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Yu X, Li S. Specific regulation of epigenome landscape by metabolic enzymes and metabolites. Biol Rev Camb Philos Soc 2024; 99:878-900. [PMID: 38174803 DOI: 10.1111/brv.13049] [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: 02/07/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Metabolism includes anabolism and catabolism, which play an essential role in many biological processes. Chromatin modifications are post-translational modifications of histones and nucleic acids that play important roles in regulating chromatin-associated processes such as gene transcription. There is a tight connection between metabolism and chromatin modifications. Many metabolic enzymes and metabolites coordinate cellular activities with alterations in nutrient availability by regulating gene expression through epigenetic mechanisms such as DNA methylation and histone modifications. The dysregulation of gene expression by metabolism and epigenetic modifications may lead to diseases such as diabetes and cancer. Recent studies reveal that metabolic enzymes and metabolites specifically regulate chromatin modifications, including modification types, modification residues and chromatin regions. This specific regulation has been implicated in the development of human diseases, yet the underlying mechanisms are only beginning to be uncovered. In this review, we summarise recent studies of the molecular mechanisms underlying the metabolic regulation of histone and DNA modifications and discuss how they contribute to pathogenesis. We also describe recent developments in technologies used to address the key questions in this field. We hope this will inspire further in-depth investigations of the specific regulatory mechanisms involved, and most importantly will shed lights on the development of more effective disease therapies.
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Affiliation(s)
- Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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2
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Stötzel M, Cheng CY, IIik IA, Kumar AS, Omgba PA, van der Weijden VA, Zhang Y, Vingron M, Meissner A, Aktaş T, Kretzmer H, Bulut-Karslioğlu A. TET activity safeguards pluripotency throughout embryonic dormancy. Nat Struct Mol Biol 2024:10.1038/s41594-024-01313-7. [PMID: 38783076 DOI: 10.1038/s41594-024-01313-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Dormancy is an essential biological process for the propagation of many life forms through generations and stressful conditions. Early embryos of many mammals are preservable for weeks to months within the uterus in a dormant state called diapause, which can be induced in vitro through mTOR inhibition. Cellular strategies that safeguard original cell identity within the silent genomic landscape of dormancy are not known. Here we show that the protection of cis-regulatory elements from silencing is key to maintaining pluripotency in the dormant state. We reveal a TET-transcription factor axis, in which TET-mediated DNA demethylation and recruitment of methylation-sensitive transcription factor TFE3 drive transcriptionally inert chromatin adaptations during dormancy transition. Perturbation of TET activity compromises pluripotency and survival of mouse embryos under dormancy, whereas its enhancement improves survival rates. Our results reveal an essential mechanism for propagating the cellular identity of dormant cells, with implications for regeneration and disease.
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Affiliation(s)
- Maximilian Stötzel
- Stem Cell Chromatin Lab, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Chieh-Yu Cheng
- Stem Cell Chromatin Lab, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Ibrahim A IIik
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Abhishek Sampath Kumar
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Persia Akbari Omgba
- Stem Cell Chromatin Lab, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | | | - Yufei Zhang
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tuğçe Aktaş
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
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3
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Shen X, Wang J, Deng B, Zhao Z, Chen S, Kong W, Zhou C, Bae-Jump V. Review of the Potential Role of Ascorbate in the Prevention and Treatment of Gynecological Cancers. Antioxidants (Basel) 2024; 13:617. [PMID: 38790722 PMCID: PMC11118910 DOI: 10.3390/antiox13050617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Ascorbate (vitamin C) is an essential vitamin for the human body and participates in various physiological processes as an important coenzyme and antioxidant. Furthermore, the role of ascorbate in the prevention and treatment of cancer including gynecological cancer has gained much more interest recently. The bioavailability and certain biological functions of ascorbate are distinct in males versus females due to differences in lean body mass, sex hormones, and lifestyle factors. Despite epidemiological evidence that ascorbate-rich foods and ascorbate plasma concentrations are inversely related to cancer risk, ascorbate has not demonstrated a significant protective effect in patients with gynecological cancers. Adequate ascorbate intake may have the potential to reduce the risk of human papillomavirus (HPV) infection and high-risk HPV persistence status. High-dose ascorbate exerts antitumor activity and synergizes with chemotherapeutic agents in preclinical cancer models of gynecological cancer. In this review, we provide evidence for the biological activity of ascorbate in females and discuss the potential role of ascorbate in the prevention and treatment of ovarian, endometrial, and cervical cancers.
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Affiliation(s)
- Xiaochang Shen
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100006, China; (X.S.); (J.W.); (B.D.); (Z.Z.); (S.C.); (W.K.)
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jiandong Wang
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100006, China; (X.S.); (J.W.); (B.D.); (Z.Z.); (S.C.); (W.K.)
| | - Boer Deng
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100006, China; (X.S.); (J.W.); (B.D.); (Z.Z.); (S.C.); (W.K.)
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ziyi Zhao
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100006, China; (X.S.); (J.W.); (B.D.); (Z.Z.); (S.C.); (W.K.)
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shuning Chen
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100006, China; (X.S.); (J.W.); (B.D.); (Z.Z.); (S.C.); (W.K.)
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Weimin Kong
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100006, China; (X.S.); (J.W.); (B.D.); (Z.Z.); (S.C.); (W.K.)
| | - Chunxiao Zhou
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Victoria Bae-Jump
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Maruta T, Tanaka Y, Yamamoto K, Ishida T, Hamada A, Ishikawa T. Evolutionary insights into strategy shifts for the safe and effective accumulation of ascorbate in plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2664-2681. [PMID: 38452239 DOI: 10.1093/jxb/erae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/06/2024] [Indexed: 03/09/2024]
Abstract
Plants accumulate high concentrations of ascorbate, commonly in their leaves, as a redox buffer. While ascorbate levels have increased during plant evolution, the mechanisms behind this phenomenon are unclear. Moreover, has the increase in ascorbate concentration been achieved without imposing any detrimental effects on the plants? In this review, we focus on potential transitions in two regulatory mechanisms related to ascorbate biosynthesis and the availability of cellular dehydroascorbate (DHA) during plant evolution. The first transition might be that the trigger for the transcriptional induction of VTC2, which encodes the rate-limiting enzyme in ascorbate biosynthesis, has shifted from oxidative stress (in green algae) to light/photosynthesis (in land plants), probably enabling the continuous accumulation of ascorbate under illumination. This could serve as a preventive system against the unpredictable occurrence of oxidative stress. The second transition might be that DHA-degrading enzymes, which protect cells from the highly reactive DHA in green algae and mosses, have been lost in ferns or flowering plants. Instead, flowering plants may have increased glutathione concentrations to reinforce the DHA reduction capacity, possibly allowing ascorbate accumulation and avoiding the toxicity of DHA. These potential transitions may have contributed to strategies for plants' safe and effective accumulation of ascorbate.
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Affiliation(s)
- Takanori Maruta
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
- Bioresource and Life Sciences, The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Yasuhiro Tanaka
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
- Bioresource and Life Sciences, The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan
| | - Kojiro Yamamoto
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Tetsuya Ishida
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Akane Hamada
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Takahiro Ishikawa
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
- Bioresource and Life Sciences, The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
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Missong H, Joshi R, Khullar N, Thareja S, Navik U, Bhatti GK, Bhatti JS. Nutrient-epigenome interactions: Implications for personalized nutrition against aging-associated diseases. J Nutr Biochem 2024; 127:109592. [PMID: 38325612 DOI: 10.1016/j.jnutbio.2024.109592] [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: 10/15/2023] [Revised: 01/28/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Aging is a multifaceted process involving genetic and environmental interactions often resulting in epigenetic changes, potentially leading to aging-related diseases. Various strategies, like dietary interventions and calorie restrictions, have been employed to modify these epigenetic landscapes. A burgeoning field of interest focuses on the role of microbiota in human health, emphasizing system biology and computational approaches. These methods help decipher the intricate interplay between diet and gut microbiota, facilitating the creation of personalized nutrition strategies. In this review, we analysed the mechanisms related to nutritional interventions while highlighting the influence of dietary strategies, like calorie restriction and intermittent fasting, on microbial composition and function. We explore how gut microbiota affects the efficacy of interventions using tools like multi-omics data integration, network analysis, and machine learning. These tools enable us to pinpoint critical regulatory elements and generate individualized models for dietary responses. Lastly, we emphasize the need for a deeper comprehension of nutrient-epigenome interactions and the potential of personalized nutrition informed by individual genetic and epigenetic profiles. As knowledge and technology advance, dietary epigenetics stands on the cusp of reshaping our strategy against aging and related diseases.
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Affiliation(s)
- Hemi Missong
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Riya Joshi
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Umashanker Navik
- Department of Pharmacology, Central University of Punjab, Bathinda, Punjab, India
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, Punjab, India.
| | - Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India.
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Da W, Song Z, Liu X, Wang Y, Wang S, Ma J. The role of TET2 in solid tumors and its therapeutic potential: a comprehensive review. Clin Transl Oncol 2024:10.1007/s12094-024-03478-5. [PMID: 38598002 DOI: 10.1007/s12094-024-03478-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024]
Abstract
Indeed, tumors are a significant health concern worldwide, and understanding the underlying mechanisms of tumor development is crucial for effective prevention and treatment. Epigenetics, which refers to changes in gene expression that are not caused by alterations in the DNA sequence itself, plays a critical role in the entire process of tumor development. It goes without saying that the effect of methylation on tumors is a significant aspect of epigenetics. Among the methylation modifications, DNA methylation is an important part, which plays a regulatory role in tumor-related genes. Ten-eleven translocation 2 (TET2) is a highly influential protein involved in the modification of DNA methylation. Its primary role is associated with the suppression of tumor development, making it a significant player in cancer research. However, TET2 is frequently mentioned in hematological diseases, its role in solid tumors has received little attention. Studying the changes of TET2 in solid tumors and the regulatory mechanism will facilitate its investigation as a clinical target for targeted therapy and may also provide directions for clinical treatment of malignant tumors.
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Affiliation(s)
- Wenxin Da
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Xuefu Road No. 301, Zhenjiang, 212013, China
| | - Ziyu Song
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Xuefu Road No. 301, Zhenjiang, 212013, China
| | - Xiaodong Liu
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Xuefu Road No. 301, Zhenjiang, 212013, China
| | - Yahui Wang
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Xuefu Road No. 301, Zhenjiang, 212013, China
| | - Shengjun Wang
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Xuefu Road No. 301, Zhenjiang, 212013, China
| | - Jie Ma
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Xuefu Road No. 301, Zhenjiang, 212013, China.
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7
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Liu X, He W, Hu L. Exploring transient global transcriptional changes induced by ascorbic acid revealed via atKAS-seq profiling. Funct Integr Genomics 2024; 24:66. [PMID: 38526630 DOI: 10.1007/s10142-024-01349-4] [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: 02/01/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024]
Abstract
Transcription initiates the formation of single-stranded DNA (ssDNA) regions within the genome, delineating transcription bubbles, a highly dynamic genomic process. Kethoxal-assisted single-stranded DNA sequencing (KAS-seq) utilizing N3-kethoxal has emerged as a potent tool for mapping specific guanine positions in ssDNA on a genome-wide scale. However, the original KAS-seq method required the costly Accel-NGS Methyl-seq DNA library kit. This study introduces an optimized iteration of the KAS-seq technique, referred to as adapter-tagged KAS-seq (atKAS-seq), incorporating an adapter tagging strategy. This modification involves integrating sequencing adapters via complementary strand synthesis using random N9 tagging. Additionally, by harnessing the potential of ascorbic acid (ASC), recognized for inducing global epigenetic changes, we employed the atKAS-seq methodology to elucidate critical pathways influenced by short-term, high-dose ASC treatment. Our findings underscore that atKAS-seq enables rapid and precise analyses of transcription dynamics and enhancer activities concurrently. This method offers a streamlined, cost-efficient, and low-input approach, affirming its utility in probing intricate genomic regulatory mechanisms.
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Affiliation(s)
- Xiangyue Liu
- Cancer Institute, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Weizhi He
- Cancer Institute, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Lulu Hu
- Cancer Institute, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai, 200032, China.
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8
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Du P, Wu J. Hallmarks of totipotent and pluripotent stem cell states. Cell Stem Cell 2024; 31:312-333. [PMID: 38382531 PMCID: PMC10939785 DOI: 10.1016/j.stem.2024.01.009] [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: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Though totipotency and pluripotency are transient during early embryogenesis, they establish the foundation for the development of all mammals. Studying these in vivo has been challenging due to limited access and ethical constraints, particularly in humans. Recent progress has led to diverse culture adaptations of epiblast cells in vitro in the form of totipotent and pluripotent stem cells, which not only deepen our understanding of embryonic development but also serve as invaluable resources for animal reproduction and regenerative medicine. This review delves into the hallmarks of totipotent and pluripotent stem cells, shedding light on their key molecular and functional features.
