1
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Wang D, Zhang Y, Li Q, Li Y, Li W, Zhang A, Xu J, Meng J, Tang L, Lyu S. Epigenetics: Mechanisms, potential roles, and therapeutic strategies in cancer progression. Genes Dis 2024; 11:101020. [PMID: 38988323 PMCID: PMC11233905 DOI: 10.1016/j.gendis.2023.04.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/20/2023] [Accepted: 04/14/2023] [Indexed: 07/12/2024] Open
Abstract
Mutations or abnormal expression of oncogenes and tumor suppressor genes are known to cause cancer. Recent studies have shown that epigenetic modifications are key drivers of cancer development and progression. Nevertheless, the mechanistic role of epigenetic dysregulation in the tumor microenvironment is not fully understood. Here, we reviewed the role of epigenetic modifications of cancer cells and non-cancer cells in the tumor microenvironment and recent research advances in cancer epigenetic drugs. In addition, we discussed the great potential of epigenetic combination therapies in the clinical treatment of cancer. However, there are still some challenges in the field of cancer epigenetics, such as epigenetic tumor heterogeneity, epigenetic drug heterogeneity, and crosstalk between epigenetics, proteomics, metabolomics, and other omics, which may be the focus and difficulty of cancer treatment in the future. In conclusion, epigenetic modifications in the tumor microenvironment are essential for future epigenetic drug development and the comprehensive treatment of cancer. Epigenetic combination therapy may be a novel strategy for the future clinical treatment of cancer.
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Affiliation(s)
- Dong Wang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yan Zhang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Qingbo Li
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yu Li
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Wen Li
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ao Zhang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jingxuan Xu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jingyan Meng
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Lin Tang
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Shuhua Lyu
- Department of Pathology, Tianjin Union Medical Center, Tianjin 300121, China
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2
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Liu Y, Tan X, Wang R, Fan L, Yan Q, Chen C, Wang W, Ren Z, Ning X, Ku T, Sang N. Retinal Degeneration Response to Graphene Quantum Dots: Disruption of the Blood-Retina Barrier Modulated by Surface Modification-Dependent DNA Methylation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39102579 DOI: 10.1021/acs.est.4c02179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Graphene quantum dots (GQDs) are used in diverse fields from chemistry-related materials to biomedicines, thus causing their substantial release into the environment. Appropriate visual function is crucial for facilitating the decision-making process within the nervous system. Given the direct interaction of eyes with the environment and even nanoparticles, herein, GQDs, sulfonic acid-doped GQDs (S-GQDs), and amino-functionalized GQDs (A-GQDs) were employed to understand the potential optic neurotoxicity disruption mechanism by GQDs. The negatively charged GQDs and S-GQDs disturbed the response to light stimulation and impaired the structure of the retinal nuclear layer of zebrafish larvae, causing vision disorder and retinal degeneration. Albeit with sublethal concentrations, a considerably reduced expression of the retinal vascular sprouting factor sirt1 through increased DNA methylation damaged the blood-retina barrier. Importantly, the regulatory effect on vision function was influenced by negatively charged GQDs and S-GQDs but not positively charged A-GQDs. Moreover, cluster analysis and computational simulation studies indicated that binding affinities between GQDs and the DNMT1-ligand binding might be the dominant determinant of the vision function response. The previously unknown pathway of blood-retinal barrier interference offers opportunities to investigate the biological consequences of GQD-based nanomaterials, guiding innovation in the industry toward environmental sustainability.
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Affiliation(s)
- Yutong Liu
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Xin Tan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Rui Wang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Lifan Fan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Qiqi Yan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Chen Chen
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Wenhao Wang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Zhihua Ren
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Xia Ning
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingting Ku
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Nan Sang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, China
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3
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Wang X, Xue X, Pang M, Yu L, Qian J, Li X, Tian M, Lyu A, Lu C, Liu Y. Epithelial-mesenchymal plasticity in cancer: signaling pathways and therapeutic targets. MedComm (Beijing) 2024; 5:e659. [PMID: 39092293 PMCID: PMC11292400 DOI: 10.1002/mco2.659] [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: 01/27/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
Currently, cancer is still a leading cause of human death globally. Tumor deterioration comprises multiple events including metastasis, therapeutic resistance and immune evasion, all of which are tightly related to the phenotypic plasticity especially epithelial-mesenchymal plasticity (EMP). Tumor cells with EMP are manifest in three states as epithelial-mesenchymal transition (EMT), partial EMT, and mesenchymal-epithelial transition, which orchestrate the phenotypic switch and heterogeneity of tumor cells via transcriptional regulation and a series of signaling pathways, including transforming growth factor-β, Wnt/β-catenin, and Notch. However, due to the complicated nature of EMP, the diverse process of EMP is still not fully understood. In this review, we systematically conclude the biological background, regulating mechanisms of EMP as well as the role of EMP in therapy response. We also summarize a range of small molecule inhibitors, immune-related therapeutic approaches, and combination therapies that have been developed to target EMP for the outstanding role of EMP-driven tumor deterioration. Additionally, we explore the potential technique for EMP-based tumor mechanistic investigation and therapeutic research, which may burst vigorous prospects. Overall, we elucidate the multifaceted aspects of EMP in tumor progression and suggest a promising direction of cancer treatment based on targeting EMP.
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Affiliation(s)
- Xiangpeng Wang
- School of Materia MedicaBeijing University of Chinese MedicineBeijingChina
| | - Xiaoxia Xue
- School of Materia MedicaBeijing University of Chinese MedicineBeijingChina
| | - Mingshi Pang
- School of Materia MedicaBeijing University of Chinese MedicineBeijingChina
| | - Liuchunyang Yu
- School of Materia MedicaBeijing University of Chinese MedicineBeijingChina
| | - Jinxiu Qian
- School of Materia MedicaBeijing University of Chinese MedicineBeijingChina
| | - Xiaoyu Li
- School of Materia MedicaBeijing University of Chinese MedicineBeijingChina
| | - Meng Tian
- School of Materia MedicaBeijing University of Chinese MedicineBeijingChina
| | - Aiping Lyu
- School of Chinese MedicineHong Kong Baptist UniversityKowloonHong KongChina
| | - Cheng Lu
- Institute of Basic Research in Clinical MedicineChina Academy of Chinese Medical SciencesBeijingChina
| | - Yuanyan Liu
- School of Materia MedicaBeijing University of Chinese MedicineBeijingChina
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4
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Guynes K, Sarre LA, Carrillo-Baltodano AM, Davies BE, Xu L, Liang Y, Martín-Zamora FM, Hurd PJ, de Mendoza A, Martín-Durán JM. Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria. Genome Biol 2024; 25:204. [PMID: 39090757 PMCID: PMC11292947 DOI: 10.1186/s13059-024-03346-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND DNA methylation in the form of 5-methylcytosine (5mC) is the most abundant base modification in animals. However, 5mC levels vary widely across taxa. While vertebrate genomes are hypermethylated, in most invertebrates, 5mC concentrates on constantly and highly transcribed genes (gene body methylation; GbM) and, in some species, on transposable elements (TEs), a pattern known as "mosaic". Yet, the role and developmental dynamics of 5mC and how these explain interspecies differences in DNA methylation patterns remain poorly understood, especially in Spiralia, a large clade of invertebrates comprising nearly half of the animal phyla. RESULTS Here, we generate base-resolution methylomes for three species with distinct genomic features and phylogenetic positions in Annelida, a major spiralian phylum. All possible 5mC patterns occur in annelids, from typical invertebrate intermediate levels in a mosaic distribution to hypermethylation and methylation loss. GbM is common to annelids with 5mC, and methylation differences across species are explained by taxon-specific transcriptional dynamics or the presence of intronic TEs. Notably, the link between GbM and transcription decays during development, alongside a gradual and global, age-dependent demethylation in adult stages. Additionally, reducing 5mC levels with cytidine analogs during early development impairs normal embryogenesis and reactivates TEs in the annelid Owenia fusiformis. CONCLUSIONS Our study indicates that global epigenetic erosion during development and aging is an ancestral feature of bilateral animals. However, the tight link between transcription and gene body methylation is likely more important in early embryonic stages, and 5mC-mediated TE silencing probably emerged convergently across animal lineages.
