental processes and sex determination such as SRY and ESR1. CONCLUSION Our study reports a reliable catalogue of sex-associated CpG sites and elucidates several characteristics of these sites using large-scale discovery and validation data sets. This resource will benefit future studies aiming to investigate sex specific epigenetic signatures and further our understanding of the role of DNA methylation in sex differences in human whole blood.
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Affiliation(s)
- Olivia A Grant
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
- Institute of Social and Economic Research, University of Essex, Colchester, CO4 3SQ, UK
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Yucheng Wang
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, CO4 3SQ, UK
| | - Meena Kumari
- Institute of Social and Economic Research, University of Essex, Colchester, CO4 3SQ, UK
| | - Nicolae Radu Zabet
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK.
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
| | - Leonard Schalkwyk
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK.
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Choudhury J, Pandey D, Chaturvedi PK, Gupta S. Epigenetic regulation of epithelial to mesenchymal transition: a trophoblast perspective. Mol Hum Reprod 2022; 28:6572349. [PMID: 35451485 DOI: 10.1093/molehr/gaac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/31/2022] [Indexed: 11/12/2022] Open
Abstract
Epigenetic changes alter expression of genes at both pre- and post-transcriptional levels without changing their DNA sequence. Accumulating evidence suggests that such changes can modify cellular behaviour and characteristics required during development and in response to various extracellular stimuli. Trophoblast cells develop from the outermost trophectoderm layer of the blastocyst and undergo many phenotypic changes as the placenta develops. One such phenotypic change is differentiation of the epithelial natured cytotrophoblasts into the mesenchymal natured extravillous trophoblasts. The extravillous trophoblasts are primarily responsible for invading into the maternal decidua and thus establishing connection with the maternal spiral arteries. Any dysregulation of this process can have adverse effects on the pregnancy outcome. Hence, tight regulation of this epithelial-mesenchymal transition is critical for successful pregnancy. This review summarizes the recent research on the epigenetic regulation of the epithelial-mesenchymal transition occurring in the trophoblast cells during placental development. The functional significance of chemical modifications of DNA and histone, which regulate transcription, as well as non-coding RNAs, which control gene expression post-transcriptionally, is discussed in relation to trophoblast biology.
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Affiliation(s)
- Jaganmoy Choudhury
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi-, 110029, India
| | - Deepak Pandey
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi-, 110029, India
| | - Pradeep Kumar Chaturvedi
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi-, 110029, India
| | - Surabhi Gupta
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi-, 110029, India
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Hallberg I, Persson S, Olovsson M, Moberg M, Ranefall P, Laskowski D, Damdimopoulou P, Sirard MA, Rüegg J, Sjunnesson YC. Bovine oocyte exposure to perfluorohexane sulfonate (PFHxS) induces phenotypic, transcriptomic, and DNA methylation changes in resulting embryos in vitro. Reprod Toxicol 2022; 109:19-30. [DOI: 10.1016/j.reprotox.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 10/19/2022]
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Disatham J, Brennan L, Jiao X, Ma Z, Hejtmancik JF, Kantorow M. Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation. Epigenetics Chromatin 2022; 15:8. [PMID: 35246225 PMCID: PMC8897925 DOI: 10.1186/s13072-022-00440-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/16/2022] [Indexed: 12/13/2022] Open
Abstract