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Affiliation(s)
- Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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9
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Kriukienė E, Tomkuvienė M, Klimašauskas S. 5-Hydroxymethylcytosine: the many faces of the sixth base of mammalian DNA. Chem Soc Rev 2024; 53:2264-2283. [PMID: 38205583 DOI: 10.1039/d3cs00858d] [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: 01/12/2024]
Abstract
Epigenetic phenomena play a central role in cell regulatory processes and are important factors for understanding complex human disease. One of the best understood epigenetic mechanisms is DNA methylation. In the mammalian genome, cytosines (C) in CpG dinucleotides were long known to undergo methylation at the 5-position of the pyrimidine ring (mC). Later it was found that mC can be oxidized to 5-hydroxymethylcytosine (hmC) or even further to 5-formylcytosine (fC) and to 5-carboxylcytosine (caC) by the action of 2-oxoglutarate-dependent dioxygenases of the TET family. These findings unveiled a long elusive mechanism of active DNA demethylation and bolstered a wave of studies in the area of epigenetic regulation in mammals. This review is dedicated to critical assessment of recent data on biochemical and chemical aspects of the formation and conversion of hmC in DNA, analytical techniques used for detection and mapping of this nucleobase in mammalian genomes as well as epigenetic roles of hmC in DNA replication, transcription, cell differentiation and human disease.
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Affiliation(s)
- Edita Kriukienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
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10
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Loh KM, Ang LT. Building human artery and vein endothelial cells from pluripotent stem cells, and enduring mysteries surrounding arteriovenous development. Semin Cell Dev Biol 2024; 155:62-75. [PMID: 37393122 DOI: 10.1016/j.semcdb.2023.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/07/2023] [Indexed: 07/03/2023]
Abstract
Owing to their manifold roles in health and disease, there have been intense efforts to synthetically generate blood vessels in vitro from human pluripotent stem cells (hPSCs). However, there are multiple types of blood vessel, including arteries and veins, which are molecularly and functionally different. How can we specifically generate either arterial or venous endothelial cells (ECs) from hPSCs in vitro? Here, we summarize how arterial or venous ECs arise during embryonic development. VEGF and NOTCH arbitrate the bifurcation of arterial vs. venous ECs in vivo. While manipulating these two signaling pathways biases hPSC differentiation towards arterial and venous identities, efficiently generating these two subtypes of ECs has remained challenging until recently. Numerous questions remain to be fully addressed. What is the complete identity, timing and combination of extracellular signals that specify arterial vs. venous identities? How do these extracellular signals intersect with fluid flow to modulate arteriovenous fate? What is a unified definition for endothelial progenitors or angioblasts, and when do arterial vs. venous potentials segregate? How can we regulate hPSC-derived arterial and venous ECs in vitro, and generate organ-specific ECs? In turn, answers to these questions could avail the production of arterial and venous ECs from hPSCs, accelerating vascular research, tissue engineering, and regenerative medicine.
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Affiliation(s)
- Kyle M Loh
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
| | - Lay Teng Ang
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
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11
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Ye C, Jiang N, Zheng J, Zhang S, Zhang J, Zhou J. Epigenetic therapy: Research progress of decitabine in the treatment of solid tumors. Biochim Biophys Acta Rev Cancer 2024; 1879:189066. [PMID: 38163523 DOI: 10.1016/j.bbcan.2023.189066] [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: 08/03/2023] [Revised: 12/06/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Decitabine's early successful therapeutic outcomes in hematologic malignancies have led to regulatory approvals from the Food and Drug Administration (FDA) and the European Medicines Agency (EMA) for addressing myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). These approvals have sparked keen interest in exploring the potential of decitabine for treating solid tumors. Continuous preclinical and clinical trials have proved that low doses of decitabine also bring benefits in treating solid tumors, and various proposed mechanisms attempt to explain the potential efficacy. It is important to note that the application of decitabine in solid tumors is still considered investigational. This article reviews the application mechanism and current status of decitabine in the treatment of solid tumors.
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Affiliation(s)
- Chenlin Ye
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Nan Jiang
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jing Zheng
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shumeng Zhang
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jingchen Zhang
- Department of Critical Care Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jianya Zhou
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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Liu J, Chu M, Zhang J, He J, Yang Q, Tao L, Wang Z, Yao F, Zhao W, Ouyang S, Chen L, Zhang S, Gao S, Tian J, Ren L, An L. Glutathione safeguards TET-dependent DNA demethylation and is critical for the acquisition of totipotency and pluripotency during preimplantation development. FASEB J 2024; 38:e23453. [PMID: 38318639 DOI: 10.1096/fj.202301220r] [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: 06/18/2023] [Revised: 12/21/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024]
Abstract
During early development, both genome-wide epigenetic reprogramming and metabolic remodeling are hallmark changes of normal embryogenesis. However, little is known about their relationship and developmental functions during the preimplantation window, which is essential for the acquisition of totipotency and pluripotency. Herein, we reported that glutathione (GSH), a ubiquitous intracellular protective antioxidant that maintains mitochondrial function and redox homeostasis, plays a critical role in safeguarding postfertilization DNA demethylation and is essential for establishing developmental potential in preimplantation embryos. By profiling mitochondria-related transcriptome that coupled with different pluripotency, we found GSH is a potential marker that is tightly correlated with full pluripotency, and its beneficial effect on prompting developmental potential was functionally conformed using in vitro fertilized mouse and bovine embryos as the model. Mechanistic study based on preimplantation embryos and embryonic stem cells further revealed that GSH prompts the acquisition of totipotency and pluripotency by facilitating ten-eleven-translocation (TET)-dependent DNA demethylation, and ascorbic acid (AsA)-GSH cycle is implicated in the process. In addition, we also reported that GSH serves as an oviductal paracrine factor that supports development potential of preimplantation embryos. Thus, our results not only advance the current knowledge of functional links between epigenetic reprogramming and metabolic remodeling during preimplantation development but also provided a promising approach for improving current in vitro culture system for assisted reproductive technology.
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Affiliation(s)
- Juan Liu
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha, China
| | - Meiqiang Chu
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Agriculture and Forestry Science, Linyi University, Linyi, Shandong, China
| | - Jingyu Zhang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiale He
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qianying Yang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Li Tao
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhaochen Wang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Fusheng Yao
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wei Zhao
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Si Ouyang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Chen
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuai Zhang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuai Gao
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianhui Tian
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Likun Ren
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Lei An
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
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13
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Guarnera L, Jha BK. TET2 mutation as prototypic clonal hematopoiesis lesion. Semin Hematol 2024; 61:51-60. [PMID: 38431463 PMCID: PMC10978279 DOI: 10.1053/j.seminhematol.2024.01.013] [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: 10/30/2023] [Revised: 01/12/2024] [Accepted: 01/28/2024] [Indexed: 03/05/2024]
Abstract
Loss of function TET2 mutation (TET2MT) is one of the most frequently observed lesions in clonal hematopoiesis (CH). TET2 a member TET-dioxygenase family of enzymes that along with TET1 and TET3, progressively oxidize 5-methyl cytosine (mC) resulting in regulated demethylation of promoter, enhancer and silencer elements of the genome. This process is critical for efficient transcription that determine cell lineage fate, proliferation and survival and the maintenance of the genomic fidelity with aging of the organism. Partial or complete loss-of-function TET2 mutations create regional and contextual DNA hypermethylation leading to gene silencing or activation that result in skewed myeloid differentiation and clonal expansion. In addition to myeloid skewing, loss of TET2 creates differentiation block and provides proliferative advantage to hematopoietic stem and progenitor cells (HSPCs). TET2MT is a prototypical lesion in CH, since the mutant clones dominate during stress hematopoiesis and often associates with evolution of myeloid malignancies. TET2MT clones has unique privilege to create and persist in pro-inflammatory milieu. Despite extensive knowledge regarding biochemical mechanisms underlying distorted myeloid differentiation, and enhanced self-replication of TET2MT HSPC, the mechanistic link of various pathogenesis associated with TET2 loss in CHIP is less understood. Here we review the recent development in TET2 biology and its probable mechanistic link in CH with aging and inflammation. We also explored the therapeutic strategies of targeting TET2MT associated CHIP and the utility of targeting TET2 in normal hematopoiesis and somatic cell reprograming. We explore the biochemical mechanisms and candidate therapies that emerged in last decade of research.
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Affiliation(s)
- Luca Guarnera
- Department of Biomedicine and Prevention, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy; Department of Translational Haematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Babal K Jha
- Department of Translational Haematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH; Center for Immunotherapy and Precision Immuno-Oncology (CITI), Lerner Research Institute (LRI) Cleveland Clinic, Cleveland, OH.
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14
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Jackson BT, Finley LWS. Metabolic regulation of the hallmarks of stem cell biology. Cell Stem Cell 2024; 31:161-180. [PMID: 38306993 PMCID: PMC10842269 DOI: 10.1016/j.stem.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Stem cells perform many different functions, each of which requires specific metabolic adaptations. Over the past decades, studies of pluripotent and tissue stem cells have uncovered a range of metabolic preferences and strategies that correlate with or exert control over specific cell states. This review aims to describe the common themes that emerge from the study of stem cell metabolism: (1) metabolic pathways supporting stem cell proliferation, (2) metabolic pathways maintaining stem cell quiescence, (3) metabolic control of cellular stress responses and cell death, (4) metabolic regulation of stem cell identity, and (5) metabolic requirements of the stem cell niche.
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Affiliation(s)
- Benjamin T Jackson
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Lydia W S Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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15
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Coker SJ, Berry MJ, Vissers MCM, Dyson RM. Maternal Vitamin C Intake during Pregnancy Influences Long-Term Offspring Growth with Timing- and Sex-Specific Effects in Guinea Pigs. Nutrients 2024; 16:369. [PMID: 38337653 PMCID: PMC10857109 DOI: 10.3390/nu16030369] [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: 12/18/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Our previous work in guinea pigs revealed that low vitamin C intake during preconception and pregnancy adversely affects fertility, pregnancy outcomes, and foetal and neonatal growth in a sex-dependent manner. To investigate the long-term impact on offspring, we monitored their growth from birth to adolescence (four months), recorded organ weights at childhood equivalence (28 days) and adolescence, and assessed physiological parameters like oral glucose tolerance and basal cortisol concentrations. We also investigated the effects of the timing of maternal vitamin C restriction (early vs. late gestation) on pregnancy outcomes and the health consequences for offspring. Dunkin Hartley guinea pigs were fed an optimal (900 mg/kg feed) or low (100 mg/kg feed) vitamin C diet ad libitum during preconception. Pregnant dams were then randomised into four feeding regimens: consistently optimal, consistently low, low during early pregnancy, or low during late pregnancy. We found that low maternal vitamin C intake during early pregnancy accelerated foetal and neonatal growth in female offspring and altered glucose homeostasis in the offspring of both sexes at an age equivalent to early childhood. Conversely, low maternal vitamin C intake during late pregnancy resulted in foetal growth restriction and reduced weight gain in male offspring throughout their lifespan. We conclude that altered vitamin C during development has long-lasting, sex-specific consequences for offspring and that the timing of vitamin C depletion is also critical, with low levels during early development being associated with the development of a metabolic syndrome-related phenotype, while later deprivation appears to be linked to a growth-faltering phenotype.
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Affiliation(s)
- Sharna J. Coker
- Perinatal and Developmental Physiology Group, Department of Paediatrics and Child Health, University of Otago, Wellington 6242, New Zealand; (M.J.B.); (R.M.D.)
| | - Mary J. Berry
- Perinatal and Developmental Physiology Group, Department of Paediatrics and Child Health, University of Otago, Wellington 6242, New Zealand; (M.J.B.); (R.M.D.)
| | - Margreet C. M. Vissers
- Mātai Hāora-Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8140, New Zealand;
| | - Rebecca M. Dyson
- Perinatal and Developmental Physiology Group, Department of Paediatrics and Child Health, University of Otago, Wellington 6242, New Zealand; (M.J.B.); (R.M.D.)