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Affiliation(s)
- Kero Guynes
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, 1030, Austria
| | - Luke A Sarre
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Allan M Carrillo-Baltodano
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Billie E Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Lan Xu
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Yan Liang
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- Altos Labs, Cambridge, UK
| | - Paul J Hurd
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
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5
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Xie Y, Xie J, Li L. The Role of Methylation in Ferroptosis. J Cardiovasc Transl Res 2024:10.1007/s12265-024-10539-1. [PMID: 39075241 DOI: 10.1007/s12265-024-10539-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 06/21/2024] [Indexed: 07/31/2024]
Abstract
Methylation modification is a crucial epigenetic alteration encompassing RNA methylation, DNA methylation, and histone methylation. Ferroptosis represents a newly discovered form of programmed cell death (PCD) in 2012, which is characterized by iron-dependent lipid peroxidation. The comprehensive investigation of ferroptosis is therefore imperative for a more profound comprehension of the pathological and pathophysiological mechanisms implicated in a wide array of diseases. Researches show that methylation modifications can exert either promotive or inhibitory effects on cell ferroptosis. Consequently, this review offers a comprehensive overview of the pivotal role played by methylation in ferroptosis, elucidating its associated factors and underlying mechanisms.
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Affiliation(s)
- Yushu Xie
- Class of Clinical Medicine, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Jie Xie
- Class of Excellent Doctor, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Liang Li
- Department of Physiology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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6
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Kisliouk T, Ravi PM, Rosenberg T, Meiri N. Embryonic manipulations shape life-long, heritable stress responses through complex epigenetic mechanisms: a review. Front Neurosci 2024; 18:1435065. [PMID: 39099633 PMCID: PMC11294202 DOI: 10.3389/fnins.2024.1435065] [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: 05/19/2024] [Accepted: 07/02/2024] [Indexed: 08/06/2024] Open
Abstract
Enhancing an organism's likelihood of survival hinges on fostering a balanced and adaptable development of robust stress response systems. This critical process is significantly influenced by the embryonic environment, which plays a pivotal role in shaping neural circuits that define the stress response set-point. While certain embryonic conditions offer advantageous outcomes, others can lead to maladaptive responses. The establishment of this response set-point during embryonic development can exert life-long and inheritable effects on an organism's physiology and behavior. This review highlights the significance of multilevel epigenetic regulation and the intricate cross-talk among these layers in response to heat stress during the embryonic period, with a particular focus on insights gained from the avian model.
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Affiliation(s)
- Tatiana Kisliouk
- Institute of Animal Science, Agricultural Research Organization, Volcani Center, Rishon Leziyyon, Israel
| | - Padma Malini Ravi
- Institute of Animal Science, Agricultural Research Organization, Volcani Center, Rishon Leziyyon, Israel
| | - Tali Rosenberg
- Department of Animal Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Noam Meiri
- Institute of Animal Science, Agricultural Research Organization, Volcani Center, Rishon Leziyyon, Israel
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7
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Cristalli C, Scotlandi K. Targeting DNA Methylation Machinery in Pediatric Solid Tumors. Cells 2024; 13:1209. [PMID: 39056791 PMCID: PMC11275080 DOI: 10.3390/cells13141209] [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: 05/20/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
DNA methylation is a key epigenetic regulatory mechanism that plays a critical role in a variety of cellular processes, including the regulation of cell fate during development, maintenance of cell identity, and genome stability. DNA methylation is tightly regulated by enzymatic reactions and its deregulation plays an important role in the development of cancer. Specific DNA methylation alterations have been found in pediatric solid tumors, providing new insights into the development of these tumors. In addition, DNA methylation profiles have greatly contributed to tune the diagnosis of pediatric solid tumors and to define subgroups of patients with different risks of progression, leading to the reduction in unwanted toxicity and the improvement of treatment efficacy. This review highlights the dysregulated DNA methylome in pediatric solid tumors and how this information provides promising targets for epigenetic therapies, particularly inhibitors of DNMT enzymes (DNMTis). Opportunities and limitations are considered, including the ability of DNMTis to induce viral mimicry and immune signaling by tumors. Besides intrinsic action against cancer cells, DNMTis have the potential to sensitize immune-cold tumors to immunotherapies and may represent a remarkable option to improve the treatment of challenging pediatric solid tumors.
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Affiliation(s)
- Camilla Cristalli
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
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8
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Du J, Goodisman MAD. The role of epigenetics in insects in changing environments. INSECT MOLECULAR BIOLOGY 2024. [PMID: 39023396 DOI: 10.1111/imb.12947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/10/2024] [Indexed: 07/20/2024]
Affiliation(s)
- Juan Du
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Michael A D Goodisman
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, Georgia, USA
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9
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Jovanska L, Lin IC, Yao JS, Chen CL, Liu HC, Li WC, Chuang YC, Chuang CN, Yu ACH, Lin HN, Pong WL, Yu CI, Su CY, Chen YP, Chen RS, Hsueh YP, Yuan HS, Timofejeva L, Wang TF. DNA cytosine methyltransferases differentially regulate genome-wide hypermutation and interhomolog recombination in Trichoderma reesei meiosis. Nucleic Acids Res 2024:gkae611. [PMID: 39021337 DOI: 10.1093/nar/gkae611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/20/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024] Open
Abstract
Trichoderma reesei is an economically important enzyme producer with several unique meiotic features. spo11, the initiator of meiotic double-strand breaks (DSBs) in most sexual eukaryotes, is dispensable for T. reesei meiosis. T. reesei lacks the meiosis-specific recombinase Dmc1. Rad51 and Sae2, the activator of the Mre11 endonuclease complex, promote DSB repair and chromosome synapsis in wild-type and spo11Δ meiosis. DNA methyltransferases (DNMTs) perform multiple tasks in meiosis. Three DNMT genes (rid1, dim2 and dimX) differentially regulate genome-wide cytosine methylation and C:G-to-T:A hypermutations in different chromosomal regions. We have identified two types of DSBs: type I DSBs require spo11 or rid1 for initiation, whereas type II DSBs do not rely on spo11 and rid1 for initiation. rid1 (but not dim2) is essential for Rad51-mediated DSB repair and normal meiosis. rid1 and rad51 exhibit a locus heterogeneity (LH) relationship, in which LH-associated proteins often regulate interconnectivity in protein interaction networks. This LH relationship can be suppressed by deleting dim2 in a haploid rid1Δ (but not rad51Δ) parental strain, indicating that dim2 and rid1 share a redundant function that acts earlier than rad51 during early meiosis. In conclusion, our studies provide the first evidence of the involvement of DNMTs during meiotic initiation and recombination.
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Affiliation(s)
| | - I-Chen Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Chi-Mei Medical Center, Tainan 71004, Taiwan
| | - Jhong-Syuan Yao
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Ling Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hou-Cheng Liu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wan-Chen Li
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Chien Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chi-Ning Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | | | - Hsin-Nan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Li Pong
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chang-I Yu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ching-Yuan Su
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ping Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ruey-Shyang Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ljudmilla Timofejeva
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Centre of Estonian Rural Research and Knowledge, J. Aamisepa 1, Jõgeva 48309, Estonia
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
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10
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Wang K, He Z, Jin G, Jin S, Du Y, Yuan S, Zhang J. Targeting DNA methyltransferases for cancer therapy. Bioorg Chem 2024; 151:107652. [PMID: 39024804 DOI: 10.1016/j.bioorg.2024.107652] [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: 05/09/2024] [Revised: 06/29/2024] [Accepted: 07/14/2024] [Indexed: 07/20/2024]
Abstract
DNA methyltransferases (DNMTs) play a crucial role in genomic DNA methylation. In mammals, DNMTs regulate the dynamic patterns of DNA methylation in embryonic and adult cells. Abnormal functions of DNMTs are often indicative of cancers, including overall hypomethylation and partial hypermethylation of tumor suppressor genes (TSG), which accelerate the malignancy of tumors, worsen the condition of patients, and significantly exacerbate the difficulty of cancer treatment. Currently, nucleoside DNMT inhibitors such as Azacytidine and Decitabine have been approved by the FDA and EMA for the treatment of acute myeloid leukemia (AML), chronic myelomonocytic leukemia (CMML), and myelodysplastic syndrome (MDS). Therefore, targeting DNMTs is a very promising anti-tumor strategy. This review mainly summarizes the therapeutic effects of DNMT inhibitors on cancers. It aims to provide more possibilities for the treatment of cancers by discovering more DNMT inhibitors with high activity, high selectivity, and good drug-like properties in the future.