Background Methylation at cytosines (mCG) is a well-known regulator of gene expression, but its requirements for cellular differentiation have yet to be fully elucidated. A well-studied cellular differentiation model system is the eye lens, consisting of a single anterior layer of epithelial cells that migrate laterally and differentiate into a core of fiber cells. Here, we explore the genome-wide relationships between mCG methylation, chromatin accessibility and gene expression during differentiation of eye lens epithelial cells into fiber cells. Results Whole genome bisulfite sequencing identified 7621 genomic loci exhibiting significant differences in mCG levels between lens epithelial and fiber cells. Changes in mCG levels were inversely correlated with the differentiation state-specific expression of 1285 genes preferentially expressed in either lens fiber or lens epithelial cells (Pearson correlation r = − 0.37, p < 1 × 10–42). mCG levels were inversely correlated with chromatin accessibility determined by assay for transposase-accessible sequencing (ATAC-seq) (Pearson correlation r = − 0.86, p < 1 × 10–300). Many of the genes exhibiting altered regions of DNA methylation, chromatin accessibility and gene expression levels in fiber cells relative to epithelial cells are associated with lens fiber cell structure, homeostasis and transparency. These include lens crystallins (CRYBA4, CRYBB1, CRYGN, CRYBB2), lens beaded filament proteins (BFSP1, BFSP2), transcription factors (HSF4, SOX2, HIF1A), and Notch signaling pathway members (NOTCH1, NOTCH2, HEY1, HES5). Analysis of regions exhibiting cell-type specific alterations in DNA methylation revealed an overrepresentation of consensus sequences of multiple transcription factors known to play key roles in lens cell differentiation including HIF1A, SOX2, and the MAF family of transcription factors. Conclusions Collectively, these results link DNA methylation with control of chromatin accessibility and gene expression changes required for eye lens differentiation. The results also point to a role for DNA methylation in the regulation of transcription factors previously identified to be important for lens cell differentiation. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00440-z.
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Affiliation(s)
- Joshua Disatham
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Lisa Brennan
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhiwei Ma
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - J Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marc Kantorow
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA.
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Ehrlich M. Risks and rewards of big-data in epigenomics research: an interview with Melanie Ehrlich. Epigenomics 2022; 14:351-358. [PMID: 35255735 DOI: 10.2217/epi-2022-0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Melanie Ehrlich, PhD, is a professor in the Tulane Cancer Center, the Tulane Center for Medical Bioinformatics and Genomics and the Hayward Human Genetics Program at Tulane Medical School, New Orleans, LA. She obtained her PhD in molecular biology in 1971 from the State University of New York at Stony Brook and completed postdoctoral research at Albert Einstein College of Medicine in 1972. She has been working on various aspects of epigenetics, starting with DNA methylation, since 1973. Her group made many first findings about DNA methylation (see below). For example, in 1982 and 1983, in collaboration with Charles Gehrke at the University of Missouri, she was the first to report tissue-specific and cancer-specific differences in overall DNA methylation in humans. In 1985, Xian-Yang Zhang and Richard Wang in her lab discovered a class of human DNA sequences specifically hypomethylated in sperm. In 1998, her group was the first to describe extensive losses of DNA methylation in pericentromeric and centromeric DNA repeats in human cancer. Her lab's many publications on the prevalence of both DNA hypermethylation and hypomethylation in the same cancers brought needed balance to our understanding of the epigenetics of cancer and to its clinical implications [1]. Besides working on cancer epigenetics, her research group has helped elucidate cytogenetic and gene expression abnormalities in the immunodeficiency, centromeric and facial anomalies (ICF) syndrome, a rare recessive disease often caused by mutations in DNMT3B. Her group also studied the epigenetics and transcriptomics of facioscapulohumeral muscular dystrophy (FSHD), whose disease locus is a tandem 3.3-kb repeat at subtelomeric 4q (that happens to be hypomethylated in ICF DNA [2]). Her study of FSHD has taken her in the direction of muscle (skeletal muscle, heart and aorta) epigenetics [3-6]. Recently, she has led research that applies epigenetics much more rigorously than usual to the evaluation of genetic variants from genome-wide association studies (GWAS) of osteoporosis and obesity. In continued collaboration with Sriharsa Pradhan at New England Biolabs and Michelle Lacey at Tulane University, she has compared 5-hydroxymethylcytosine and 5-methylcytosine clustering in various human tissues [7] and is studying myoblast methylomes that they generated by a new high-resolution enzymatic technique (enzymatic methyl-seq).