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16
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He W, Yin X, Xu C, Liu X, Huang Y, Yang C, Xu Y, Hu L. Ascorbic Acid Reprograms Epigenome and Epitranscriptome by Reducing Fe(III) in the Catalytic Cycle of Dioxygenases. ACS Chem Biol 2024; 19:129-140. [PMID: 38100359 DOI: 10.1021/acschembio.3c00567] [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: 12/17/2023]
Abstract
Ascorbic acid (ASC) has been reported to stimulate DNA iterative oxidase ten-eleven translocation (TET) enzymes, Jumonji C-domain-containing histone demethylases, and potentially RNA m6A demethylases FTO and ALKBH5 as a cofactor. Although ascorbic acid has been widely investigated in reprogramming DNA and histone methylation status in vitro, in cultured cells and mouse models, its specific role in the catalytic cycle of dioxygenases remains enigmatic. Here, we systematically investigated the stimulation of ASC toward TET2, ALKBH3, histone demethylases, and FTO. We find that ASC reprograms epitranscriptome by erasing the hypermethylated m6A sites in mRNA. Biochemistry and electron spin resonance assays demonstrate that ASC enters the active pocket of dioxygenases and reduces Fe(III), either incorporated upon protein synthesis or generated upon rebounding the hydroxyl radical during oxidation, into Fe(II). Finally, we propose a remedied model for the catalytic cycle of dioxygenases by adding in the essential cofactor, ASC, which refreshes and regenerates inactive dioxygenase through recycling Fe(III) into Fe(II) in a dynamic "hit-and-run" manner.
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Affiliation(s)
- Weizhi He
- Cancer Institute, Fudan university Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xiaotong Yin
- Cancer Institute, Fudan university Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Chu Xu
- Cancer Institute, Fudan university Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xiangyue Liu
- Cancer Institute, Fudan university Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yue Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Caiguang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanhui Xu
- Cancer Institute, Fudan university Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Lulu Hu
- Cancer Institute, Fudan university Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai 200032, China
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17
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Treadway CJ, Boyer JA, Yang S, Yang H, Liu M, Li Z, Cheng M, Marzluff WF, Ye D, Xiong Y, Baldwin AS, Zhang Q, Brown NG. Using NMR to Monitor TET-Dependent Methylcytosine Dioxygenase Activity and Regulation. ACS Chem Biol 2024; 19:15-21. [PMID: 38193366 PMCID: PMC11075173 DOI: 10.1021/acschembio.3c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The active removal of DNA methylation marks is governed by the ten-eleven translocation (TET) family of enzymes (TET1-3), which iteratively oxidize 5-methycytosine (5mC) into 5-hydroxymethycytosine (5hmC), and then 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TET proteins are frequently mutated in myeloid malignancies or inactivated in solid tumors. These methylcytosine dioxygenases are α-ketoglutarate (αKG)-dependent and are, therefore, sensitive to metabolic homeostasis. For example, TET2 is activated by vitamin C (VC) and inhibited by specific oncometabolites. However, understanding the regulation of the TET2 enzyme by different metabolites and its activity remains challenging because of limitations in the methods used to simultaneously monitor TET2 substrates, products, and cofactors during catalysis. Here, we measure TET2-dependent activity in real time using NMR. Additionally, we demonstrate that in vitro activity of TET2 is highly dependent on the presence of VC in our system and is potently inhibited by an intermediate metabolite of the TCA cycle, oxaloacetate (OAA). Despite these opposing effects on TET2 activity, the binding sites of VC and OAA on TET2 are shared with αKG. Overall, our work suggests that NMR can be effectively used to monitor TET2 catalysis and illustrates how TET activity is regulated by metabolic and cellular conditions at each oxidation step.
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Affiliation(s)
- Colton J Treadway
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joshua A Boyer
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Shiyue Yang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Hui Yang
- Molecular & Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai College of Medicine, Fudan University, Shanghai 200032, China
| | - Mengxi Liu
- Molecular & Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai College of Medicine, Fudan University, Shanghai 200032, China
| | - Zhijun Li
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Meng Cheng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William F Marzluff
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Dan Ye
- Molecular & Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai College of Medicine, Fudan University, Shanghai 200032, China
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Albert S Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nicholas G Brown
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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18
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Tseng YJ, Kageyama Y, Murdaugh RL, Kitano A, Kim JH, Hoegenauer KA, Tiessen J, Smith MH, Uryu H, Takahashi K, Martin JF, Samee MAH, Nakada D. Increased iron uptake by splenic hematopoietic stem cells promotes TET2-dependent erythroid regeneration. Nat Commun 2024; 15:538. [PMID: 38225226 PMCID: PMC10789814 DOI: 10.1038/s41467-024-44718-0] [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: 10/01/2021] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Hematopoietic stem cells (HSCs) are capable of regenerating the blood system, but the instructive cues that direct HSCs to regenerate particular lineages lost to the injury remain elusive. Here, we show that iron is increasingly taken up by HSCs during anemia and induces erythroid gene expression and regeneration in a Tet2-dependent manner. Lineage tracing of HSCs reveals that HSCs respond to hemolytic anemia by increasing erythroid output. The number of HSCs in the spleen, but not bone marrow, increases upon anemia and these HSCs exhibit enhanced proliferation, erythroid differentiation, iron uptake, and TET2 protein expression. Increased iron in HSCs promotes DNA demethylation and expression of erythroid genes. Suppressing iron uptake or TET2 expression impairs erythroid genes expression and erythroid differentiation of HSCs; iron supplementation, however, augments these processes. These results establish that the physiological level of iron taken up by HSCs has an instructive role in promoting erythroid-biased differentiation of HSCs.
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Affiliation(s)
- Yu-Jung Tseng
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yuki Kageyama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rebecca L Murdaugh
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ayumi Kitano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jong Hwan Kim
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kevin A Hoegenauer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jonathan Tiessen
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mackenzie H Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hidetaka Uryu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - James F Martin
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Cardiomyocyte Renewal Laboratory, Texas Heart Institute, Houston, TX, 77030, USA
| | - Md Abul Hassan Samee
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daisuke Nakada
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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19
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Schwarz SD, Xu J, Gunasekera K, Schürmann D, Vågbø CB, Ferrari E, Slupphaug G, Hottiger MO, Schär P, Steinacher R. Covalent PARylation of DNA base excision repair proteins regulates DNA demethylation. Nat Commun 2024; 15:184. [PMID: 38167803 PMCID: PMC10762122 DOI: 10.1038/s41467-023-44209-8] [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: 08/18/2022] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
The intracellular ATP-ribosyltransferases PARP1 and PARP2, contribute to DNA base excision repair (BER) and DNA demethylation and have been implicated in epigenetic programming in early mammalian development. Recently, proteomic analyses identified BER proteins to be covalently poly-ADP-ribosylated by PARPs. The role of this posttranslational modification in the BER process is unknown. Here, we show that PARP1 senses AP-sites and SSBs generated during TET-TDG mediated active DNA demethylation and covalently attaches PAR to each BER protein engaged. Covalent PARylation dissociates BER proteins from DNA, which accelerates the completion of the repair process. Consistently, inhibition of PARylation in mESC resulted both in reduced locus-specific TET-TDG-targeted DNA demethylation, and in reduced general repair of random DNA damage. Our findings establish a critical function of covalent protein PARylation in coordinating molecular processes associated with dynamic DNA methylation.
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Affiliation(s)
- Simon D Schwarz
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Jianming Xu
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Kapila Gunasekera
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - David Schürmann
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Cathrine B Vågbø
- Proteomics and Modomics Experimental Core Facility (PROMEC), Norwegian University of Science and Technology and St. Olavs Hospital, Trondheim, Norway
| | - Elena Ferrari
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Geir Slupphaug
- Proteomics and Modomics Experimental Core Facility (PROMEC), Norwegian University of Science and Technology and St. Olavs Hospital, Trondheim, Norway
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland.
| | - Roland Steinacher
- Department of Biomedicine, University of Basel, Basel, Switzerland.
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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20
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Kondoh H. Molecular Basis of Cell Reprogramming into iPSCs with Exogenous Transcription Factors. Results Probl Cell Differ 2024; 72:193-218. [PMID: 38509259 DOI: 10.1007/978-3-031-39027-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
A striking discovery in recent decades concerning the transcription factor (TF)-dependent process was the production of induced pluripotent stem cell (iPSCs) from fibroblasts by the exogenous expression of the TF cocktail containing Oct3/4 (Pou5f1), Sox2, Klf4, and Myc, collectively called OSKM. How fibroblast cells can be remodeled into embryonic stem cell (ESC)-like iPSCs despite high epigenetic barriers has opened a new essential avenue to understanding the action of TFs in developmental regulation. Two forerunning investigations preceded the iPSC phenomenon: exogenous TF-mediated cell remodeling driven by the action of MyoD, and the "pioneer TF" action to preopen chromatin, allowing multiple TFs to access enhancer sequences. The process of remodeling somatic cells into iPSCs has been broken down into multiple subprocesses: the initial attack of OSKM on closed chromatin, sequential changes in cytosine modification, enhancer usage, and gene silencing and activation. Notably, the OSKM TFs change their genomic binding sites extensively. The analyses are still at the descriptive stage, but currently available information is discussed in this chapter.
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Affiliation(s)
- Hisato Kondoh
- Osaka University, Suita, Osaka, Japan
- Biohistory Research Hall, Takatsuki, Osaka, Japan
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21
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Mishra S, Sharma A, Srivastava AK. Ascorbic acid: a metabolite switch for designing stress-smart crops. Crit Rev Biotechnol 2024:1-17. [PMID: 38163756 DOI: 10.1080/07388551.2023.2286428] [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: 07/27/2023] [Accepted: 11/02/2023] [Indexed: 01/03/2024]
Abstract
Plant growth and productivity are continually being challenged by a diverse array of abiotic stresses, including: water scarcity, extreme temperatures, heavy metal exposure, and soil salinity. A common theme in these stresses is the overproduction of reactive oxygen species (ROS), which disrupts cellular redox homeostasis causing oxidative damage. Ascorbic acid (AsA), commonly known as vitamin C, is an essential nutrient for humans, and also plays a crucial role in the plant kingdom. AsA is synthesized by plants through the d-mannose/l-galactose pathway that functions as a powerful antioxidant and protects plant cells from ROS generated during photosynthesis. AsA controls several key physiological processes, including: photosynthesis, respiration, and carbohydrate metabolism, either by acting as a co-factor for metabolic enzymes or by regulating cellular redox-status. AsA's multi-functionality uniquely positions it to integrate and recalibrate redox-responsive transcriptional/metabolic circuits and essential biological processes, in accordance to developmental and environmental cues. In recognition of this, we present a systematic overview of current evidence highlighting AsA as a central metabolite-switch in plants. Further, a comprehensive overview of genetic manipulation of genes involved in AsA metabolism has been provided along with the bottlenecks and future research directions, that could serve as a framework for designing "stress-smart" crops in future.
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Affiliation(s)
- Shefali Mishra
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ankush Sharma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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22
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Schulz M, Teissandier A, De La Mata Santaella E, Armand M, Iranzo J, El Marjou F, Gestraud P, Walter M, Kinston S, Göttgens B, Greenberg MVC, Bourc'his D. DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation. Nat Struct Mol Biol 2024; 31:102-114. [PMID: 38177678 DOI: 10.1038/s41594-023-01162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 10/26/2023] [Indexed: 01/06/2024]
Abstract
As embryonic stem cells (ESCs) transition from naive to primed pluripotency during early mammalian development, they acquire high DNA methylation levels. During this transition, the germline is specified and undergoes genome-wide DNA demethylation, while emergence of the three somatic germ layers is preceded by acquisition of somatic DNA methylation levels in the primed epiblast. DNA methylation is essential for embryogenesis, but the point at which it becomes critical during differentiation and whether all lineages equally depend on it is unclear. Here, using culture modeling of cellular transitions, we found that DNA methylation-free mouse ESCs with triple DNA methyltransferase knockout (TKO) progressed through the continuum of pluripotency states but demonstrated skewed differentiation abilities toward neural versus other somatic lineages. More saliently, TKO ESCs were fully competent for establishing primordial germ cell-like cells, even showing temporally extended and self-sustained capacity for the germline fate. By mapping chromatin states, we found that neural and germline lineages are linked by a similar enhancer dynamic upon exit from the naive state, defined by common sets of transcription factors, including methyl-sensitive ones, that fail to be decommissioned in the absence of DNA methylation. We propose that DNA methylation controls the temporality of a coordinated neural-germline axis of the preferred differentiation route during early development.
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Affiliation(s)
- Mathieu Schulz
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | - Aurélie Teissandier
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | | | - Mélanie Armand
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | - Julian Iranzo
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | - Fatima El Marjou
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | - Pierre Gestraud
- INSERM U900, MINES ParisTech, Institut Curie, PSL Research University, Paris, France
| | | | - Sarah Kinston
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Deborah Bourc'his
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France.