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Affiliation(s)
- Kaiyue Wang
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Zhangxu He
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China.
| | - Gang Jin
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Sasa Jin
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Yuanbing Du
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Shuo Yuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, PR China.
| | - Jingyu Zhang
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China.
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11
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Wang A, Wan X, Zhu F, Liu H, Song X, Huang Y, Zhu L, Ao Y, Zeng J, Wang B, Wu Y, Xu Z, Wang J, Yao W, Li H, Zhuang P, Jiao J, Zhang Y. Habitual Daily Intake of Fried Foods Raises Transgenerational Inheritance Risk of Heart Failure Through NOTCH1-Triggered Apoptosis. RESEARCH (WASHINGTON, D.C.) 2024; 7:0401. [PMID: 39010883 PMCID: PMC11246838 DOI: 10.34133/research.0401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/15/2024] [Indexed: 07/17/2024]
Abstract
Consumption of fried foods is highly prevalent in the Western dietary pattern. Western diet has been unfavorably linked with high risk of developing cardiovascular diseases. Heart failure (HF) as a cardiovascular disease subtype is a growing global pandemic with high morbidity and mortality. However, the causal relationship between long-term fried food consumption and incident HF remains unclear. Our population-based study revealed that frequent fried food consumption is strongly associated with 15% higher risk of HF. The causal relationship may be ascribed to the dietary acrylamide exposure in fried foods. Further cross-sectional study evidenced that acrylamide exposure is associated with an increased risk of HF. Furthermore, we discover and demonstrate that chronic acrylamide exposure may induce HF in zebrafish and mice. Mechanistically, we reveal that acrylamide induces energy metabolism disturbance in heart due to the mitochondria dysfunction and metabolic remodeling. Moreover, acrylamide exposure induces myocardial apoptosis via inhibiting NOTCH1-phosphatidylinositol 3-kinase/AKT signaling. In addition, acrylamide exposure could affect heart development during early life stage, and the adverse effect of acrylamide exposure is a threat for next generation via epigenetic change evoked by DNA methyltransferase 1 (DNMT1). In this study, we reveal the adverse effects and underlying mechanism of fried foods and acrylamide as a typical food processing contaminant on HF from population-based observations to experimental validation. Collectively, these results both epidemiologically and mechanistically provide strong evidence to unravel the mechanism of acrylamide-triggered HF and highlight the significance of reducing fried food consumption for lower the risk of HF.
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Affiliation(s)
- Anli Wang
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xuzhi Wan
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fanghuan Zhu
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haoyin Liu
- Department of Endocrinology, The Second Affiliated Hospital, Department of Nutrition, School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaoran Song
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yingyu Huang
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Li Zhu
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yang Ao
- Department of Endocrinology, The Second Affiliated Hospital, Department of Nutrition, School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jia Zeng
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Binjie Wang
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, China
| | - Yuanzhao Wu
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, China
| | - Zhongshi Xu
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, China
| | - Jiye Wang
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, China
| | - Weixuan Yao
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, China
| | - Haoyu Li
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Pan Zhuang
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingjing Jiao
- Department of Endocrinology, The Second Affiliated Hospital, Department of Nutrition, School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yu Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
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12
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Hong Z, Xu Y, Wu J. Bisphenol A: Epigenetic effects on the male reproductive system and male offspring. Reprod Toxicol 2024; 129:108656. [PMID: 39004383 DOI: 10.1016/j.reprotox.2024.108656] [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: 07/28/2023] [Revised: 06/23/2024] [Accepted: 07/03/2024] [Indexed: 07/16/2024]
Abstract
Bisphenol A (BPA) is a commonly used organic compound. Over the past decades, many studies have examined the mechanisms of BPA toxicity, with BPA-induced alterations in epigenetic modifications receiving considerable attention. Particularly in the male reproductive system, abnormal alterations in epigenetic markers can adversely affect reproductive function. Furthermore, these changes in epigenetic markers can be transmitted to offspring through the father. Here, we review the effects of BPA exposure on various epigenetic markers in the male reproductive system, including DNA methylation, histone modifications, and noncoding RNA, as well as associated changes in the male reproductive function. We also reviewed the effects of father's exposure to BPA on offspring epigenetic modification patterns.
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Affiliation(s)
- Zhilin Hong
- The center of clinical laboratory, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, PR China.
| | - Yingpei Xu
- Department of Reproductive Medicine, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, Fujian 364000, PR China
| | - Jinxiang Wu
- Department of reproductive medicine, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, PR China.
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13
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Sarre LA, Kim IV, Ovchinnikov V, Olivetta M, Suga H, Dudin O, Sebé-Pedrós A, de Mendoza A. DNA methylation enables recurrent endogenization of giant viruses in an animal relative. SCIENCE ADVANCES 2024; 10:eado6406. [PMID: 38996012 PMCID: PMC11244446 DOI: 10.1126/sciadv.ado6406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/07/2024] [Indexed: 07/14/2024]
Abstract
5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. The causes for 5mC retention and its genomic consequences are still poorly understood. Here, we show that the protist closely related to animals Amoebidium appalachense features both transposon and gene body methylation, a pattern reminiscent of invertebrates and plants. Unexpectedly, hypermethylated genomic regions in Amoebidium derive from viral insertions, including hundreds of endogenized giant viruses, contributing 14% of the proteome. Using a combination of inhibitors and genomic assays, we demonstrate that 5mC silences these giant virus insertions. Moreover, alternative Amoebidium isolates show polymorphic giant virus insertions, highlighting a dynamic process of infection, endogenization, and purging. Our results indicate that 5mC is critical for the controlled coexistence of newly acquired viral DNA into eukaryotic genomes, making Amoebidium a unique model to understand the hybrid origins of eukaryotic DNA.
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Affiliation(s)
- Luke A. Sarre
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Iana V. Kim
- CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Vladimir Ovchinnikov
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Marine Olivetta
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara, Japan
| | - Omaya Dudin
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Arnau Sebé-Pedrós
- CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- ICREA, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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14
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Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang CK, Chou SH, Neidle S, Hou MH. Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation. Nucleic Acids Res 2024:gkae594. [PMID: 38989613 DOI: 10.1093/nar/gkae594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.
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Affiliation(s)
- Shan-Meng Lin
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsiang-Ti Huang
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Pei-Ju Fang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Roshan Satange
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-Ke Chang
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan
| | - Stephen Neidle
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Ming-Hon Hou
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
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15
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Tang Y. Single-Molecule Mixture: A Concept in Polymer Science. Int J Mol Sci 2024; 25:7571. [PMID: 39062814 PMCID: PMC11277297 DOI: 10.3390/ijms25147571] [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: 06/20/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
In theory, two extreme forms of substances exist: the pure form and the single-molecule mixture form. The latter contains a mixture of molecules with molecularly different structures. Inspired by the "chemical space" concept, in this paper, I report a study of the single-molecule mixture state that combines model construction and mathematical analysis, obtaining some interesting results. These results provide theoretical evidence that the single-molecule mixture state may indeed exist in realistic synthetic or natural polymer systems.
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Affiliation(s)
- Yu Tang
- State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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16
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Deng F, Lei J, Qiu J, Zhao C, Wang X, Li M, Sun M, Zhang M, Gao Q. DNA methylation landscape in pregnancy-induced hypertension: progress and challenges. Reprod Biol Endocrinol 2024; 22:77. [PMID: 38978060 PMCID: PMC11229300 DOI: 10.1186/s12958-024-01248-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/24/2024] [Indexed: 07/10/2024] Open
Abstract
Gestational hypertension (PIH), especially pre-eclampsia (PE), is a common complication of pregnancy. This condition poses significant risks to the health of both the mother and the fetus. Emerging evidence suggests that epigenetic modifications, particularly DNA methylation, may play a role in initiating the earliest pathophysiology of PIH. This article describes the relationship between DNA methylation and placental trophoblast function, genes associated with the placental microenvironment, the placental vascular system, and maternal blood and vascular function, abnormalities of umbilical cord blood and vascular function in the onset and progression of PIH, as well as changes in DNA methylation in the progeny of PIH, in terms of maternal, fetal, and offspring. We also explore the latest research on DNA methylation-based early detection, diagnosis and potential therapeutic strategies for PIH. This will enable the field of DNA methylation research to continue to enhance our understanding of the epigenetic regulation of PIH genes and identify potential therapeutic targets.