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center, Center for Medical Bioinformatics & Genomics, & Hayward Genetics Center, Tulane University, New Orleans, LA 70112, USA
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Zhang B, Yuan L, Chen G, Chen X, Yang X, Fan T, Sun C, Fan D, Chen Z. Deciphering Obesity-Related Gene Clusters Unearths SOCS3 Immune Infiltrates and 5mC/m6A Modifiers in Ossification of Ligamentum Flavum Pathogenesis. Front Endocrinol (Lausanne) 2022; 13:861567. [PMID: 35712246 PMCID: PMC9196192 DOI: 10.3389/fendo.2022.861567] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Ossification of ligamentum flavum (OLF) is an insidious and debilitating heterotopic ossifying disease with etiological heterogeneity and undefined pathogenesis. Obese individuals predispose to OLF, whereas the underlying connections between obesity phenotype and OLF pathomechanism are not fully understood. Therefore, this study aims to explore distinct obesity-related genes and their functional signatures in OLF. METHODS The transcriptome sequencing data related to OLF were downloaded from the GSE106253 in the Gene Expression Omnibus (GEO) database. The obesity-related differentially expressed genes (ORDEGs) in OLF were screened, and functional and pathway enrichment analysis were applied for these genes. Furthermore, protein-protein interactions (PPI), module analysis, transcription factor enrichment analysis (TFEA), and experiment validation were used to identify hub ORDEGs. The immune infiltration landscape in OLF was depicted, and correlation analysis between core gene SOCS3 and OLF-related infiltrating immune cells (OIICs) as well as 5mC/m6A modifiers in OLF was constructed. RESULTS Ninety-nine ORDEGs were preliminarily identified, and functional annotations showed these genes were mainly involved in metabolism, inflammation, and immune-related biological functions and pathways. Integrative bioinformatic algorithms determined a crucial gene cluster associated with inflammatory/immune responses, such as TNF signaling pathway, JAK-STAT signaling pathway, and regulation of interferon-gamma-mediated signaling. Eight hub ORDEGs were validated, including 6 down-regulated genes (SOCS3, PPARG, ICAM-1, CCL2, MYC, and NT5E) and 2 up-regulated genes (PTGS2 and VEGFA). Furthermore, 14 differential OIICs were identified by ssGSEA and xCell, and SOCS3 was overlapped to be the core gene, which was associated with multiple immune infiltrates (dendritic cells, macrophage, and T cells) and six m6A modifiers as well as four 5mC regulators in OLF. Reduced SOCS3 and FTO expression and up-regulated DNMT1 level in OLF were validated by Western blotting. CONCLUSION This study deciphered immune/inflammatory signatures of obesity-related gene clusters for the first time, and defined SOCS3 as one core gene. The crosstalk between 5mC/m6A methylation may be a key mediator of SOCS3 expression and immune infiltration. These findings will provide more insights into molecular mechanisms and therapeutic targets of obesity-related OLF.