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23
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Sadida HQ, Abdulla A, Marzooqi SA, Hashem S, Macha MA, Akil ASAS, Bhat AA. Epigenetic modifications: Key players in cancer heterogeneity and drug resistance. Transl Oncol 2024; 39:101821. [PMID: 37931371 PMCID: PMC10654239 DOI: 10.1016/j.tranon.2023.101821] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/12/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
Cancer heterogeneity and drug resistance remain pivotal obstacles in effective cancer treatment and management. One major contributor to these challenges is epigenetic modifications - gene regulation that does not involve changes to the DNA sequence itself but significantly impacts gene expression. As we elucidate these phenomena, we underscore the pivotal role of epigenetic modifications in regulating gene expression, contributing to cellular diversity, and driving adaptive changes that can instigate therapeutic resistance. This review dissects essential epigenetic modifications - DNA methylation, histone modifications, and chromatin remodeling - illustrating their significant yet complex contributions to cancer biology. While these changes offer potential avenues for therapeutic intervention due to their reversible nature, the interplay of epigenetic and genetic changes in cancer cells presents unique challenges that must be addressed to harness their full potential. By critically analyzing the current research landscape, we identify knowledge gaps and propose future research directions, exploring the potential of epigenetic therapies and discussing the obstacles in translating these concepts into effective treatments. This comprehensive review aims to stimulate further research and aid in developing innovative, patient-centered cancer therapies. Understanding the role of epigenetic modifications in cancer heterogeneity and drug resistance is critical for scientific advancement and paves the way towards improving patient outcomes in the fight against this formidable disease.
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Affiliation(s)
- Hana Q Sadida
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Alanoud Abdulla
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Sara Al Marzooqi
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Sheema Hashem
- Laboratory of Genomic Medicine, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Jammu & Kashmir, India
| | - Ammira S Al-Shabeeb Akil
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar.
| | - Ajaz A Bhat
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar.
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24
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Manesia JK, Maganti HB, Almoflehi S, Jahan S, Hasan T, Pasha R, McGregor C, Dumont N, Laganière J, Audet J, Pineault N. AA2P-mediated DNA demethylation synergizes with stem cell agonists to promote expansion of hematopoietic stem cells. CELL REPORTS METHODS 2023; 3:100663. [PMID: 38070507 PMCID: PMC10783628 DOI: 10.1016/j.crmeth.2023.100663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 06/28/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023]
Abstract
Small molecules have enabled expansion of hematopoietic stem and progenitor cells (HSPCs), but limited knowledge is available on whether these agonists can act synergistically. In this work, we identify a stem cell agonist in AA2P and optimize a series of stem cell agonist cocktails (SCACs) to help promote robust expansion of human HSPCs. We find that SCACs provide strong growth-promoting activities while promoting retention and function of immature HSPC. We show that AA2P-mediated HSPC expansion is driven through DNA demethylation leading to enhanced expression of AXL and GAS6. Further, we demonstrate that GAS6 enhances the serial engraftment activity of HSPCs and show that the GAS6/AXL pathway is critical for robust HSPC expansion.
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Affiliation(s)
- Javed K Manesia
- Canadian Blood Services, Centre for Innovation, Ottawa, ON, Canada
| | - Harinad B Maganti
- Canadian Blood Services, Centre for Innovation, Ottawa, ON, Canada; Biochemistry, Microbiology and Immunology Department, University of Ottawa, Ottawa, ON, Canada
| | - Sakhar Almoflehi
- Canadian Blood Services, Centre for Innovation, Ottawa, ON, Canada; Biochemistry, Microbiology and Immunology Department, University of Ottawa, Ottawa, ON, Canada
| | - Suria Jahan
- Canadian Blood Services, Centre for Innovation, Ottawa, ON, Canada; Biochemistry, Microbiology and Immunology Department, University of Ottawa, Ottawa, ON, Canada
| | - Tanvir Hasan
- Canadian Blood Services, Centre for Innovation, Ottawa, ON, Canada; Biochemistry, Microbiology and Immunology Department, University of Ottawa, Ottawa, ON, Canada
| | - Roya Pasha
- Canadian Blood Services, Centre for Innovation, Ottawa, ON, Canada
| | - Chelsea McGregor
- Canadian Blood Services, Centre for Innovation, Ottawa, ON, Canada
| | | | | | - Julie Audet
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Nicolas Pineault
- Canadian Blood Services, Centre for Innovation, Ottawa, ON, Canada; Biochemistry, Microbiology and Immunology Department, University of Ottawa, Ottawa, ON, Canada.
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25
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Keshawarz A, Joehanes R, Ma J, Lee GY, Costeira R, Tsai PC, Masachs OM, Bell JT, Wilson R, Thorand B, Winkelmann J, Peters A, Linseisen J, Waldenberger M, Lehtimäki T, Mishra PP, Kähönen M, Raitakari O, Helminen M, Wang CA, Melton PE, Huang RC, Pennell CE, O’Sullivan TA, Ochoa-Rosales C, Voortman T, van Meurs JB, Young KL, Graff M, Wang Y, Kiel DP, Smith CE, Jacques PF, Levy D. Dietary and supplemental intake of vitamins C and E is associated with altered DNA methylation in an epigenome-wide association study meta-analysis. Epigenetics 2023; 18:2211361. [PMID: 37233989 PMCID: PMC10228397 DOI: 10.1080/15592294.2023.2211361] [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: 08/11/2022] [Accepted: 04/28/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Dietary intake of antioxidants such as vitamins C and E protect against oxidative stress, and may also be associated with altered DNA methylation patterns. METHODS We meta-analysed epigenome-wide association study (EWAS) results from 11,866 participants across eight population-based cohorts to evaluate the association between self-reported dietary and supplemental intake of vitamins C and E with DNA methylation. EWAS were adjusted for age, sex, BMI, caloric intake, blood cell type proportion, smoking status, alcohol consumption, and technical covariates. Significant results of the meta-analysis were subsequently evaluated in gene set enrichment analysis (GSEA) and expression quantitative trait methylation (eQTM) analysis. RESULTS In meta-analysis, methylation at 4,656 CpG sites was significantly associated with vitamin C intake at FDR ≤ 0.05. The most significant CpG sites associated with vitamin C (at FDR ≤ 0.01) were enriched for pathways associated with systems development and cell signalling in GSEA, and were associated with downstream expression of genes enriched in the immune response in eQTM analysis. Furthermore, methylation at 160 CpG sites was significantly associated with vitamin E intake at FDR ≤ 0.05, but GSEA and eQTM analysis of the top most significant CpG sites associated with vitamin E did not identify significant enrichment of any biological pathways investigated. CONCLUSIONS We identified significant associations of many CpG sites with vitamin C and E intake, and our results suggest that vitamin C intake may be associated with systems development and the immune response.
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Affiliation(s)
| | - Roby Joehanes
- Framingham Heart Study, Framingham, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jiantao Ma
- Framingham Heart Study, Framingham, Framingham, MA, USA
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Gha Young Lee
- Framingham Heart Study, Framingham, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Olatz M. Masachs
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg, Germany
| | - Barbara Thorand
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Chair of Neurogenetics, School of Medicine, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
- Chair of Epidemiology, Medical Faculty, Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Cardiovascular Research (DZHK), München Heart Alliance, Munich, Germany
| | - Jakob Linseisen
- Chair of Epidemiology, University Augsburg at University Hospital Augsburg, Augsburg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), München Heart Alliance, Munich, Germany
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Pashupati P. Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Mika Helminen
- Tays Research Services, Tampere University Hospital, Tampere, Finland
- Faculty of Social Sciences, Health Sciences, Tampere University, Tampere, Finland
| | - Carol A. Wang
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Phillip E. Melton
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- School of Population and Global Health, University of Western Australia, Perth, Australia
| | - Rae-Chi Huang
- Nutrition & Health Innovation Research Institute, Edith Cowan University, Perth, Australia
| | - Craig E. Pennell
- Faculty of Social Sciences, Health Sciences, Tampere University, Tampere, Finland
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | | | - Carolina Ochoa-Rosales
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Centro de Vida Saludable, Universidad de Concepción, Concepción, Chile
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Joyce B.J. van Meurs
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Kristin L. Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Hebrew Senior Life, Chapel Hill, North Carolina, USA
| | - Misa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Hebrew Senior Life, Chapel Hill, North Carolina, USA
| | - Yujie Wang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Hebrew Senior Life, Chapel Hill, North Carolina, USA
| | - Douglas P. Kiel
- Department of Medicine, Beth Israel Deaconess Medical Center, Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Caren E. Smith
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - Paul F. Jacques
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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26
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Gao J, Wang H, Shen J, Liu X, Zhu X, Huang C, Li G, Sun Y, Liu Z, Sun YE, Liu H. Mutual regulation between GDF11 and TET2 prevents senescence of mesenchymal stem cells. J Cell Physiol 2023; 238:2827-2840. [PMID: 37801347 DOI: 10.1002/jcp.31132] [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: 05/22/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
Growth differentiation factor 11 (GDF11) is a putative systemic rejuvenation factor. In this study, we characterized the mechanism by which GDF11 reversed aging of mesenchymal stem cells (MSCs). In culture, aged MSCs proliferate slower and are positive for senescence markers senescence-associated β-galactosidase and P16ink4a . They have shortened telomeres, decreased GDF11 expression, and reduced osteogenic potential. GDF11 can block MSC aging in vitro and reverse age-dependent bone loss in vivo. The antiaging effect of GDF11 is via activation of the Smad2/3-PI3K-AKT-mTOR pathway. Unexpectedly, GDF11 also upregulated a DNA demethylase Tet2, which served as a key mediator for GDF11 to autoregulate itself via demethylation of the GDF11 promoter. Mutation of Tet2 facilitates MSC aging by blocking GDF11 expression. Mutagenesis of Tet2-regulated CpG sites also blocks GDF11 expression, leading to MSC aging. Together, a novel mutual regulatory relationship between GDF11 and an epigenetic factor Tet2 unveiled their antiaging roles.
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Affiliation(s)
- Jiaming Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hao Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Junyan Shen
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaojing Liu
- Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoqi Zhu
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ce Huang
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Gongchen Li
- Department of Implantology, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, School of Stomatology, Tongji University, Shanghai, China
| | - Yao Sun
- Department of Implantology, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, School of Stomatology, Tongji University, Shanghai, China
| | - Zhongmin Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Eve Sun
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Implantology, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, School of Stomatology, Tongji University, Shanghai, China
- Department of Psychiatry and Biobehavioral Sciences, UCLA Medical School, Los Angeles, California, USA
| | - Hailiang Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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27
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Chang A, Martin KA, Colvin M, Bellumkonda L. Role of ascorbic acid in cardiac allograft vasculopathy. Clin Transplant 2023; 37:e15153. [PMID: 37792313 DOI: 10.1111/ctr.15153] [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: 06/08/2023] [Revised: 09/04/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023]
Abstract
PURPOSE OF THE REVIEW Cardiac allograft vasculopathy (CAV) is a progressive fibroproliferative disease which occurs after heart transplantation and is associated with significant long-term morbidity and mortality. Currently available strategies including statins, mammalian target of rapamycin (mTOR) inhibitors, and revascularization, have limited overall effectiveness in treating this pathology once the disease process is established. mTOR inhibitors, while effective when used early in the disease process, are not well tolerated, and hence not routinely used in post-transplant care. RECENT DATA Recent work on rodent models have given us a novel mechanistic understanding of effects of ascorbic acid in preventing CAV. TET methyl cytosine dioxygenase2 (TET2) reduces vascular smooth muscle cell (VSMC) apoptosis and intimal thickening. TET2 is repressed by interferon γ (IFNγ) in the setting of CAV. Ascorbic acid has been shown to promote TET2 activity and attenuate allograft vasculopathy in animal models and CAV progression in a small clinical trial. SUMMARY CAV remains a challenging disease process and needs better preventative strategies. Ascorbic acid improves endothelial dysfunction, reduces reactive oxygen species, and prevents development of intimal hyperplasia by preventing smooth muscle cell apoptosis and hyperproliferation. Further large-scale randomized control studies of ascorbic acid are needed to establish the role in routine post-transplant management.
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Affiliation(s)
- Alyssa Chang
- Department of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Kathleen A Martin
- Division of Cardiology, Department of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Monica Colvin
- Division of Cardiology, Department of Medicine, Yale University, New Haven, Connecticut, USA
| | - Lavanya Bellumkonda
- Division of Cardiology, Department of Medicine, University of Michigan, Ann Arbor, Michigan, USA
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28
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Ussishkin N, Nachmani D. A Bloody Feast-Nutritional Regulation of Hematopoiesis. Exp Hematol 2023; 127:1-7. [PMID: 37582454 DOI: 10.1016/j.exphem.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 08/17/2023]
Abstract
Hematopoietic stem cells provide us with a lifelong supply of blood cells. Hence, their proper function is absolutely essential for life, and their dysfunction can lead to infectious and malignant diseases. These cells have specific metabolic requirements to enable their lifelong function and blood-producing capacity. With the words of the Roman poet Juvenal "a healthy mind in a healthy body" in mind, it is intriguing to understand the connection between our daily diet and the quality of our blood, with the hope that through specific dietary adjustments we can improve our hematopoietic stem cell function and prevent disease. Nowadays, dietary supplements are an expanding market filled with potential and promises for better health. However, the link between many of those supplements and human physiology is obscure. Several groups have begun to shed light on this by investigating the metabolic regulation of hematopoiesis by specific nutrients. Beyond the link to dietary supplementation, these studies have also significantly improved our understanding of basic hematopoietic stem cell biology. Herein we summarize recent knowledge on the effect of specific vitamins and amino acids, which might be considered as dietary supplements, on normal hematopoiesis and hematopoietic stem cell function. We propose that improving our understanding of the link between nutrition in general and blood physiology can ultimately lead to the optimization of health-care policies, protocols, and standards of care.