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Affiliation(s)
- Fengying Deng
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, 215006, P. R. China
| | - Jiahui Lei
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, 215006, P. R. China
| | - Junlan Qiu
- Department of Oncology and Hematology, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, Jiangsu, 215153, P.R. China
| | - Chenxuan Zhao
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, 215006, P. R. China
| | - Xietong Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250014, China
| | - Min Li
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, 215006, P. R. China
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Soochow University, Suzhou, 215006, P. R. China
| | - Miao Sun
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, 215006, P. R. China.
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250014, China.
| | - Meihua Zhang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250014, China.
| | - Qinqin Gao
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, 215006, P. R. China.
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250014, China.
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17
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Li C, Liu Y, Luo S, Yang M, Li L, Sun L. A review of CDKL: An underestimated protein kinase family. Int J Biol Macromol 2024:133604. [PMID: 38964683 DOI: 10.1016/j.ijbiomac.2024.133604] [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: 06/25/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
Cyclin-dependent kinase-like (CDKL) family proteins are serine/threonine protein kinases and is a specific branch of CMGC (including CDK, MAPK, GSK). Its name is due to the sequence similarity with CDK and it consists of 5 members. Their function in protein phosphorylation underpins their important role in cellular activities, including cell cycle, apoptosis, autophagy and microtubule dynamics. CDKL proteins have been demonstrated to regulate the length of primary cilium, which is a dynamic and diverse signaling hub and closely associated with multiple diseases. Furthermore, CDKL proteins have been shown to be involved in the development and progression of several diseases, including cancer, neurodegenerative diseases and kidney disease. In this review, we summarize the structural characteristics and discovered functions of CDKL proteins and their role in diseases, which might be helpful for the development of innovative therapeutic strategies for disease.
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Affiliation(s)
- Chenrui Li
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Yan Liu
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Shilu Luo
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Ming Yang
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Li Li
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China.
| | - Lin Sun
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China.
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18
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Totten V, Teixido-Tura G, Lopez-Grondona F, Fernandez-Alvarez P, Lasa-Aranzasti A, Muñoz-Cabello P, Kosaki R, Tizzano EF, Dewals W, Borràs E, Cañas EG, Almoguera B, Loeys B, Valenzuena I. Arterial aneurysm and dissection: toward the evolving phenotype of Tatton-Brown-Rahman syndrome. J Med Genet 2024:jmg-2024-109861. [PMID: 38960581 DOI: 10.1136/jmg-2024-109861] [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: 01/08/2024] [Accepted: 06/17/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND Tatton-Brown-Rahman syndrome (TBRS) is a rare disorder, caused by DNMT3A heterozygous pathogenic variants, and first described in 2014. TBRS is characterised by overgrowth, intellectual disability, facial dysmorphism, hypotonia and musculoskeletal features, as well as neurological and psychiatric features. Cardiac manifestations have also been reported, mainly congenital malformations such as atrial septal defect, ventricular septal defect and cardiac valvular disease. Aortic dilatation has rarely been described. METHODS Here we have undertaken a detailed clinical and molecular description of eight previously unreported individuals, who had TBRS and arterial dilatation and/or dissection, mainly thoracic aortic aneurysm (TAA). We have also reviewed the seven previously published cases of TAA in individuals with TBRS to try to better delineate the vascular phenotype and to determine specific follow-up for this condition. RESULTS We include eight new patients with TBRS who presented with arterial aneurysms mainly involving aorta. Three of these patients presented with dissection that required critical surgery. CONCLUSIONS Arterial aneurysms and dissections are a potentially lethal, age-dependent manifestation. The prevalence of aortic disease in individuals with TBRS is far in excess of that expected in the general population. This cohort, together with individuals previously published, illustrates the importance to consider dilatation/dissection, mainly in aorta but also in other arteries. Arterial vascular weakness may therefore also be a cardinal feature of TBRS and vascular surveillance is recommended.
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Affiliation(s)
- Vicken Totten
- Kaweah Health System, Visalia, California, USA
- Kayenta Health Center of the Indian Health Service, Kayenta, Arizona, USA
| | - Gisela Teixido-Tura
- Department of Cardiology, Hospital Universitari Vall d'Hebron, CIBER-CV, Vall d'Hebron institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Genetics and Genomics, Hospital Universitario Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain
| | - Fermina Lopez-Grondona
- European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Barcelona, Spain
| | - Paula Fernandez-Alvarez
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital. Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability (ERN-ITHACA), Barcelona, Spain
| | - Amaia Lasa-Aranzasti
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital. Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability (ERN-ITHACA), Barcelona, Spain
| | - Patricia Muñoz-Cabello
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital. Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability (ERN-ITHACA), Barcelona, Spain
| | - Rika Kosaki
- Division of Medical Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Eduardo F Tizzano
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital. Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability (ERN-ITHACA), Barcelona, Spain
| | - Wendy Dewals
- Pediatric Cardiology Department, Antwerp University Hospital, Edegem, Belgium
| | - Emma Borràs
- Molecular Genetics Unit, Consorci Sanitari de Terrassa, Terrassa, Spain
| | - Elena Gonzalez Cañas
- Angiology and Vascular Surgery, Hospital Universitari Parc Tauli, Sabadell, Spain
| | - Berta Almoguera
- European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Barcelona, Spain
- Centro de Investigacion Biomedica en Red de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Bart Loeys
- Center for Medical Genetics, Antwerp University Hospital/University of Antwerp, Antwerp, Belgium
| | - Irene Valenzuena
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital. Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability (ERN-ITHACA), Barcelona, Spain
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19
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Cai X, Liu Y, Li H, Que Y, Xiao M, Wang Y, Wang X, Li D. XPO1 inhibition displays anti-leukemia efficacy against DNMT3A-mutant acute myeloid leukemia via downregulating glutathione pathway. Ann Hematol 2024; 103:2311-2322. [PMID: 38519605 DOI: 10.1007/s00277-024-05706-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024]
Abstract
Acute myeloid leukemia (AML) patients with DNA methyltransferase 3A (DNMT3A) mutation display poor prognosis, and targeted therapy is not available currently. Our previous study identified increased expression of Exportin1 (XPO1) in DNMT3AR882H AML patients. Therefore, we further investigated the therapeutic effect of XPO1 inhibition on DNMT3AR882H AML. Three types of DNMT3AR882H AML cell lines were generated, and XPO1 was significantly upregulated in all DNMT3AR882H cells compared with the wild-type (WT) cells. The XPO1 inhibitor selinexor displayed higher potential in the inhibition of proliferation, promotion of apoptosis, and blockage of the cell cycle in DNMT3AR882H cells than WT cells. Selinexor also significantly inhibited the proliferation of subcutaneous tumors in DNMT3AR882H AML model mice. Primary cells with DNMT3A mutations were more sensitive to selinexor in chemotherapy-naive AML patients. RNA sequencing of selinexor treated AML cells revealed that the majority of metabolic pathways were downregulated after selinexor treatment, with the most significant change in the glutathione metabolic pathway. Glutathione inhibitor L-Buthionine-(S, R)-sulfoximine (BSO) significantly enhanced the apoptosis-inducing effect of selinexor in DNMT3AWT/DNMT3AR882H AML cells. In conclusion, our work reveals that selinexor displays anti-leukemia efficacy against DNMT3AR882H AML via downregulating glutathione pathway. Combination of selinexor and BSO provides novel therapeutic strategy for AML treatment.