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Affiliation(s)
- Baoliang Zhang
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease Research, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, China
| | - Lei Yuan
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease Research, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, China
| | - Guanghui Chen
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease Research, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, China
| | - Xi Chen
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease Research, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, China
| | - Xiaoxi Yang
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease Research, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, China
| | - Tianqi Fan
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease Research, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, China
| | - Chuiguo Sun
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease Research, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, China
| | - Dongwei Fan
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease Research, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, China
| | - Zhongqiang Chen
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease Research, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, China
- *Correspondence: Zhongqiang Chen,
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Cao Q, Feng Y, Dai X, Huang L, Li J, Tao P, Crabbe MJC, Zhang T, Qiao Q. Dynamic Changes of DNA Methylation During Wild Strawberry ( Fragaria nilgerrensis) Tissue Culture. FRONTIERS IN PLANT SCIENCE 2021; 12:765383. [PMID: 34917103 PMCID: PMC8669611 DOI: 10.3389/fpls.2021.765383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Tissue culture is an important tool for asexual propagation and genetic transformation of strawberry plants. In plant tissue culture, variation of DNA methylation is a potential source of phenotypic variation in regenerated plants. However, the genome wide dynamic methylation patterns of strawberry tissue culture remain unclear. In this study, we used whole-genome bisulfite sequencing (WGBS) to study genomic DNA methylation changes of a wild strawberry Fragaria nilgerrensis at six stages: from explants of shoot tips to outplanting and acclimation. Global methylation levels showed that CG sites exhibited the highest methylation level in all stages with an average of 49.5%, followed by CHG (33.2%) and CHH (12.4%). Although CHH accounted for the lowest proportion of total cytosine methylation, it showed the most obvious methylation change and the most of these changes occurred in the transposable element regions. The overall methylation levels alternately decreased and increased during the entire tissue culture process and the distribution of DNA methylation was non-uniform among different genetic regions. Furthermore, much more differentially methylated regions (DMRs) were detected in dedifferentiation and redifferentiation stages and most of them were transposable elements, suggesting these processes involved activating or silencing of amounts of transposons. The functional enrichment of the DMR-related genes indicated that genes involved in hormone metabolic processes, plant development and the stress response changed methylation throughout the tissue culture process. Finally, the quantitative real-time PCR (qRT-PCR) was conducted to examine the association of methylation and gene expression of a set of different methylated genes. Our findings give deeper insight into the epigenetic regulation of gene expression during the plant tissue cultures process, which will be useful in the efficient control of somaclonal variations and in crop improvement.
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Affiliation(s)
- Qiang Cao
- School of Agriculture, Yunnan University, Kunming, China
| | - Yuxi Feng
- School of Agriculture, Yunnan University, Kunming, China
| | - Xiongwei Dai
- School of Agriculture, Yunnan University, Kunming, China
| | - Lin Huang
- School of Agriculture, Yunnan University, Kunming, China
| | - Jiamin Li
- School of Agriculture, Yunnan University, Kunming, China
| | - Pang Tao
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Qin Qiao
- School of Agriculture, Yunnan University, Kunming, China
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Hallberg I, Persson S, Olovsson M, Sirard MA, Damdimopoulou P, Rüegg J, Sjunnesson YCB. Perfluorooctane sulfonate (PFOS) exposure of bovine oocytes affects early embryonic development at human-relevant levels in an in vitro model. Toxicology 2021; 464:153028. [PMID: 34762985 DOI: 10.1016/j.tox.2021.153028] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/20/2021] [Accepted: 11/04/2021] [Indexed: 02/02/2023]
Abstract
Perfluorooctane sulfonate (PFOS) has been added to Stockholm Convention for global phase out, but will continue to contribute to the chemical burden in humans for a long time to come due to extreme persistence in the environment. In the body, PFOS is transferred into to the ovarian follicular fluid that surrounds the maturing oocyte. In the present study, bovine cumulus oocyte complexes were exposed to PFOS during 22 h in vitro maturation. Concentrations of 2 ng g-1 (PFOS-02) representing average human exposure and 53 ng g-1 (PFOS-53) relevant to highly exposed groups were used. After exposure, developmental competence was recorded until day 8 after fertilisation. Blastocysts were fixed and either stained to evaluate blastomere number and lipid distribution using confocal microscopy or frozen and pooled for microarray-based gene expression and DNA methylation analyses. PFOS-53 delayed the first cleavage to two-cell stage and beyond at 44 h after fertilisation (p < .01). No reduction of proportion blastocysts were seen at day 8 in either of the groups, but PFOS-53 exposure resulted in delayed development into more advanced stages of blastocysts seen as both reduced developmental stage (p = .001) and reduced number of blastomeres (p = .04). Blastocysts showed an altered lipid distribution that was more pronounced after exposure to PFOS-53 (increased total lipid volume, p=.0003, lipid volume/cell p < .0001) than PFOS-02, where only decreased average lipid droplet size (p=.02) was observed. Gene expression analyses revealed pathways differently regulated in the PFOS-treated groups compared to the controls, which were related to cell death and survival through e.g., P38 mitogen-activated protein kinases and signal transducer and activator of transcription 3, which in turn activates tumour protein 53 (TP53). Transcriptomic changes were also associated with metabolic stress response, differentiation and proliferation, which could help to explain the phenotypic changes seen in the blastocysts. The gene expression changes were more pronounced after exposure to PFOS-53 compared to PFOS-02. DNA-methylation changes were associated with similar biological functions as the transcriptomic data, with the most significantly associated pathway being TP53. Collectively, these results reveal that brief PFOS exposure during oocyte maturation alters the early embryo development at concentrations relevant to humans. This study adds to the evidence that PFOS has the potential to affect female fertility.