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Affiliation(s)
- Noga Ussishkin
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Daphna Nachmani
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel.
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29
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Aarabi F, Ghigi A, Ahchige MW, Bulut M, Geigenberger P, Neuhaus HE, Sampathkumar A, Alseekh S, Fernie AR. Genome-wide association study unveils ascorbate regulation by PAS/LOV PROTEIN during high light acclimation. PLANT PHYSIOLOGY 2023; 193:2037-2054. [PMID: 37265123 PMCID: PMC10602610 DOI: 10.1093/plphys/kiad323] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 06/03/2023]
Abstract
Varying light conditions elicit metabolic responses as part of acclimation with changes in ascorbate levels being an important component. Here, we adopted a genome-wide association-based approach to characterize the response in ascorbate levels on high light (HL) acclimation in a panel of 315 Arabidopsis (Arabidopsis thaliana) accessions. These studies revealed statistically significant SNPs for total and reduced ascorbate under HL conditions at a locus in chromosome 2. Ascorbate levels under HL and the region upstream and within PAS/LOV PROTEIN (PLP) were strongly associated. Intriguingly, subcellular localization analyses revealed that the PLPA and PLPB splice variants co-localized with VITAMIN C DEFECTIVE2 (VTC2) and VTC5 in both the cytosol and nucleus. Yeast 2-hybrid and bimolecular fluorescence complementation analyses revealed that PLPA and PLPB interact with VTC2 and that blue light diminishes this interaction. Furthermore, PLPB knockout mutants were characterized by 1.5- to 1.7-fold elevations in their ascorbate levels, whereas knockout mutants of the cry2 cryptochromes displayed 1.2- to 1.3-fold elevations compared to WT. Our results collectively indicate that PLP plays a critical role in the elevation of ascorbate levels, which is a signature response of HL acclimation. The results strongly suggest that this is achieved via the release of the inhibitory effect of PLP on VTC2 upon blue light illumination, as the VTC2-PLPB interaction is stronger under darkness. The conditional importance of the cryptochrome receptors under different environmental conditions suggests a complex hierarchy underpinning the environmental control of ascorbate levels. However, the data we present here clearly demonstrate that PLP dominates during HL acclimation.
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Affiliation(s)
- Fayezeh Aarabi
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Andrea Ghigi
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Micha Wijesingha Ahchige
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Mustafa Bulut
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Peter Geigenberger
- Department Biology I, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
| | - H Ekkehard Neuhaus
- Plant Physiology, University of Kaiserslautern, Kaiserslautern D-67653, Germany
| | - Arun Sampathkumar
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Saleh Alseekh
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Crop Quantitative Genetics, Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Alisdair R Fernie
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Crop Quantitative Genetics, Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
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30
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Cheng KCL, Frost JM, Sánchez-Luque FJ, García-Canãdas M, Taylor D, Yang WR, Irayanar B, Sampath S, Patani H, Agger K, Helin K, Ficz G, Burns KH, Ewing A, García-Pérez JL, Branco MR. Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation. Epigenetics Chromatin 2023; 16:39. [PMID: 37845773 PMCID: PMC10578016 DOI: 10.1186/s13072-023-00514-6] [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: 08/07/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Vitamin C (vitC) enhances the activity of 2-oxoglutarate-dependent dioxygenases, including TET enzymes, which catalyse DNA demethylation, and Jumonji-domain histone demethylases. The epigenetic remodelling promoted by vitC improves the efficiency of induced pluripotent stem cell derivation, and is required to attain a ground-state of pluripotency in embryonic stem cells (ESCs) that closely mimics the inner cell mass of the early blastocyst. However, genome-wide DNA and histone demethylation can lead to upregulation of transposable elements (TEs), and it is not known how vitC addition in culture media affects TE expression in pluripotent stem cells. RESULTS Here we show that vitC increases the expression of several TE families, including evolutionarily young LINE-1 (L1) elements, in mouse ESCs. We find that TET activity is dispensable for L1 upregulation, and that instead it occurs largely as a result of H3K9me3 loss mediated by KDM4A/C histone demethylases. Despite increased L1 levels, we did not detect increased somatic insertion rates in vitC-treated cells. Notably, treatment of human ESCs with vitC also increases L1 protein levels, albeit through a distinct, post-transcriptional mechanism. CONCLUSION VitC directly modulates the expression of mouse L1s and other TEs through epigenetic mechanisms, with potential for downstream effects related to the multiple emerging roles of L1s in cellular function.
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Affiliation(s)
- Kevin C L Cheng
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jennifer M Frost
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Francisco J Sánchez-Luque
- Institute of Parasitology and Biomedicine "Lopez-Neyra" (IPBLN), Spanish National Research Council (CSIC), PTS Granada, Granada, Spain
| | - Marta García-Canãdas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Darren Taylor
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Wan R Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Branavy Irayanar
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Swetha Sampath
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Hemalvi Patani
- Barts Cancer Institute, Faculty of Medicine and Dentistry, QMUL, London, EC1M 6BQ, UK
| | - Karl Agger
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
- The Institute of Cancer Research, London, UK
| | - Gabriella Ficz
- Barts Cancer Institute, Faculty of Medicine and Dentistry, QMUL, London, EC1M 6BQ, UK
| | - Kathleen H Burns
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Adam Ewing
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - José L García-Pérez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Miguel R Branco
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK.
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31
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Tu WB, Christofk HR, Plath K. Nutrient regulation of development and cell fate decisions. Development 2023; 150:dev199961. [PMID: 37260407 PMCID: PMC10281554 DOI: 10.1242/dev.199961] [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] [Indexed: 06/02/2023]
Abstract
Diet contributes to health at all stages of life, from embryonic development to old age. Nutrients, including vitamins, amino acids, lipids and sugars, have instructive roles in directing cell fate and function, maintaining stem cell populations, tissue homeostasis and alleviating the consequences of aging. This Review highlights recent findings that illuminate how common diets and specific nutrients impact cell fate decisions in healthy and disease contexts. We also draw attention to new models, technologies and resources that help to address outstanding questions in this emerging field and may lead to dietary approaches that promote healthy development and improve disease treatments.
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Affiliation(s)
- William B. Tu
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Heather R. Christofk
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
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32
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Jeong S, Chokkalla AK, Davis CK, Vemuganti R. Post-stroke depression: epigenetic and epitranscriptomic modifications and their interplay with gut microbiota. Mol Psychiatry 2023; 28:4044-4055. [PMID: 37188778 PMCID: PMC10646155 DOI: 10.1038/s41380-023-02099-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
Epigenetic and epitranscriptomic modifications that regulate physiological processes of an organism at the DNA and RNA levels, respectively, are novel therapeutic candidates for various neurological diseases. Gut microbiota and its metabolites are known to modulate DNA methylation and histone modifications (epigenetics), as well as RNA methylation especially N6-methyladenosine (epitranscriptomics). As gut microbiota as well as these modifications are highly dynamic across the lifespan of an organism, they are implicated in the pathogenesis of stroke and depression. The lack of specific therapeutic interventions for managing post-stroke depression emphasizes the need to identify novel molecular targets. This review highlights the interaction between the gut microbiota and epigenetic/epitranscriptomic pathways and their interplay in modulating candidate genes that are involved in post-stroke depression. This review further focuses on the three candidates, including brain-derived neurotrophic factor, ten-eleven translocation family proteins, and fat mass and obesity-associated protein based on their prevalence and pathoetiologic role in post-stroke depression.
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Affiliation(s)
- Soomin Jeong
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
- Neuroscience Training Program, University of Wisconsin, Madison, WI, USA
| | - Anil K Chokkalla
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Charles K Davis
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA.
- Neuroscience Training Program, University of Wisconsin, Madison, WI, USA.
- William S. Middleton Veterans Hospital, Madison, WI, USA.
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33
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Canat A, Veillet A, Batrin R, Dubourg C, Lhoumaud P, Arnau-Romero P, Greenberg MVC, Bonhomme F, Arimondo PB, Illingworth R, Fabre E, Therizols P. DAXX safeguards heterochromatin formation in embryonic stem cells. J Cell Sci 2023; 136:jcs261092. [PMID: 37655670 DOI: 10.1242/jcs.261092] [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: 02/24/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023] Open
Abstract
Genomes comprise a large fraction of repetitive sequences folded into constitutive heterochromatin, which protect genome integrity and cell identity. De novo formation of heterochromatin during preimplantation development is an essential step for preserving the ground-state of pluripotency and the self-renewal capacity of embryonic stem cells (ESCs). However, the molecular mechanisms responsible for the remodeling of constitutive heterochromatin are largely unknown. Here, we identify that DAXX, an H3.3 chaperone essential for the maintenance of mouse ESCs in the ground state, accumulates in pericentromeric regions independently of DNA methylation. DAXX recruits PML and SETDB1 to promote the formation of heterochromatin, forming foci that are hallmarks of ground-state ESCs. In the absence of DAXX or PML, the three-dimensional (3D) architecture and physical properties of pericentric and peripheral heterochromatin are disrupted, resulting in de-repression of major satellite DNA, transposable elements and genes associated with the nuclear lamina. Using epigenome editing tools, we observe that H3.3, and specifically H3.3K9 modification, directly contribute to maintaining pericentromeric chromatin conformation. Altogether, our data reveal that DAXX is crucial for the maintenance and 3D organization of the heterochromatin compartment and protects ESC viability.
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Affiliation(s)
- Antoine Canat
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Adeline Veillet
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Renaud Batrin
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Clara Dubourg
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | | | - Pol Arnau-Romero
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | | | - Frédéric Bonhomme
- Institut Pasteur, Université Paris Cité, CNRS, Epigenetic Chemical Biology, UMR 3523, F-75724 Paris, France
| | - Paola B Arimondo
- Institut Pasteur, Université Paris Cité, CNRS, Epigenetic Chemical Biology, UMR 3523, F-75724 Paris, France
| | - Robert Illingworth
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Emmanuelle Fabre
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Pierre Therizols
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
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de Aguiar ÉS, Dias AN, Sousa RM, Germano TA, de Sousa RO, Miranda RDS, Costa JH, dos Santos CP. Genome and Transcriptome Analyses of Genes Involved in Ascorbate Biosynthesis in Pepper Indicate Key Genes Related to Fruit Development, Stresses, and Phytohormone Exposures. PLANTS (BASEL, SWITZERLAND) 2023; 12:3367. [PMID: 37836106 PMCID: PMC10574469 DOI: 10.3390/plants12193367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/10/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Pepper (Capsicum annuum L.) is a vegetable consumed worldwide, primarily used for vitamin C uptake and condiment purposes. Ascorbate (Asc) is a multifunctional metabolite, acting as an antioxidant and enzymatic cofactor involved in multiple cellular processes. Nevertheless, there is no evidence about the contribution of biosynthesis pathways and regulatory mechanisms responsible for Asc reserves in pepper plants. Here, we present a genome- and transcriptome-wide investigation of genes responsible for Asc biosynthesis in pepper during fruit development, stresses, and phytohormone exposures. A total of 21 genes, scattered in ten of twelve pepper chromosomes were annotated. Gene expression analyses of nine transcriptomic experiments supported the primary role of the L-galactose pathway in the Asc-biosynthesizing process, given its constitutive, ubiquitous, and high expression profile observed in all studied conditions. However, genes from alternative pathways generally exhibited low expression or were unexpressed and appeared to play some secondary role under specific stress conditions and phytohormone treatments. Taken together, our findings provide a deeper spatio-temporal understanding of expression levels of genes involved in Asc biosynthesis, and they highlight GGP2, GME1 and 2, and GalLDH members from L-galactose pathway as promising candidates for future wet experimentation, addressing the attainment of increase in ascorbate content of peppers and other crops.