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Affiliation(s)
- Xiaoya Cai
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Liu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huimin Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yimei Que
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiong Wang
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Dengju Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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20
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Czajka N, Northrup JM, Jones MJ, Shafer ABA. Epigenetic clocks, sex markers and age-class diagnostics in three harvested large mammals. Mol Ecol Resour 2024; 24:e13956. [PMID: 38553977 DOI: 10.1111/1755-0998.13956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/05/2024] [Accepted: 03/14/2024] [Indexed: 06/04/2024]
Abstract
The development of epigenetic clocks, or the DNA methylation-based inference of age, is an emerging tool for ageing in free ranging populations. In this study, we developed epigenetic clocks for three species of large mammals that are the focus of extensive management throughout their range in North America: white-tailed deer, black bear and mountain goat. We quantified differential DNA methylation patterns at over 30,000 cytosine-guanine sites (CpGs) from tissue samples of all three species (black bear n = 49; white-tailed deer n = 47; mountain goat n = 45). We used a penalized regression model (elastic net) to build explanatory (black bear r = .95; white-tailed deer r = .99; mountain goat r = .97) and robust (black bear Median Absolute Error or MAE = 1.33; white-tailed deer MAE = 0.29; mountain goat MAE = 0.61) models of age or clocks. We also characterized individual CpG sites within each species that demonstrated clear differences in methylation levels between age classes and sex, which can be used to develop a suite of accessible diagnostic markers. This tool has the potential to contribute to wildlife monitoring by providing easily obtainable representations of age structure in managed populations.
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Affiliation(s)
- Natalie Czajka
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Joseph M Northrup
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Meaghan J Jones
- Department of Biochemistry and Medical Genetics, Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Aaron B A Shafer
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
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21
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Thomas H, Alix T, Renard É, Renaud M, Wourms J, Zuily S, Leheup B, Geneviève D, Dreumont N, Schmitt E, Bronner M, Muller M, Divoux M, Wandzel M, Ravel JM, Dexheimer M, Becker A, Roth V, Willems M, Coubes C, Vieville G, Devillard F, Schaefer É, Baer S, Piton A, Gérard B, Vincent M, Nizon M, Cogné B, Ruaud L, Couque N, Putoux A, Edery P, Lesca G, Chatron N, Till M, Faivre L, Tran-Mau-Them F, Alessandri JL, Lebrun M, Quélin C, Odent S, Dubourg C, David V, Faoucher M, Mignot C, Keren B, Pisan É, Afenjar A, Julia S, Bieth É, Banneau G, Goldenberg A, Husson T, Campion D, Lecoquierre F, Nicolas G, Charbonnier C, De Saint Martin A, Naudion S, Degoutin M, Rondeau S, Michot C, Cormier-Daire V, Oussalah A, Pourié C, Lambert L, Bonnet C. Expanding the genetic and clinical spectrum of Tatton-Brown-Rahman syndrome in a series of 24 French patients. J Med Genet 2024:jmg-2024-110031. [PMID: 38937076 DOI: 10.1136/jmg-2024-110031] [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: 04/02/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Tatton-Brown-Rahman syndrome (TBRS; OMIM 615879), also known as DNA methyltransferase 3 alpha (DNMT3A)-overgrowth syndrome (DOS), was first described by Tatton-Brown in 2014. This syndrome is characterised by overgrowth, intellectual disability and distinctive facial features and is the consequence of germline loss-of-function variants in DNMT3A, which encodes a DNA methyltransferase involved in epigenetic regulation. Somatic variants of DNMT3A are frequently observed in haematological malignancies, including acute myeloid leukaemia (AML). To date, 100 individuals with TBRS with de novo germline variants have been described. We aimed to further characterise this disorder clinically and at the molecular level in a nationwide series of 24 French patients and to investigate the correlation between the severity of intellectual disability and the type of variant. METHODS We collected genetic and medical information from 24 individuals with TBRS using a questionnaire released through the French National AnDDI-Rares Network. RESULTS Here, we describe the first nationwide French cohort of 24 individuals with germline likely pathogenic/pathogenic variants in DNMT3A, including 17 novel variants. We confirmed that the main phenotypic features were intellectual disability (100% of individuals), distinctive facial features (96%) and overgrowth (87%). We highlighted novel clinical features, such as hypertrichosis, and further described the neurological features and EEG results. CONCLUSION This study of a nationwide cohort of individuals with TBRS confirms previously published data and provides additional information and clarifies clinical features to facilitate diagnosis and improve care. This study adds value to the growing body of knowledge on TBRS and broadens its clinical and molecular spectrum.
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Affiliation(s)
- Hortense Thomas
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- Service de Génétique Clinique, CHRU de Nancy, Nancy, France
| | - Tom Alix
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Émeline Renard
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
- Endocrinologie pédiatrique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Mathilde Renaud
- Service de Génétique Clinique, CHRU de Nancy, Nancy, France
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
- Service de Neurologie, CHRU de Nancy, Nancy, France
| | - Justine Wourms
- Service de Génétique Clinique, CHRU de Nancy, Nancy, France
| | - Stéphane Zuily
- Médecine Vasculaire, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- UMR_S 916 DCAC, INSERM, Vandœuvre-lès-Nancy, France
| | - Bruno Leheup
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - David Geneviève
- Centre de référence anomalies du développement et syndromes malformatifs, Département de Génétique Medicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
- Inserm U1183, Université Montpellier 1, Faculté de Médecine Montpellier-Nîmes, Montpellier, France
| | - Natacha Dreumont
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Myriam Bronner
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Marc Muller
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Marion Divoux
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Marion Wandzel
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Jean-Marie Ravel
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Mylène Dexheimer
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Aurélie Becker
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Virginie Roth
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Marjolaine Willems
- Centre de référence anomalies du développement et syndromes malformatifs, Département de Génétique Medicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Christine Coubes
- Centre de référence anomalies du développement et syndromes malformatifs, Département de Génétique Medicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Gaëlle Vieville
- Département de Génétique et Procréation, Hôpital Couple Enfant, CHU Grenoble Alpes, Grenoble, France
| | - Françoise Devillard
- Département de Génétique et Procréation, Hôpital Couple Enfant, CHU Grenoble Alpes, Grenoble, France
| | - Élise Schaefer
- Service de Génétique médicale, Institut de Génétique Médicale d'Alsace, CHU de Strasbourg, Strasbourg, France
| | - Sarah Baer
- Service de Génétique médicale, Institut de Génétique Médicale d'Alsace, CHU de Strasbourg, Strasbourg, France
| | - Amélie Piton
- Service de Génétique médicale, Institut de Génétique Médicale d'Alsace, CHU de Strasbourg, Strasbourg, France
| | - Bénédicte Gérard
- Service de Génétique médicale, Institut de Génétique Médicale d'Alsace, CHU de Strasbourg, Strasbourg, France
| | - Marie Vincent
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
- CNRS, INSERM, Institut du thorax, Nantes Université, Nantes, France
| | - Mathilde Nizon
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
- CNRS, INSERM, Institut du thorax, Nantes Université, Nantes, France
| | - Benjamin Cogné
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
- CNRS, INSERM, Institut du thorax, Nantes Université, Nantes, France
| | - Lyse Ruaud
- Département de Génétique, Hôpital Robert Debré, APHP Nord, Paris, France
| | - Nathalie Couque
- Département de Génétique, Hôpital Robert Debré, APHP Nord, Paris, France
| | - Audrey Putoux
- Service de Génétique, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France
- CNRS UMR5310, INSERM U1217, Institut NeuroMyoGene PNMG, Université Claude Bernard Lyon 1, Lyon, France
| | - Patrick Edery
- Service de Génétique, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France
- CNRS UMR5310, INSERM U1217, Institut NeuroMyoGene PNMG, Université Claude Bernard Lyon 1, Lyon, France
| | - Gaëtan Lesca
- Service de Génétique, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France
- CNRS UMR5310, INSERM U1217, Institut NeuroMyoGene PNMG, Université Claude Bernard Lyon 1, Lyon, France
| | - Nicolas Chatron
- Service de Génétique, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France