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Affiliation(s)
- Ida Hallberg
- Department of Clinical Sciences, Division of Reproduction, The Centre for Reproductive Biology in Uppsala, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
| | - Sara Persson
- Department of Clinical Sciences, Division of Reproduction, The Centre for Reproductive Biology in Uppsala, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Matts Olovsson
- Department of Women's and Children's Health, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Marc-André Sirard
- Department of Animal Sciences, Laval University, QC G1V 0A6, Quebec, Canada
| | - Pauliina Damdimopoulou
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, SE-141 86, Stockholm, Sweden
| | - Joëlle Rüegg
- Department of Organismal Biology, Program of Environmental Toxicology, Uppsala University, SE-752 36, Uppsala, Sweden
| | - Ylva C B Sjunnesson
- Department of Clinical Sciences, Division of Reproduction, The Centre for Reproductive Biology in Uppsala, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
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Rabaglino MB, Bojsen-Møller Secher J, Sirard MA, Hyttel P, Kadarmideen HN. Epigenomic and transcriptomic analyses reveal early activation of the HPG axis in in vitro-produced male dairy calves. FASEB J 2021; 35:e21882. [PMID: 34460963 DOI: 10.1096/fj.202101067r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/03/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022]
Abstract
In cattle, several calves born after IVP ("in vitro" embryo production) present similar birthweight to those generated after MOET (multiple ovulation and embryo transfer). However, the underlying molecular patterns in organs involved in the developmental process are unknown and could indicate physiological programming. The objectives of this study were: (1) to compare epigenomic and transcriptomic modifications in the hypothalamus, pituitary, gonadal and adrenal organs between 3 months old ovum pick-up-IVP and MOET male calves (n = 4 per group) and (2) to use blood epigenomic data to proxy methylation of the inner organs. Extracted gDNA and RNA were sequenced through whole-genome bisulfite sequencing and RNA sequencing, respectively. Next, bioinformatic analyses determined differentially methylated cytosines (DMC) and differentially expressed genes (DEG) (FDR < 0.05) in IVP versus MOET samples and the KEGG pathways that were overrepresented by genes associated with DMC or DEG (FDR < 0.1). Pathways related to hypothalamus, pituitary, gonadal (HPG) axis activation (GnRH secretion in the hypothalamus, GnRH signaling in the pituitary, and steroidogenesis in the testicle) were enriched in IVP calves. Modeling the effect of the methylation levels and the group on the expression of all the genes involved in these pathways confirmed their upregulation in HPG organs in IVP calves. The application of the DIABLO method allowed the identification of 15 epigenetic and five transcriptomic biomarkers, which were able to predict the embryo origin using the epigenomic data from the blood. In conclusion, the use of an integrated epigenomic-transcriptomic approach suggested an early activation of the HPG axis in male IVP calves compared to MOET counterparts, and the identification of potential biomarkers allowed the use of blood samples to proxy methylation levels of the relevant internal organs.