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Affiliation(s)
- Évelyn Silva de Aguiar
- Postgraduate Program in Environmental Sciences, Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil;
| | - Abigailde Nascimento Dias
- Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil; (A.N.D.); (R.M.S.)
| | - Raquel Mendes Sousa
- Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil; (A.N.D.); (R.M.S.)
| | - Thais Andrade Germano
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451-970, Ceará, Brazil; (T.A.G.); (J.H.C.)
| | - Renato Oliveira de Sousa
- Postgraduate Program in Agricultural Sciences, Campus Professora Cinobelina Elvas, Federal University of Piauí, Bom Jesus 64900-000, Piauí, Brazil; (R.O.d.S.); (R.d.S.M.)
| | - Rafael de Souza Miranda
- Postgraduate Program in Agricultural Sciences, Campus Professora Cinobelina Elvas, Federal University of Piauí, Bom Jesus 64900-000, Piauí, Brazil; (R.O.d.S.); (R.d.S.M.)
- Plant Science Department, Federal University of Piauí, Teresina 64049-550, Piauí, Brazil
| | - José Hélio Costa
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451-970, Ceará, Brazil; (T.A.G.); (J.H.C.)
| | - Clesivan Pereira dos Santos
- Postgraduate Program in Environmental Sciences, Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil;
- Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil; (A.N.D.); (R.M.S.)
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35
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Coker SJ, Dyson RM, Smith-Díaz CC, Vissers MCM, Berry MJ. Effects of Low Vitamin C Intake on Fertility Parameters and Pregnancy Outcomes in Guinea Pigs. Nutrients 2023; 15:4107. [PMID: 37836389 PMCID: PMC10574174 DOI: 10.3390/nu15194107] [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: 08/17/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Identifying how specific nutrients can impact fertility, pregnancy, and neonatal outcomes will yield important insights into the biological mechanisms linking diet and reproductive health. Our study investigates how dietary vitamin C intake affects various fertility parameters and pregnancy and neonatal outcomes in the guinea pig, a natural model of vitamin C dependency. Dunkin Hartley guinea pigs were fed an optimal (900 mg/kg feed) or low (100 mg/kg feed) vitamin C diet ad libitum for at least three weeks prior to mating and throughout pregnancy. We found that animals receiving the low vitamin C diet had an increased number of unsuccessful matings, a higher incidence of foetal reabsorption, and, among pregnancies resulting in delivery at term, produced fewer offspring. Neonates from mothers on the low vitamin C diet had significantly decreased plasma vitamin C concentrations at birth and exhibited mild growth impairments in a sex-dependent manner. We conclude that a diet low of vitamin C induces a state of subfertility, reduces overall fecundity, and adversely impacts both pregnancy outcomes and growth in the offspring. Our study provides an essential foundation for future investigations to determine whether these findings translate to humans. If so, they could have important clinical implications for assisted reproductive technologies and nutritional recommendations for couples trying to conceive, pregnant women, and breastfeeding mothers.
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Affiliation(s)
- Sharna J. Coker
- Perinatal and Developmental Physiology Group, Department of Paediatrics and Child Health, University of Otago, Wellington 6242, New Zealand; (S.J.C.); (R.M.D.)
| | - Rebecca M. Dyson
- Perinatal and Developmental Physiology Group, Department of Paediatrics and Child Health, University of Otago, Wellington 6242, New Zealand; (S.J.C.); (R.M.D.)
| | - Carlos C. Smith-Díaz
- Mātai Hāora—Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8140, New Zealand;
| | - Margreet C. M. Vissers
- Mātai Hāora—Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8140, New Zealand;
| | - Mary J. Berry
- Perinatal and Developmental Physiology Group, Department of Paediatrics and Child Health, University of Otago, Wellington 6242, New Zealand; (S.J.C.); (R.M.D.)
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Pesti-Asbóth G, Szilágyi E, Bíróné Molnár P, Oláh J, Babinszky L, Czeglédi L, Cziáky Z, Paholcsek M, Stündl L, Remenyik J. Monitoring physiological processes of fast-growing broilers during the whole life cycle: Changes of redox-homeostasis effected to trassulfuration pathway predicting the development of non-alcoholic fatty liver disease. PLoS One 2023; 18:e0290310. [PMID: 37590293 PMCID: PMC10434899 DOI: 10.1371/journal.pone.0290310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/06/2023] [Indexed: 08/19/2023] Open
Abstract
In the broiler industry, the average daily gain and feed conversion ratio are extremely favorable, but the birds are beginning to approach the maximum of their genetic capacity. However, as a consequence of strong genetic selection, the occurrence of certain metabolic diseases, such as myopathies, ascites, sudden cardiac death and tibial dyschondroplasia, is increasing. These metabolic diseases can greatly affect the health status and welfare of birds, as well as the quality of meat. The main goal of this study was to investigate the changes in the main parameters of redox homeostasis during the rearing (1-42 days of age) of broilers with high genetic capacity, such as the concentrations of malondialdehyde, vitamin C, vitamin E, and reduced glutathione, the activities of glutathione peroxidase and glutathione reductase, and the inhibition rate of superoxide dismutase. Damage to the transsulfuration pathway during growth and the reason for changes in the level of homocysteine were investigated. Further, the parameters that can characterize the biochemical changes occurring in the birds were examined. Our study is the first characterize plasma albumin saturation. A method was developed to measure the levels of other small molecule thiol components of plasma. Changes in redox homeostasis induce increases in the concentrations of tumor necrosis factor alpha and inflammatory interleukins interleukin 2, interleukin 6 and interleukin 8 in broilers reared according to current large-scale husbandry technology and feeding protocols. A significant difference in all parameters tested was observed on the 21st day. The concentrations of cytokines and homocysteine increased, while the concentrations of glutathione and cysteine in the plasma decreased. Our findings suggest that observed changes in the abovementioned biochemical indices have a negative effect on poultry health.
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Affiliation(s)
- Georgina Pesti-Asbóth
- Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Food Technology, University of Debrecen, Debrecen, Hungary
| | - Endre Szilágyi
- Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Food Technology, University of Debrecen, Debrecen, Hungary
| | - Piroska Bíróné Molnár
- Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Food Technology, University of Debrecen, Debrecen, Hungary
| | - János Oláh
- Farm and Regional Research Institute of Debrecen, University of Debrecen, Debrecen, Hungary
| | - László Babinszky
- Faculty of Agricultural and Food Sciences and Environmental Management, Department of Animal Nutrition Physiology, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
| | - Levente Czeglédi
- Faculty of Agricultural and Food Sciences and Environmental Management, Department of Animal Science, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
| | - Zoltán Cziáky
- Agricultural and Molecular Research and Service Group, University of Nyíregyháza; Nyíregyháza, Hungary
| | - Melinda Paholcsek
- Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Food Technology, University of Debrecen, Debrecen, Hungary
| | - László Stündl
- Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Food Technology, University of Debrecen, Debrecen, Hungary
| | - Judit Remenyik
- Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Food Technology, University of Debrecen, Debrecen, Hungary
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37
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Stuckey R, Bilbao-Sieyro C, Segura-Díaz A, Gómez-Casares MT. Molecular Studies for the Early Detection of Philadelphia-Negative Myeloproliferative Neoplasms. Int J Mol Sci 2023; 24:12700. [PMID: 37628880 PMCID: PMC10454334 DOI: 10.3390/ijms241612700] [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: 07/23/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
JAK2 V617F is the predominant driver mutation in patients with Philadelphia-negative myeloproliferative neoplasms (MPN). JAK2 mutations are also frequent in clonal hematopoiesis of indeterminate potential (CHIP) in otherwise "healthy" individuals. However, the period between mutation acquisition and MPN diagnosis (known as latency) varies widely between individuals, with JAK2 mutations detectable several decades before diagnosis and even from birth in some individuals. Here, we will review the current evidence on the biological factors, such as additional mutations and chronic inflammation, which influence clonal expansion and may determine why some JAK2-mutated individuals will progress to an overt neoplasm during their lifetime while others will not. We will also introduce several germline variants that predispose individuals to CHIP (as well as MPN) identified from genome-wide association studies. Finally, we will explore possible mutation screening or interventions that could help to minimize MPN-associated cardiovascular complications or even delay malignant progression.
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Affiliation(s)
- Ruth Stuckey
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (R.S.); (C.B.-S.); (A.S.-D.)
| | - Cristina Bilbao-Sieyro
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (R.S.); (C.B.-S.); (A.S.-D.)
- Morphology Department, Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain
| | - Adrián Segura-Díaz
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (R.S.); (C.B.-S.); (A.S.-D.)
| | - María Teresa Gómez-Casares
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (R.S.); (C.B.-S.); (A.S.-D.)
- Department of Medical Sciences, Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain
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38
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Zhang X, Zhang Y, Wang C, Wang X. TET (Ten-eleven translocation) family proteins: structure, biological functions and applications. Signal Transduct Target Ther 2023; 8:297. [PMID: 37563110 PMCID: PMC10415333 DOI: 10.1038/s41392-023-01537-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 08/12/2023] Open
Abstract
Ten-eleven translocation (TET) family proteins (TETs), specifically, TET1, TET2 and TET3, can modify DNA by oxidizing 5-methylcytosine (5mC) iteratively to yield 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC), and then two of these intermediates (5fC and 5caC) can be excised and return to unmethylated cytosines by thymine-DNA glycosylase (TDG)-mediated base excision repair. Because DNA methylation and demethylation play an important role in numerous biological processes, including zygote formation, embryogenesis, spatial learning and immune homeostasis, the regulation of TETs functions is complicated, and dysregulation of their functions is implicated in many diseases such as myeloid malignancies. In addition, recent studies have demonstrated that TET2 is able to catalyze the hydroxymethylation of RNA to perform post-transcriptional regulation. Notably, catalytic-independent functions of TETs in certain biological contexts have been identified, further highlighting their multifunctional roles. Interestingly, by reactivating the expression of selected target genes, accumulated evidences support the potential therapeutic use of TETs-based DNA methylation editing tools in disorders associated with epigenetic silencing. In this review, we summarize recent key findings in TETs functions, activity regulators at various levels, technological advances in the detection of 5hmC, the main TETs oxidative product, and TETs emerging applications in epigenetic editing. Furthermore, we discuss existing challenges and future directions in this field.
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Affiliation(s)
- Xinchao Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Long Y, Yi C, Wu R, Zhang Y, Zhang B, Shi X, Zhang X, Zha Z. Biodistribution and radiation dosimetry in cancer patients of the ascorbic acid analogue 6-Deoxy-6-[ 18F] fluoro-L-ascorbic acid PET imaging: first-in-human study. Eur J Nucl Med Mol Imaging 2023; 50:3072-3083. [PMID: 37191679 DOI: 10.1007/s00259-023-06262-9] [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: 12/25/2022] [Accepted: 05/06/2023] [Indexed: 05/17/2023]
Abstract
PURPOSE Clinical studies on the use of ascorbic acid (AA) have become a hot spot in cancer research. There remains an unmet need to assess AA utilization in normal tissues and tumors. 6-Deoxy-6-[18F]fluoro-L-ascorbic acid ([18F]DFA) displayed distinctive tumor localization and similar distribution as AA in mice. In this study, to evaluate the distribution, tumor detecting ability and radiation dosimetry of [18F]DFA in humans, we performed the first-in-human PET imaging study. METHODS Six patients with a variety of cancers underwent whole-body PET/CT scans after injection of 313-634 MBq of [18F]DFA. Five sequential dynamic emission scans in each patient were acquired at 5-60 min. Regions of interest (ROI) were delineated along the edge of the source-organ and tumor on the transverse PET slice. Tumor-to-background ratio (TBR) was obtained using the tumor SUVmax to background SUVmean. Organ residence times were calculated via time-activity curves, and human absorbed doses were estimated from organ residence time using the medical internal radiation dosimetry method. RESULTS [18F]DFA was well tolerated in all subjects without serious adverse event. The high uptake was found in the liver, adrenal glands, kidneys, choroid plexus, and pituitary gland. [18F]DFA accumulated in tumor rapidly and the TBR increased over time. The average SUVmax of [18F]DFA in tumor lesions was 6.94 ± 3.92 (range 1.62-22.85, median 5.94). The organs with the highest absorbed doses were the liver, spleen, adrenal glands, and kidneys. The mean effective dose was estimated to be 1.68 ± 0.36 E-02 mSv/MBq. CONCLUSIONS [18F]DFA is safe to be used in humans. It showed a similar distribution pattern as AA, and displayed high uptake and retention in tumors with appropriate kinetics. [18F]DFA might be a promising radiopharmaceutical in identifying tumors with high affinity for SVCT2 and monitoring AA distribution in both normal tissues and tumors. TRIAL REGISTRATION Chinese Clinical Trial Registry; Registered Number: ChiCTR2200057842 (registered 19 March 2022).