- CNRS UMR5310, INSERM U1217, Institut NeuroMyoGene PNMG, Université Claude Bernard Lyon 1, Lyon, France
| | - Marianne Till
- Service de Génétique, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France
- CNRS UMR5310, INSERM U1217, Institut NeuroMyoGene PNMG, Université Claude Bernard Lyon 1, Lyon, France
| | - Laurence Faivre
- Centre de référence anomalies du développement et syndromes malformatifs et Centre de référence Déficiences Intellectuelles de causes rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UMR1231 GAD, Inserm, Université Bourgogne Franche-Comté, Dijon, France
| | - Frédéric Tran-Mau-Them
- UMR1231 GAD, Inserm, Université Bourgogne Franche-Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Jean-Luc Alessandri
- Service de génétique médicale, CHU de La Réunion, Hôpital Félix Guyon, Bellepierre, Saint-Denis, Réunion
| | - Marine Lebrun
- Département de Génétique, Centre Hospitalier Universitaire de Saint-Etienne, Saint-Etienne, France
| | - Chloé Quélin
- Département de génétique moléculaire et génomique, CHU Rennes, Rennes, France
| | - Sylvie Odent
- Département de génétique moléculaire et génomique, CHU Rennes, Rennes, France
| | - Christèle Dubourg
- Département de génétique moléculaire et génomique, CHU Rennes, Rennes, France
| | - Véronique David
- Département de génétique moléculaire et génomique, CHU Rennes, Rennes, France
| | - Marie Faoucher
- Département de génétique moléculaire et génomique, CHU Rennes, Rennes, France
| | - Cyril Mignot
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Boris Keren
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Élise Pisan
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Alexandra Afenjar
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Sophie Julia
- Département de Génétique médicale, CHU Toulouse, Toulouse, France
| | - Éric Bieth
- Département de Génétique médicale, CHU Toulouse, Toulouse, France
| | | | - Alice Goldenberg
- Department of Genetics and Reference Center for Developmental Disorders, CHU de Rouen, Rouen, France
- Inserm U1245, Université de Rouen Normandie, Rouen, France
| | - Thomas Husson
- Inserm U1245, Université de Rouen Normandie, Rouen, France
- Department of Psychiatry, CHU de Rouen, Rouen, France
- Department of Research, Centre hospitalier du Rouvray, Sotteville-Lès-Rouen, France
| | - Dominique Campion
- Inserm U1245, Université de Rouen Normandie, Rouen, France
- Department of Psychiatry, CHU de Rouen, Rouen, France
- Department of Research, Centre hospitalier du Rouvray, Sotteville-Lès-Rouen, France
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, CHU de Rouen, Rouen, France
- Inserm U1245, Université de Rouen Normandie, Rouen, France
| | - Gaël Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, CHU de Rouen, Rouen, France
- Inserm U1245, Université de Rouen Normandie, Rouen, France
| | - Camille Charbonnier
- Inserm U1245, Université de Rouen Normandie, Rouen, France
- Department of Biotatistics, CHU de Rouen, Rouen, France
| | - Anne De Saint Martin
- Centre de Référence des épilepsies Rares, Hopitaux universitaires de Strasbourg, Strasbourg, France
| | - Sophie Naudion
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Groupe hospitalier Pellegrin, Bordeaux, France
| | - Manon Degoutin
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Groupe hospitalier Pellegrin, Bordeaux, France
| | - Sophie Rondeau
- Centre de référence des maladies osseuses constitutionnelles, Necker-Enfants Malades Hospitals, Paris, France
- INSERM UMR 1163, Imagine Institute, Paris, France
| | - Caroline Michot
- Centre de référence des maladies osseuses constitutionnelles, Necker-Enfants Malades Hospitals, Paris, France
- INSERM UMR 1163, Imagine Institute, Paris, France
| | - Valérie Cormier-Daire
- Centre de référence des maladies osseuses constitutionnelles, Necker-Enfants Malades Hospitals, Paris, France
- INSERM UMR 1163, Imagine Institute, Paris, France
| | - Abderrahim Oussalah
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
- Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, and Nutrition, CHRU de Nancy, Nancy, France
| | - Carine Pourié
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Laëtitia Lambert
- Service de Génétique Clinique, CHRU de Nancy, Nancy, France
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Céline Bonnet
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
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22
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Ye Z, Zhong Y, Zhang Z. Pan-cancer multi-omics analysis of PTBP1 reveals it as an inflammatory, progressive and prognostic marker in glioma. Sci Rep 2024; 14:14584. [PMID: 38918441 PMCID: PMC11199703 DOI: 10.1038/s41598-024-64979-5] [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: 12/27/2023] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
PTBP1 is an oncogene that regulates the splicing of precursor mRNA. However, the relationship between PTBP1 expression and gene methylation, cancer prognosis, and tumor microenvironment remains unclear. The expression profiles of PTBP1 across various cancers were derived from the TCGA, as well as the GTEx and CGGA databases. The CGGA mRNA_325, CGGA mRNA_301, and CGGA mRNA_693 datasets were utilized as validation cohorts. Immune cell infiltration scores were approximated using the TIMER 2.0 tool. Functional enrichment analysis for groups with high and low PTBP1 expression was conducted using Gene Set Enrichment Analysis (GSEA). Methylation data were predominantly sourced from the SMART and Mexpress databases. Linked-omics analysis was employed to perform functional enrichment analysis of genes related to PTBP1 methylation, as well as to conduct protein functional enrichment analysis. Single-cell transcriptome analysis and spatial transcriptome analysis were carried out using Seurat version 4.10. Compared to normal tissues, PTBP1 is significantly overexpressed and hypomethylated in various cancers. It is implicated in prognosis, immune cell infiltration, immune checkpoint expression, genomic variation, tumor neoantigen load, and tumor mutational burden across a spectrum of cancers, with particularly notable effects in low-grade gliomas. In the context of gliomas, PTBP1 expression correlates with WHO grade and IDH1 mutation status. PTBP1 expression and methylation play an important role in a variety of cancers. PTBP1 can be used as a marker of inflammation, progression and prognosis in gliomas.
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Affiliation(s)
- Zheng Ye
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, 510006, Guangdong, China
- Zhongda Hospital, Southeast University, Nanjing, China
| | - Yan Zhong
- People's Hospital of Dongxihu District, Wuhan, China
| | - Zhiyuan Zhang
- Department of Neurosurgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
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23
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Sun S, Lu W, Zhang C, Wang G, Hou Y, Zhou J, Wang Y. Folic acid and S-adenosylmethionine reverse Homocysteine-induced Alzheimer's disease-like pathological changes in rat hippocampus by modulating PS1 and PP2A methylation levels. Brain Res 2024; 1841:149095. [PMID: 38917878 DOI: 10.1016/j.brainres.2024.149095] [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: 01/25/2024] [Revised: 06/10/2024] [Accepted: 06/22/2024] [Indexed: 06/27/2024]
Abstract
BACKGROUND Abnormally elevated homocysteine (Hcy) is recognized as a biomarker and risk factor for Alzheimer's disease (AD). However, the underlying mechanisms by which Hcy affects AD are still unclear. OBJECTIVES This study aimed to elucidate the effects and mechanisms by which Hcy affects AD-like pathological changes in the hippocampus through in vivo and in vitro experiments, and to investigate whether folic acid (FA) and S-adenosylmethionine (SAM) supplementation could improve neurodegenerative injuries. METHODS In vitro experiments hippocampal neurons of rat were treated with Hcy, FA or SAM for 24 h; while the hyperhomocysteinemia (HHcy) in Wistar rats was established by intraperitoneal injection of Hcy, and FA was added to feed. The expression of β-amyloid (Aβ), phosphorylated tau protein, presenilin 1 (PS1) at the protein level and the activity of protein phosphatase 2A (PP2A) were detected, the immunopositive cells for Aβ and phosphorylated tau protein in the rat hippocampus were also evaluated by immunohistochemical staining. RESULTS FA and SAM significantly repressed Hcy-induced AD-like pathological changes in the hippocampus, including the increased tau protein phosphorylation at Ser214, Ser396 and the expression of Aβ42. In addition, Hcy-induced PS1 expression increased at the protein level and PP2A activity decreased, while FA and SAM were able to retard that. CONCLUSIONS The increase in PS1 expression and decrease in PP2A activity may be the mechanisms underlying the Hcy-induced AD-like pathology. FA and SAM significantly repressed the Hcy-induced neurodegenerative injury by modulating PS1 and PP2A methylation levels.
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Affiliation(s)
- Shoudan Sun
- Shandong Provincial Third Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250031, China
| | - Wei Lu
- Shandong Provincial Third Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250031, China
| | - Chunhong Zhang
- Shandong Provincial Third Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250031, China
| | - Guanyu Wang
- Institute of Environmental and Operational Medicine, Tianjin 30050, China
| | - Yue Hou
- Institute of Environmental and Operational Medicine, Tianjin 30050, China
| | - Jian Zhou
- School of Public Health, Weifang Medical College, Weifang 261053, China.
| | - Yonghui Wang
- Institute of Environmental and Operational Medicine, Tianjin 30050, China.