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Affiliation(s)
- María B Rabaglino
- Quantitative Genetics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
| | | | - Marc-André Sirard
- Departement des Sciences Animales, Centre de Recherche en Reproduction, Développement et Santé Inter-générationnelle (CRDSI), Université Laval, Laval, Quebec, Canada
| | - Poul Hyttel
- Department of Veterinary Clinical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Haja N Kadarmideen
- Quantitative Genetics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
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46
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Kubiak-Szymendera M, Pryszcz LP, Białas W, Celińska E. Epigenetic Response of Yarrowia lipolytica to Stress: Tracking Methylation Level and Search for Methylation Patterns via Whole-Genome Sequencing. Microorganisms 2021; 9:microorganisms9091798. [PMID: 34576693 PMCID: PMC8471669 DOI: 10.3390/microorganisms9091798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 01/02/2023] Open
Abstract
DNA methylation is a common, but not universal, epigenetic modification that plays an important role in multiple cellular processes. While definitely settled for numerous plant, mammalian, and bacterial species, the genome methylation in different fungal species, including widely studied and industrially-relevant yeast species, Yarrowia lipolytica, is still a matter of debate. In this paper, we report a differential DNA methylation level in the genome of Y. lipolytica subjected to sequential subculturing and to heat stress conditions. To this end, we adopted repeated batch bioreactor cultivations of Y. lipolytica subjected to thermal stress in specific time intervals. To analyze the variation in DNA methylation between stressed and control cultures, we (a) quantified the global DNA methylation status using an immuno-assay, and (b) studied DNA methylation patterns through whole-genome sequencing. Primarily, we demonstrated that 5 mC modification can be detected using a commercial immuno-assay, and that the modifications are present in Y. lipolytica’s genome at ~0.5% 5 mC frequency. On the other hand, we did not observe any changes in the epigenetic response of Y. lipolytica to heat shock (HS) treatment. Interestingly, we identified a general phenomenon of decreased 5 mC level in Y. lipolytica’s genome in the stationary phase of growth, when compared to a late-exponential epigenome. While this study provides an insight into the subculturing stress response and adaptation to the stress at epigenetic level by Y. lipolytica, it also leaves an open question of inability to detect any genomic DNA methylation level (either in CpG context or context-less) through whole-genome sequencing. The results of ONT sequencing, suggesting that 5 mC modification is either rare or non-existent in Y. lipolytica genome, are contradicted with the results of the immunoassay.
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Affiliation(s)
- Monika Kubiak-Szymendera
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
| | - Leszek P. Pryszcz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain;
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
- Correspondence:
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47
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Sahm A, Koch P, Horvath S, Hoffmann S. An analysis of methylome evolution in primates. Mol Biol Evol 2021; 38:4700-4714. [PMID: 34175932 PMCID: PMC8557466 DOI: 10.1093/molbev/msab189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Although the investigation of the epigenome becomes increasingly important, still little is known about the long-term evolution of epigenetic marks and systematic investigation strategies are still lacking. Here, we systematically demonstrate the transfer of classic phylogenetic methods such as maximum likelihood based on substitution models, parsimony, and distance-based to interval-scaled epigenetic data. Using a great apes blood data set, we demonstrate that DNA methylation is evolutionarily conserved at the level of individual CpGs in promotors, enhancers, and genic regions. Our analysis also reveals that this epigenomic conservation is significantly correlated with its transcription factor binding density. Binding sites for transcription factors involved in neuron differentiation and components of AP-1 evolve at a significantly higher rate at methylation than at the nucleotide level. Moreover, our models suggest an accelerated epigenomic evolution at binding sites of BRCA1, chromobox homolog protein 2, and factors of the polycomb repressor 2 complex in humans. For most genomic regions, the methylation-based reconstruction of phylogenetic trees is at par with sequence-based reconstruction. Most strikingly, phylogenetic reconstruction using methylation rates in enhancer regions was ineffective independently of the chosen model. We identify a set of phylogenetically uninformative CpG sites enriched in enhancers controlling immune-related genes.