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Affiliation(s)
- Yali Long
- Department of Nuclear Medicine, the First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Er Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Chang Yi
- Department of Nuclear Medicine, the First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Er Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Renbo Wu
- Department of Nuclear Medicine, the First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Er Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Yuying Zhang
- Department of Nuclear Medicine, the First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Er Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Bing Zhang
- Department of Nuclear Medicine, the First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Er Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Xinchong Shi
- Department of Nuclear Medicine, the First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Er Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Xiangsong Zhang
- Department of Nuclear Medicine, the First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Er Road, Guangzhou, 510080, Guangdong Province, People's Republic of China.
| | - Zhihao Zha
- Department of Nuclear Medicine, the First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Er Road, Guangzhou, 510080, Guangdong Province, People's Republic of China.
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Li S, Jakobs TC. Vitamin C protects retinal ganglion cells via SPP1 in glaucoma and after optic nerve damage. Life Sci Alliance 2023; 6:e202301976. [PMID: 37160307 PMCID: PMC10172762 DOI: 10.26508/lsa.202301976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/11/2023] Open
Abstract
Glaucoma is a common neurodegenerative disorder characterized by retinal ganglion cell death, astrocyte reactivity in the optic nerve, and vision loss. Currently, lowering the intraocular pressure (IOP) is the first-line treatment, but adjuvant neuroprotective approaches would be welcome. Vitamin C possesses neuroprotective activities that are thought to be related to its properties as a co-factor of enzymes and its antioxidant effects. Here, we show that vitamin C promotes a neuroprotective phenotype and increases gene expression related to neurotropic factors, phagocytosis, and mitochondrial ATP production. This effect is dependent on the up-regulation of secreted phosphoprotein 1 (SPP1) in reactive astrocytes via the transcription factor E2F1. SPP1+ astrocytes in turn promote retinal ganglion cell survival in a mouse model of glaucoma. In addition, oral administration of vitamin C lowers the IOP in mice. This study identifies an additional neuroprotective pathway for vitamin C and suggests a potential therapeutic role of vitamin C in neurodegenerative diseases such as glaucoma.
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Affiliation(s)
- Song Li
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute, Massachusetts Eye and Ear, Boston, MA, USA
| | - Tatjana C Jakobs
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute, Massachusetts Eye and Ear, Boston, MA, USA
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Gao Y, Su L, Wei Y, Tan S, Hu Z, Tao Z, Kovalik JP, Soong TW, Zhang J, Pu J, Ye L. Ascorbic acid induces MLC2v protein expression and promotes ventricular-like cardiomyocyte subtype in human induced pluripotent stem cells derived cardiomyocytes. Theranostics 2023; 13:3872-3896. [PMID: 37441603 PMCID: PMC10334833 DOI: 10.7150/thno.80801] [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: 11/13/2022] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction: The potentially unlimited number of cardiomyocyte (CMs) derived from human induced pluripotent stem cells (hiPSCs) in vitro facilitates high throughput applications like cell transplantation for myocardial repair, disease modelling, and cardiotoxicity testing during drug development. Despite promising progress in these areas, a major disadvantage that limits the use of hiPSC derived CMs (hiPSC-CMs) is their immaturity. Methods: Three hiPSC lines (PCBC-hiPSC, DP3-hiPSCs, and MLC2v-mEGFP hiPSC) were differentiated into CMs (PCBC-CMs, DP3-CMs, and MLC2v-CMs, respectively) with or without retinoic acid (RA). hiPSC-CMs were either maintained up to day 30 of contraction (D30C), or D60C, or purified using lactate acid and used for experiments. Purified hiPSC-CMs were cultured in basal maturation medium (BMM) or BMM supplemented with ascorbic acid (AA) for 14 days. The AA treated and non-treated hiPSC-CMs were characterized for sarcomeric proteins (MLC2v, TNNI3, and MYH7), ion channel proteins (Kir2.1, Nav1.5, Cav1.2, SERCA2a, and RyR), mitochondrial membrane potential, metabolomics, and action potential. Bobcat339, a selective and potent inhibitor of DNA demethylation, was used to determine whether AA promoted hiPSC-CM maturation through modulating DNA demethylation. Results: AA significantly increased MLC2v expression in PCBC-CMs, DP3-CMs, MLC2v-CMs, and RA induced atrial-like PCBC-CMs. AA treatment significantly increased mitochondrial mass, membrane potential, and amino acid and fatty acid metabolism in PCBC-CMs. Patch clamp studies showed that AA treatment induced PCBC-CMs and DP3-CMs adaptation to a ventricular-like phenotype. Bobcat339 inhibited MLC2v protein expression in AA treated PCBC-CMs and DP3-CMs. DNA demethylation inhibition was also associated with reduced TET1 and TET2 protein expressions and reduced accumulation of the oxidative product, 5 hmC, in both PCBC-CMs and DP3-CMs, in the presence of AA. Conclusions: Ascorbic acid induced MLC2v protein expression and promoted ventricular-like CM subtype in hiPSC-CMs. The effect of AA on hiPSC-CM was attenuated with inhibition of TET1/TET2 mediated DNA demethylation.
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Affiliation(s)
- Yu Gao
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
- Department of Cardiology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liping Su
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
| | - Yuhua Wei
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shihua Tan
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
| | - Zhenyu Hu
- Department of Physiology, National University of Singapore, Singapore
- Cardiovascular Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore
| | - Zhonghao Tao
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
- Department of Thoracic and Cardiovascular Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jean-Paul Kovalik
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS, Singapore
| | - Tuck Wah Soong
- Department of Physiology, National University of Singapore, Singapore
- Cardiovascular Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore
| | - Jianyi Zhang
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jun Pu
- Department of Cardiology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lei Ye
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
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He X, Wei Y, Wu J, Wang Q, Bergholz JS, Gu H, Zou J, Lin S, Wang W, Xie S, Jiang T, Lee J, Asara JM, Zhang K, Cantley LC, Zhao JJ. Lysine vitcylation is a novel vitamin C-derived protein modification that enhances STAT1-mediated immune response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546774. [PMID: 37425798 PMCID: PMC10327172 DOI: 10.1101/2023.06.27.546774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Vitamin C (vitC) is a vital nutrient for health and also used as a therapeutic agent in diseases such as cancer. However, the mechanisms underlying vitC's effects remain elusive. Here we report that vitC directly modifies lysine without enzymes to form vitcyl-lysine, termed "vitcylation", in a dose-, pH-, and sequence-dependent manner across diverse proteins in cells. We further discover that vitC vitcylates K298 site of STAT1, which impairs its interaction with the phosphatase PTPN2, preventing STAT1 Y701 dephosphorylation and leading to increased STAT1-mediated IFN pathway activation in tumor cells. As a result, these cells have increased MHC/HLA class-I expression and activate immune cells in co-cultures. Tumors collected from vitC-treated tumor-bearing mice have enhanced vitcylation, STAT1 phosphorylation and antigen presentation. The identification of vitcylation as a novel PTM and the characterization of its effect in tumor cells opens a new avenue for understanding vitC in cellular processes, disease mechanisms, and therapeutics.
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Salazar K, Jara N, Ramírez E, de Lima I, Smith-Ghigliotto J, Muñoz V, Ferrada L, Nualart F. Role of vitamin C and SVCT2 in neurogenesis. Front Neurosci 2023; 17:1155758. [PMID: 37424994 PMCID: PMC10324519 DOI: 10.3389/fnins.2023.1155758] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023] Open
Abstract
Different studies have established the fundamental role of vitamin C in proliferation, differentiation, and neurogenesis in embryonic and adult brains, as well as in in vitro cell models. To fulfill these functions, the cells of the nervous system regulate the expression and sorting of sodium-dependent vitamin C transporter 2 (SVCT2), as well as the recycling of vitamin C between ascorbic acid (AA) and dehydroascorbic acid (DHA) via a bystander effect. SVCT2 is a transporter preferentially expressed in neurons and in neural precursor cells. In developmental stages, it is concentrated in the apical region of the radial glia, and in adult life, it is expressed preferentially in motor neurons of the cerebral cortex, starting on postnatal day 1. In neurogenic niches, SVCT2 is preferentially expressed in precursors with intermediate proliferation, where a scorbutic condition reduces neuronal differentiation. Vitamin C is a potent epigenetic regulator in stem cells; thus, it can induce the demethylation of DNA and histone H3K27m3 in the promoter region of genes involved in neurogenesis and differentiation, an effect mediated by Tet1 and Jmjd3 demethylases, respectively. In parallel, it has been shown that vitamin C induces the expression of stem cell-specific microRNA, including the Dlk1-Dio3 imprinting region and miR-143, which promotes stem cell self-renewal and suppresses de novo expression of the methyltransferase gene Dnmt3a. The epigenetic action of vitamin C has also been evaluated during gene reprogramming of human fibroblasts to induced pluripotent cells, where it has been shown that vitamin C substantially improves the efficiency and quality of reprogrammed cells. Thus, for a proper effect of vitamin C on neurogenesis and differentiation, its function as an enzymatic cofactor, modulator of gene expression and antioxidant is essential, as is proper recycling from DHA to AA by various supporting cells in the CNS.
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Affiliation(s)
- Katterine Salazar
- Laboratory of Neurobiology and Stem Cells, NeuroCellT, Department of Cellular Biology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
- Center for Advanced Microscopy CMA BIO, University of Concepcion, Concepcion, Chile
| | - Nery Jara
- Department of Pharmacology, University of Concepcion, Concepcion, Chile
| | - Eder Ramírez
- Laboratory of Neurobiology and Stem Cells, NeuroCellT, Department of Cellular Biology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
| | - Isabelle de Lima
- Laboratory of Neurobiology and Stem Cells, NeuroCellT, Department of Cellular Biology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
| | - Javiera Smith-Ghigliotto
- Laboratory of Neurobiology and Stem Cells, NeuroCellT, Department of Cellular Biology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
| | - Valentina Muñoz
- Department of Pharmacology, University of Concepcion, Concepcion, Chile
| | - Luciano Ferrada
- Center for Advanced Microscopy CMA BIO, University of Concepcion, Concepcion, Chile
| | - Francisco Nualart
- Laboratory of Neurobiology and Stem Cells, NeuroCellT, Department of Cellular Biology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
- Center for Advanced Microscopy CMA BIO, University of Concepcion, Concepcion, Chile
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Gómez de Cedrón M, Moreno Palomares R, Ramírez de Molina A. Metabolo-epigenetic interplay provides targeted nutritional interventions in chronic diseases and ageing. Front Oncol 2023; 13:1169168. [PMID: 37404756 PMCID: PMC10315663 DOI: 10.3389/fonc.2023.1169168] [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: 02/18/2023] [Accepted: 05/24/2023] [Indexed: 07/06/2023] Open
Abstract
Epigenetic modifications are chemical modifications that affect gene expression without altering DNA sequences. In particular, epigenetic chemical modifications can occur on histone proteins -mainly acetylation, methylation-, and on DNA and RNA molecules -mainly methylation-. Additional mechanisms, such as RNA-mediated regulation of gene expression and determinants of the genomic architecture can also affect gene expression. Importantly, depending on the cellular context and environment, epigenetic processes can drive developmental programs as well as functional plasticity. However, misbalanced epigenetic regulation can result in disease, particularly in the context of metabolic diseases, cancer, and ageing. Non-communicable chronic diseases (NCCD) and ageing share common features including altered metabolism, systemic meta-inflammation, dysfunctional immune system responses, and oxidative stress, among others. In this scenario, unbalanced diets, such as high sugar and high saturated fatty acids consumption, together with sedentary habits, are risk factors implicated in the development of NCCD and premature ageing. The nutritional and metabolic status of individuals interact with epigenetics at different levels. Thus, it is crucial to understand how we can modulate epigenetic marks through both lifestyle habits and targeted clinical interventions -including fasting mimicking diets, nutraceuticals, and bioactive compounds- which will contribute to restore the metabolic homeostasis in NCCD. Here, we first describe key metabolites from cellular metabolic pathways used as substrates to "write" the epigenetic marks; and cofactors that modulate the activity of the epigenetic enzymes; then, we briefly show how metabolic and epigenetic imbalances may result in disease; and, finally, we show several examples of nutritional interventions - diet based interventions, bioactive compounds, and nutraceuticals- and exercise to counteract epigenetic alterations.