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24
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Hu X, Ye Q, Lu H, Wu Z, Chen S, Zheng R. Estrogen-mediated DNMT1 and DNMT3A recruitment by EZH2 silences miR-570-3p that contributes to papillary thyroid malignancy through DPP4. Clin Epigenetics 2024; 16:81. [PMID: 38890707 PMCID: PMC11184720 DOI: 10.1186/s13148-024-01685-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 05/27/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) is a common endocrine malignancy. Studies have indicated that estrogen can regulate the expression of miRNAs in numerous malignancies. MiR-570-3p has been shown to have a regulatory function in various cancers. However, studies of the regulatory function of miR-570-3p and a direct link between estrogen (especially estradiol E2) and miR-570-3p in PTC have not been done. METHODS Expression of miR-570-3p and its downstream target DPP4 in PTC tissues and cells was predicted using bioinformatics and validated by qRT-PCR and western blot assays. We then performed a series of gain-and-loss experiments to assess the functional significance of miR-570-3p/DPP4 axis in PTC progression in vitro and in vivo. Additionally, the methylation of the miR-570-3p promoter region was examined via bioinformatics analysis and MSP. Finally, the effects of E2 on PTC progression and the correlation between DNMT1/DNMT3A and EZH2 were predicted by bioinformatic tools and proved by luciferase reporter, ChIP, and co-IP assays. RESULTS In PTC tumor tissues and cell lines, there was a lower expression level and a higher methylation level of miR-570-3p compared to normal tissues and cell lines. DPP4 was identified as the downstream target of miR-570-3p. Overexpression of miR-570-3p reduced the proliferative, migratory, and invasive capabilities, and promoted apoptosis, while overexpression of DPP4 reversed these effects in PTC cells. It was also discovered that DNMT1 and DNMT3A increased the CpG methylation level of the miR-570-3p promoter in an EZH2-dependent manner, which led to decreased expression of miR-570-3p. Furthermore, we observed that estrogen (E2) enhanced the methylation of miR-570-3p and suppressed its expression levels, resulting in augmented tumor growth in vivo in PTC. CONCLUSION Estrogen regulates the EZH2/DNMTs/miR-570-3p/DPP4 signaling pathway to promote PTC progression.
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Affiliation(s)
- Xiarong Hu
- Department of General Surgery, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan, 523059, Guangdong, China
| | - Qingyao Ye
- Department of General Surgery, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan, 523059, Guangdong, China
| | - HuanQuan Lu
- Department of General Surgery, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan, 523059, Guangdong, China
| | - Zhiming Wu
- Department of General Surgery, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan, 523059, Guangdong, China
| | - Siyuan Chen
- Department of General Surgery, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan, 523059, Guangdong, China
| | - Ruinian Zheng
- Department of Oncology, Dongguan Institute of Clinical Cancer Research, Dongguan Key Laboratory of Precision Diagnosis and Treatment for Tumors, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan, 523059, Guangdong, China.
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25
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Sobhiafshar U, Çakici B, Yilmaz E, Yildiz Ayhan N, Hedaya L, Ayhan MC, Yerinde C, Alankuş YB, Gürkaşlar HK, Firat-Karalar EN, Emre NCT. Interferon regulatory factor 4 modulates epigenetic silencing and cancer-critical pathways in melanoma cells. Mol Oncol 2024. [PMID: 38880659 DOI: 10.1002/1878-0261.13672] [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: 08/17/2023] [Revised: 04/14/2024] [Accepted: 05/22/2024] [Indexed: 06/18/2024] Open
Abstract
Interferon regulatory factor 4 (IRF4) was initially identified as a key controller in lymphocyte differentiation and function, and subsequently as a dependency factor and therapy target in lymphocyte-derived cancers. In melanocytes, IRF4 takes part in pigmentation. Although genetic studies have implicated IRF4 in melanoma, how IRF4 functions in melanoma cells has remained largely elusive. Here, we confirmed prevalent IRF4 expression in melanoma and showed that high expression is linked to dependency in cells and mortality in patients. Analysis of genes activated by IRF4 uncovered, as a novel target category, epigenetic silencing factors involved in DNA methylation (DNMT1, DNMT3B, UHRF1) and histone H3K27 methylation (EZH2). Consequently, we show that IRF4 controls the expression of tumour suppressor genes known to be silenced by these epigenetic modifications, for instance cyclin-dependent kinase inhibitors CDKN1A and CDKN1B, the PI3-AKT pathway regulator PTEN, and primary cilium components. Furthermore, IRF4 modulates activity of key downstream oncogenic pathways, such as WNT/β-catenin and AKT, impacting cell proliferation and survival. Accordingly, IRF4 modifies the effectiveness of pertinent epigenetic drugs on melanoma cells, a finding that encourages further studies towards therapeutic targeting of IRF4 in melanoma.
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Affiliation(s)
- Ulduz Sobhiafshar
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Betül Çakici
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Erdem Yilmaz
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Nalan Yildiz Ayhan
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Laila Hedaya
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Mustafa Can Ayhan
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Cansu Yerinde
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | | | - H Kübra Gürkaşlar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | | | - N C Tolga Emre
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
- Center for Life Sciences and Technologies, Boğaziçi University, Istanbul, Turkey
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26
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Afgar A, Keyhani A, Afgar A, Mirzaei-Parsa MJ, Kermani MRZ, Rezaei M, Ebrahimipour M, Langroudi L, Bardsiri MS, Vahidi R. Catechin-Induced changes in PODXL, DNMTs, and miRNA expression in Nalm6 cells: an integrated in silico and in vitro approach. BMC Complement Med Ther 2024; 24:234. [PMID: 38879474 PMCID: PMC11179370 DOI: 10.1186/s12906-024-04521-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND This study explored the impact of predicted miRNAs on DNA methyltransferases (DNMTs) and the PODXL gene in Nalm6 cells, revealing the significance of these miRNAs in acute lymphocytic leukemia (ALL). METHODS A comprehensive approach was adopted, integrating bioinformatic analyses encompassing protein structure prediction, molecular docking, dynamics, and ADMET profiling, in conjunction with evaluations of gene and miRNA expression patterns. This methodology was employed to elucidate the therapeutic potential of catechin compounds in modulating the activity of DNA methyltransferases (DNMTs) and the PODXL gene. RESULTS The findings from our investigation indicate that catechins possess the capability to inhibit DNMT enzymes. This inhibitory effect is associated with the upregulation of microRNAs miR-200c and miR-548 and a concurrent downregulation of PODXL gene expression. These molecular interactions culminate in an augmented apoptotic response within ALL (Nalm6) cells. CONCLUSION The study posits that catechins may represent a viable therapeutic avenue for inducing apoptosis in ALL cells. This is achieved through the modulation of epigenetic mechanisms and alterations in gene expression profiles, highlighting the potential of catechins as agents for cancer therapy.
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Affiliation(s)
- Ali Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Alireza Keyhani
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Amirreza Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohamad Javad Mirzaei-Parsa
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Science, Kerman, Iran
| | | | - Masoud Rezaei
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Ebrahimipour
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Ladan Langroudi
- Department of Immunology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mahla Sattarzadeh Bardsiri
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Science, Kerman, Iran.
- Stem Cells and Regenerative Medicine Innovation Center, Kerman University of Medical Sciences, Kerman, Iran.
- Student Research Committee, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.
| | - Reza Vahidi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran.