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Affiliation(s)
- Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Philipp Koch
- Core Facility Life Science Computing, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
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48
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Womersley JS, Nothling J, Toikumo S, Malan-Müller S, van den Heuvel LL, McGregor NW, Seedat S, Hemmings SMJ. Childhood trauma, the stress response and metabolic syndrome: A focus on DNA methylation. Eur J Neurosci 2021; 55:2253-2296. [PMID: 34169602 DOI: 10.1111/ejn.15370] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/13/2021] [Accepted: 06/12/2021] [Indexed: 12/12/2022]
Abstract
Childhood trauma (CT) is well established as a potent risk factor for the development of mental disorders. However, the potential of adverse early experiences to exert chronic and profound effects on physical health, including aberrant metabolic phenotypes, has only been more recently explored. Among these consequences is metabolic syndrome (MetS), which is characterised by at least three of five related cardiometabolic traits: hypertension, insulin resistance/hyperglycaemia, raised triglycerides, low high-density lipoprotein and central obesity. The deleterious effects of CT on health outcomes may be partially attributable to dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis, which coordinates the response to stress, and the consequent fostering of a pro-inflammatory environment. Epigenetic tags, such as DNA methylation, which are sensitive to environmental influences provide a means whereby the effects of CT can be biologically embedded and persist into adulthood to affect health and well-being. The methylome regulates the transcription of genes involved in the stress response, metabolism and inflammation. This narrative review examines the evidence for DNA methylation in CT and MetS in order to identify shared neuroendocrine and immune correlates that may mediate the increased risk of MetS following CT exposure. Our review specifically highlights differential methylation of FKBP5, the gene that encodes FK506-binding protein 51 and has pleiotropic effects on stress responding, inflammation and energy metabolism, as a central candidate to understand the molecular aetiology underlying CT-associated MetS risk.
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Affiliation(s)
- Jacqueline S Womersley
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jani Nothling
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Gender and Health Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Sylvanus Toikumo
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stefanie Malan-Müller
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Leigh L van den Heuvel
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nathaniel W McGregor
- Systems Genetics Working Group, Department of Genetics, Faculty of Agriculture, Stellenbosch University, Stellenbosch, South Africa
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Sîan M J Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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49
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Yoshioka K, Nagahisa H, Miura F, Araki H, Kamei Y, Kitajima Y, Seko D, Nogami J, Tsuchiya Y, Okazaki N, Yonekura A, Ohba S, Sumita Y, Chiba K, Ito K, Asahina I, Ogawa Y, Ito T, Ohkawa Y, Ono Y. Hoxa10 mediates positional memory to govern stem cell function in adult skeletal muscle. SCIENCE ADVANCES 2021; 7:7/24/eabd7924. [PMID: 34108202 PMCID: PMC8189581 DOI: 10.1126/sciadv.abd7924] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 04/21/2021] [Indexed: 05/04/2023]
Abstract
Muscle stem cells (satellite cells) are distributed throughout the body and have heterogeneous properties among muscles. However, functional topographical genes in satellite cells of adult muscle remain unidentified. Here, we show that expression of Homeobox-A (Hox-A) cluster genes accompanied with DNA hypermethylation of the Hox-A locus was robustly maintained in both somite-derived muscles and their associated satellite cells in adult mice, which recapitulates their embryonic origin. Somite-derived satellite cells were clearly separated from cells derived from cranial mesoderm in Hoxa10 expression. Hoxa10 inactivation led to genomic instability and mitotic catastrophe in somite-derived satellite cells in mice and human. Satellite cell-specific Hoxa10 ablation in mice resulted in a decline in the regenerative ability of somite-derived muscles, which were unobserved in cranial mesoderm-derived muscles. Thus, our results show that Hox gene expression profiles instill the embryonic history in satellite cells as positional memory, potentially modulating region-specific pathophysiology in adult muscles.