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Affiliation(s)
- Marta Gómez de Cedrón
- Molecular Oncology Group, IMDEA Food Institute, CEI UAM, CSIC, Madrid, Spain
- Cell Metabolism Unit, IMDEA Food Institute, CEI UAM, CSIC, Madrid, Spain
| | - Rocío Moreno Palomares
- Molecular Oncology Group, IMDEA Food Institute, CEI UAM, CSIC, Madrid, Spain
- FORCHRONIC S.L, Avda. Industria, Madrid, Spain
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Li C, Pang M, Li Y, Han L, Fan Y, Xin X, Zhang X, Zhang N, Qin Y. Protective effect of vitamin C against tetrachlorobenzoquinone-induced 5-hydroxymethylation-dependent apoptosis in HepG2 cells mainly via the mitochondrial apoptosis pathway. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 260:115097. [PMID: 37271103 DOI: 10.1016/j.ecoenv.2023.115097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
Tetrachlorobenzoquinone (TCBQ) is an active metabolite of pentachlorophenol, and stimulates the accumulation of ROS to trigger apoptosis. The preventive effect of vitamin C (Vc) against TCBQ-induced apoptosis in HepG2 cells is unknown. And there is little known about TCBQ-triggered 5-hydromethylcytosine (5hmC)-dependent apoptosis. Here, we confirmed that Vc alleviated TCBQ-induced apoptosis. Through investigating the underlying mechanism, we found TCBQ downregulated 5hmC levels of genomic DNA in a Tet-dependent manner, with a particularly pronounced decrease in the promoter region, using UHPLC-MS-MS analysis and hydroxymethylated DNA immunoprecipitation sequencing. Notably, TCBQ exposure resulted in alterations of 5hmC abundance to ∼91% of key genes at promoters in the mitochondrial apoptosis pathway, along with changes of mRNA expression in 87% of genes. By contrast, 5hmC abundance of genes only exhibited slight changes in the death receptor/ligand pathway. Interestingly, the pretreatment with Vc, a positive stimulator of 5hmC generation, restored 5hmC in the genomic DNA to near-normal levels. More notably, Vc pretreatment further counter-regulated TCBQ-induced alteration of 5hmC abundance in the promoter with 100% of genes, accompanying the reverse modulation of mRNA expressions in 89% of genes. These data from Vc pretreatment supported the relationship between TCBQ-induced apoptosis and the altered 5hmC abundance. Additionally, Vc also suppressed TCBQ-stimulated generation of ROS, and further increased the stability of mitochondria. Our study illuminates a new mechanism of TCBQ-induced 5hmC-dependent apoptosis, and the dual mechanisms of Vc against TCBQ-stimulated apoptosis via reversely regulating 5hmC levels and scavenging ROS. The work also provided a possible strategy for the detoxification of TCBQ.
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Affiliation(s)
- Cuiping Li
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China.
| | - Mengfan Pang
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Yaping Li
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China.
| | - Lirong Han
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Yajiao Fan
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Xuelian Xin
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Xian Zhang
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Ning Zhang
- College of Chemistry and Chemical Engineering, Dezhou University, Shandong 253023, PR China
| | - Yan Qin
- Central Laboratory, Affiliated Hospital of Hebei University, Baoding 071002, PR China
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Grady CI, Walsh LM, Heiss JD. Mitoepigenetics and gliomas: epigenetic alterations to mitochondrial DNA and nuclear DNA alter mtDNA expression and contribute to glioma pathogenicity. Front Neurol 2023; 14:1154753. [PMID: 37332990 PMCID: PMC10270738 DOI: 10.3389/fneur.2023.1154753] [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: 01/31/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023] Open
Abstract
Epigenetic mechanisms allow cells to fine-tune gene expression in response to environmental stimuli. For decades, it has been known that mitochondria have genetic material. Still, only recently have studies shown that epigenetic factors regulate mitochondrial DNA (mtDNA) gene expression. Mitochondria regulate cellular proliferation, apoptosis, and energy metabolism, all critical areas of dysfunction in gliomas. Methylation of mtDNA, alterations in mtDNA packaging via mitochondrial transcription factor A (TFAM), and regulation of mtDNA transcription via the micro-RNAs (mir 23-b) and long noncoding RNAs [RNA mitochondrial RNA processing (RMRP)] have all been identified as contributing to glioma pathogenicity. Developing new interventions interfering with these pathways may improve glioma therapy.
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Affiliation(s)
- Clare I. Grady
- Neurosurgery, MedStar Georgetown University Hospital, Washington, DC, United States
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Bethesda, MD, United States
| | - Lisa M. Walsh
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Bethesda, MD, United States
| | - John D. Heiss
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Bethesda, MD, United States
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Kietzmann T. Vitamin C: From nutrition to oxygen sensing and epigenetics. Redox Biol 2023; 63:102753. [PMID: 37263060 DOI: 10.1016/j.redox.2023.102753] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
Vitamin C is unbeatable - at least when it comes to sales. Of all the vitamin preparations, those containing vitamin C sell best. This is surprising because vitamin C deficiency is extremely rare. Nevertheless, there is still controversy about whether the additional intake of vitamin C supplements is essential for our health. In this context, the possible additional benefit is in most cases merely reduced to the known effect as an antioxidant. However, new findings in recent years on the mechanisms of oxygen-sensing and epigenetic control underpin the multifaceted role of vitamin C in a biological context and have therefore renewed interest in it. In the present article, therefore, known facts are linked to these new key data. In addition, available clinical data on vitamin C use of cancer therapy are summarized.
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Affiliation(s)
- Thomas Kietzmann
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, P.O. Box 3000, 90014, Oulu, Finland.
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48
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Glasstetter LM, Oderinde TS, Mirchandani M, Rajagopalan KS, Barsom SH, Thaler R, Siddiqi S, Zhu XY, Tang H, Jordan KL, Saadiq IM, van Wijnen AJ, Eirin A, Lerman LO. Obesity and dyslipidemia are associated with partially reversible modifications to DNA hydroxymethylation of apoptosis- and senescence-related genes in swine adipose-derived mesenchymal stem/stromal cells. Stem Cell Res Ther 2023; 14:143. [PMID: 37231414 PMCID: PMC10214739 DOI: 10.1186/s13287-023-03372-x] [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: 06/16/2022] [Accepted: 05/09/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Obesity dysregulates key biological processes underlying the functional homeostasis, fate decisions, and reparative potential of mesenchymal stem/stromal cells (MSCs). Mechanisms directing obesity-induced phenotypic alterations in MSCs remain unclear, but emerging drivers include dynamic modification of epigenetic marks, like 5-hydroxymethylcytosine (5hmC). We hypothesized that obesity and cardiovascular risk factors induce functionally relevant, locus-specific changes in 5hmC of swine adipose-derived MSCs and evaluated their reversibility using an epigenetic modulator, vitamin-C. METHODS Female domestic pigs were fed a 16-week Lean or Obese diet (n = 6 each). MSCs were harvested from subcutaneous adipose tissue, and 5hmC profiles were examined through hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq) followed by an integrative (hMeDIP and mRNA sequencing) gene set enrichment analysis. For clinical context, we compared 5hmC profiles of adipose tissue-derived human MSCs harvested from patients with obesity and healthy controls. RESULTS hMeDIP-seq revealed 467 hyper- (fold change ≥ 1.4; p-value ≤ 0.05) and 591 hypo- (fold change ≤ 0.7; p-value ≤ 0.05) hydroxymethylated loci in swine Obese- versus Lean-MSCs. Integrative hMeDIP-seq/mRNA-seq analysis identified overlapping dysregulated gene sets and discrete differentially hydroxymethylated loci with functions related to apoptosis, cell proliferation, and senescence. These 5hmC changes were associated with increased senescence in cultured MSCs (p16/CDKN2A immunoreactivity, senescence-associated β-galactosidase [SA-β-Gal] staining), were partly reversed in swine Obese-MSCs treated with vitamin-C, and shared common pathways with 5hmC changes in human Obese-MSCs. CONCLUSIONS Obesity and dyslipidemia are associated with dysregulated DNA hydroxymethylation of apoptosis- and senescence-related genes in swine and human MSCs, potentially affecting cell vitality and regenerative functions. Vitamin-C may mediate reprogramming of this altered epigenomic landscape, providing a potential strategy to improve the success of autologous MSC transplantation in obese patients.
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Affiliation(s)
- Logan M Glasstetter
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Tomiwa S Oderinde
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Mohit Mirchandani
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Samer H Barsom
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Roman Thaler
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Sarosh Siddiqi
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Xiang-Yang Zhu
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Hui Tang
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kyra L Jordan
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ishran M Saadiq
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Lilach O Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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49
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Rajagopalan KS, Kazeminia S, Glasstetter LM, Farahani RA, Zhu XY, Tang H, Jordan KL, Chade AR, Lerman A, Lerman LO, Eirin A. Metabolic Syndrome Induces Epigenetic Alterations in Mitochondria-Related Genes in Swine Mesenchymal Stem Cells. Cells 2023; 12:1274. [PMID: 37174674 PMCID: PMC10177475 DOI: 10.3390/cells12091274] [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: 01/26/2023] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Autologous mesenchymal stem/stromal cells (MSCs) have demonstrated important therapeutic effects in several diseases. Cardiovascular risk factors may impair MSC mitochondrial structure and function, but the underlying mechanisms remain unknown. We hypothesized that metabolic syndrome (MetS) induces epigenetic alterations in mitochondria-related genes in swine MSCs. Pigs were fed a Lean or MetS diet (n = 6 each) for 16 weeks. MSCs were collected from subcutaneous abdominal fat, and DNA hydroxymethylation (5 hmC) profiles of mitochondria-related genes (MitoCarta-2.0) were analyzed by hydroxymethylated DNA immunoprecipitation and next-generation sequencing (hMeDIP-seq) in Lean- and MetS-MSCs untreated or treated with the epigenetic modulator vitamin (Vit)-C (n = 3 each). Functional analysis of genes with differential 5 hmC regions was performed using DAVID6.8. Mitochondrial structure (electron microscopy), oxidative stress, and membrane potential were assessed. hMeDIP-seq identified 172 peaks (associated with 103 mitochondrial genes) with higher and 416 peaks (associated with 165 mitochondrial genes) with lower 5 hmC levels in MetS-MSCs versus Lean-MSCs (≥2-fold, p < 0.05). Genes with higher 5 hmC levels in MetS + MSCs were primarily implicated in fatty acid metabolism, whereas those with lower 5 hmC levels were associated with electron transport chain activity. Vit-C increased 5 hmC levels in mitochondrial antioxidant genes, improved mitochondrial structure and membrane potential, and decreased oxidative stress. MetS alters 5 hmC levels of mitochondria-related genes in swine MSCs. Vit-C modulated 5 hmC levels in these genes and preserved mitochondrial structure and function in MetS-MSCs. These observations may contribute to development of strategies to overcome the deleterious effects of MetS on MSCs.
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Affiliation(s)
| | - Sara Kazeminia
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Rahele A. Farahani
- Division of Endocrinology, Diabetes, Metabolism and Nutrition, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiang-Yang Zhu
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
| | - Hui Tang
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
| | - Kyra L. Jordan
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
| | - Alejandro R. Chade
- Department of Medical Pharmacology and Physiology and Department of Medicine, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Amir Lerman
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Lilach O. Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
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50
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Boughanem H, Kompella P, Tinahones FJ, Macias-Gonzalez M. An overview of vitamins as epidrugs for colorectal cancer prevention. Nutr Rev 2023; 81:455-479. [PMID: 36018754 DOI: 10.1093/nutrit/nuac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gene expression altering epigenomic modifications such as DNA methylation, histone modification, and chromosome remodeling is crucial to regulating many biological processes. Several lifestyle factors, such as diet and natural, bioactive food compounds, such as vitamins, modify epigenetic patterns. However, epigenetic dysregulation can increase the risk of many diseases, including cancer. Various studies have provided supporting and contrasting evidence on the relationship between vitamins and cancer risk. Though there is a gap in knowledge about whether dietary vitamins can induce epigenetic modifications in the context of colorectal cancer (CRC), the possibility of using them as epidrugs for CRC treatment is being explored. This is promising because such studies might be informative about the most effective way to use vitamins in combination with DNA methyltransferase inhibitors and other approved therapies to prevent and treat CRC. This review summarizes the available epidemiological and observational studies involving dietary, circulating levels, and supplementation of vitamins and their relationship with CRC risk. Additionally, using available in vitro, in vivo, and human observational studies, the role of vitamins as potential epigenetic modifiers in CRC is discussed. This review is focused on the action of vitamins as modifiers of DNA methylation because aberrant DNA methylation, together with genetic alterations, can induce the initiation and progression of CRC. Although this review presents some studies with promising results, studies with better study designs are necessary. A thorough understanding of the underlying molecular mechanisms of vitamin-mediated epigenetic regulation of CRC genes can help identify effective therapeutic targets for CRC prevention and treatment.
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Affiliation(s)
- Hatim Boughanem
- are with the Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Institute of Biomedical Research in Malaga (IBIMA), University of Malaga, Malaga, Spain.,are with the Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Pallavi Kompella
- are with the Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Institute of Biomedical Research in Malaga (IBIMA), University of Malaga, Malaga, Spain.,is with the Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
| | - Francisco J Tinahones
- are with the Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Institute of Biomedical Research in Malaga (IBIMA), University of Malaga, Malaga, Spain.,are with the Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Manuel Macias-Gonzalez
- are with the Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Institute of Biomedical Research in Malaga (IBIMA), University of Malaga, Malaga, Spain.,are with the Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
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