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Affiliation(s)
- Kiyoshi Yoshioka
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
- Musculoskeletal Molecular Biology Research Group, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
- Department of Molecular Bone Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
| | - Hiroshi Nagahisa
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Hiromitsu Araki
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Yasutomi Kamei
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Yasuo Kitajima
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
- Musculoskeletal Molecular Biology Research Group, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
| | - Daiki Seko
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
- Musculoskeletal Molecular Biology Research Group, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
- Department of Molecular Bone Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
| | - Jumpei Nogami
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshifumi Tsuchiya
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
- Musculoskeletal Molecular Biology Research Group, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
| | - Narihiro Okazaki
- Department of Orthopaedic Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Akihiko Yonekura
- Department of Orthopaedic Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Seigo Ohba
- Department of Regenerative Oral Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Yoshinori Sumita
- Department of Regenerative Oral Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Ko Chiba
- Department of Orthopaedic Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Kosei Ito
- Department of Molecular Bone Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
| | - Izumi Asahina
- Department of Regenerative Oral Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yusuke Ono
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan.
- Musculoskeletal Molecular Biology Research Group, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto 860-0811, Japan
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50
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Rabaglino MB, O’Doherty A, Bojsen-Møller Secher J, Lonergan P, Hyttel P, Fair T, Kadarmideen HN. Application of multi-omics data integration and machine learning approaches to identify epigenetic and transcriptomic differences between in vitro and in vivo produced bovine embryos. PLoS One 2021; 16:e0252096. [PMID: 34029343 PMCID: PMC8143403 DOI: 10.1371/journal.pone.0252096] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/09/2021] [Indexed: 01/16/2023] Open
Abstract
Pregnancy rates for in vitro produced (IVP) embryos are usually lower than for embryos produced in vivo after ovarian superovulation (MOET). This is potentially due to alterations in their trophectoderm (TE), the outermost layer in physical contact with the maternal endometrium. The main objective was to apply a multi-omics data integration approach to identify both temporally differentially expressed and differentially methylated genes (DEG and DMG), between IVP and MOET embryos, that could impact TE function. To start, four and five published transcriptomic and epigenomic datasets, respectively, were processed for data integration. Second, DEG from day 7 to days 13 and 16 and DMG from day 7 to day 17 were determined in the TE from IVP vs. MOET embryos. Third, genes that were both DE and DM were subjected to hierarchical clustering and functional enrichment analysis. Finally, findings were validated through a machine learning approach with two additional datasets from day 15 embryos. There were 1535 DEG and 6360 DMG, with 490 overlapped genes, whose expression profiles at days 13 and 16 resulted in three main clusters. Cluster 1 (188) and Cluster 2 (191) genes were down-regulated at day 13 or day 16, respectively, while Cluster 3 genes (111) were up-regulated at both days, in IVP embryos compared to MOET embryos. The top enriched terms were the KEGG pathway "focal adhesion" in Cluster 1 (FDR = 0.003), and the cellular component: "extracellular exosome" in Cluster 2 (FDR<0.0001), also enriched in Cluster 1 (FDR = 0.04). According to the machine learning approach, genes in Cluster 1 showed a similar expression pattern between IVP and less developed (short) MOET conceptuses; and between MOET and DKK1-treated (advanced) IVP conceptuses. In conclusion, these results suggest that early conceptuses derived from IVP embryos exhibit epigenomic and transcriptomic changes that later affect its elongation and focal adhesion, impairing post-transfer survival.
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Affiliation(s)
- Maria B. Rabaglino
- Quantitative Genetics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
| | - Alan O’Doherty
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Jan Bojsen-Møller Secher
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Poul Hyttel
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Trudee Fair
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Haja N. Kadarmideen
- Quantitative Genetics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
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