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27
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Ren L, Chang YF, Jiang SH, Li XH, Cheng HP. DNA methylation modification in Idiopathic pulmonary fibrosis. Front Cell Dev Biol 2024; 12:1416325. [PMID: 38915445 PMCID: PMC11194555 DOI: 10.3389/fcell.2024.1416325] [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: 04/12/2024] [Accepted: 05/22/2024] [Indexed: 06/26/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and irreversible interstitial lung disease with a prognosis worse than lung cancer. It is a fatal lung disease with largely unknown etiology and pathogenesis, and no effective therapeutic drugs render its treatment largely unsuccessful. With continuous in-depth research efforts, the epigenetic mechanisms in IPF pathogenesis have been further discovered and concerned. As a widely studied mechanism of epigenetic modification, DNA methylation is primarily facilitated by DNA methyltransferases (DNMTs), resulting in the addition of a methyl group to the fifth carbon position of the cytosine base, leading to the formation of 5-methylcytosine (5-mC). Dysregulation of DNA methylation is intricately associated with the advancement of respiratory disorders. Recently, the role of DNA methylation in IPF pathogenesis has also received considerable attention. DNA methylation patterns include methylation modification and demethylation modification and regulate a range of essential biological functions through gene expression regulation. The Ten-Eleven-Translocation (TET) family of DNA dioxygenases is crucial in facilitating active DNA demethylation through the enzymatic conversion of the modified genomic base 5-mC to 5-hydroxymethylcytosine (5-hmC). TET2, a member of TET proteins, is involved in lung inflammation, and its protein expression is downregulated in the lungs and alveolar epithelial type II cells of IPF patients. This review summarizes the current knowledge of pathologic features and DNA methylation mechanisms of pulmonary fibrosis, focusing on the critical roles of abnormal DNA methylation patterns, DNMTs, and TET proteins in impacting IPF pathogenesis. Researching DNA methylation will enchance comprehension of the fundamental mechanisms involved in IPF pathology and provide novel diagnostic biomarkers and therapeutic targets for pulmonary fibrosis based on the studies involving epigenetic mechanisms.
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Affiliation(s)
- Lu Ren
- Clinical Nursing Teaching and Research Section, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yan-Fen Chang
- Medicine School, Zhengzhou University of Industrial Technology, Zhengzhou, China
| | - Shi-He Jiang
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiao-Hong Li
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Hai-Peng Cheng
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
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28
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Mukherjee K, Dobrindt U. Epigenetic remodeling in insect immune memory. Front Immunol 2024; 15:1397521. [PMID: 38915407 PMCID: PMC11194310 DOI: 10.3389/fimmu.2024.1397521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/29/2024] [Indexed: 06/26/2024] Open
Abstract
The innate immune system of insects can respond more swiftly and efficiently to pathogens based on previous experience of encountering antigens. The understanding of molecular mechanisms governing immune priming, a form of immune memory in insects, including its transgenerational inheritance, remains elusive. It is still unclear if the enhanced expression of immune genes observed in primed insects can persist and be regulated through changes in chromatin structure via epigenetic modifications of DNA or histones, mirroring observations in mammals. Increasing experimental evidence suggests that epigenetic changes at the level of DNA/RNA methylation and histone acetylation can modulate the activation of insects' immune responses to pathogen exposure. Moreover, transgenerational inheritance of certain epigenetic modifications in model insect hosts can influence the transmission of pre-programmed immune responses to the offspring, leading to the development of evolved resistance. Epigenetic research in model insect hosts is on the brink of significant progress in the mechanistic understanding of chromatin remodeling within innate immunity, particularly the direct relationships between immunological priming and epigenetic alterations. In this review, we discuss the latest discoveries concerning the involvement of DNA methylation and histone acetylation in shaping the development, maintenance, and inheritance of immune memory in insects, culminating in the evolution of resistance against pathogens.
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Affiliation(s)
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
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29
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Zebrauskiene D, Sadauskiene E, Dapkunas J, Kairys V, Balciunas J, Konovalovas A, Masiuliene R, Petraityte G, Valeviciene N, Mataciunas M, Barysiene J, Mikstiene V, Tomkuviene M, Preiksaitiene E. Aortic disease and cardiomyopathy in patients with a novel DNMT3A gene variant causing Tatton-Brown-Rahman syndrome. Clin Epigenetics 2024; 16:76. [PMID: 38845031 PMCID: PMC11157947 DOI: 10.1186/s13148-024-01686-y] [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: 04/05/2024] [Accepted: 05/27/2024] [Indexed: 06/09/2024] Open
Abstract
Tatton-Brown-Rahman syndrome (TBRS) is a rare congenital genetic disorder caused by autosomal dominant pathogenic variants in the DNA methyltransferase DNMT3A gene. Typical TBRS clinical features are overgrowth, intellectual disability, and minor facial anomalies. However, since the syndrome was first described in 2014, a widening spectrum of abnormalities is being described. Cardiovascular abnormalities are less commonly reported but can be a major complication of the syndrome. This article describes a family of three individuals diagnosed with TBRS in adulthood and highlights the variable expression of cardiovascular features. A 34-year-old proband presented with progressive aortic dilatation, mitral valve (MV) regurgitation, left ventricular (LV) dilatation, and ventricular arrhythmias. The affected family members (mother and brother) were diagnosed with MV regurgitation, LV dilatation, and arrhythmias. Exome sequencing and computational protein analysis suggested that the novel familial DNMT3A mutation Ser775Tyr is located in the methyltransferase domain, however, distant from the active site or DNA-binding loops. Nevertheless, this bulky substitution may have a significant effect on DNMT3A protein structure, dynamics, and function. Analysis of peripheral blood cfDNA and transcriptome showed shortened mononucleosome fragments and altered gene expression in a number of genes related to cardiovascular health and of yet undescribed function, including several lncRNAs. This highlights the importance of epigenetic regulation by DNMT3A on cardiovascular system development and function. From the clinical perspective, we suggest that new patients diagnosed with congenital DNMT3A variants and TBRS require close examination and follow-up for aortic dilatation and valvular disease because these conditions can progress rapidly. Moreover, personalized treatments, based on the specific DNMT3A variants and the different pathways of their function loss, can be envisioned in the future.
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Affiliation(s)
- Dovile Zebrauskiene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania.
| | - Egle Sadauskiene
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Justas Dapkunas
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Joris Balciunas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | | | | | - Gunda Petraityte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania
| | - Nomeda Valeviciene
- Department of Radiology, Nuclear Medicine and Medical Physics, Institute of Biomedical Sciences, Vilnius University Faculty of Medicine, Vilnius, Lithuania
| | - Mindaugas Mataciunas
- Department of Radiology, Nuclear Medicine and Medical Physics, Institute of Biomedical Sciences, Vilnius University Faculty of Medicine, Vilnius, Lithuania
| | - Jurate Barysiene
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Violeta Mikstiene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania
| | - Migle Tomkuviene
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania.
| | - Egle Preiksaitiene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania
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Fernandes P, Waldron N, Chatzilygeroudi T, Naji NS, Karantanos T. Acute Erythroid Leukemia: From Molecular Biology to Clinical Outcomes. Int J Mol Sci 2024; 25:6256. [PMID: 38892446 PMCID: PMC11172574 DOI: 10.3390/ijms25116256] [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: 04/12/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Acute Erythroid Leukemia (AEL) is a rare and aggressive subtype of Acute Myeloid Leukemia (AML). In 2022, the World Health Organization (WHO) defined AEL as a biopsy with ≥30% proerythroblasts and erythroid precursors that account for ≥80% of cellularity. The International Consensus Classification refers to this neoplasm as "AML with mutated TP53". Classification entails ≥20% blasts in blood or bone marrow biopsy and a somatic TP53 mutation (VAF > 10%). This type of leukemia is typically associated with biallelic TP53 mutations and a complex karyotype, specifically 5q and 7q deletions. Transgenic mouse models have implicated several molecules in the pathogenesis of AEL, including transcriptional master regulator GATA1 (involved in erythroid differentiation), master oncogenes, and CDX4. Recent studies have also characterized AEL by epigenetic regulator mutations and transcriptome subgroups. AEL patients have overall poor clinical outcomes, mostly related to their poor response to the standard therapies, which include hypomethylating agents and intensive chemotherapy. Allogeneic bone marrow transplantation (AlloBMT) is the only potentially curative approach but requires deep remission, which is very challenging for these patients. Age, AlloBMT, and a history of antecedent myeloid neoplasms further affect the outcomes of these patients. In this review, we will summarize the diagnostic criteria of AEL, review the current insights into the biology of AEL, and describe the treatment options and outcomes of patients with this disease.
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Affiliation(s)
- Priyanka Fernandes
- Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (P.F.); (N.W.)
| | - Natalie Waldron
- Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (P.F.); (N.W.)
| | - Theodora Chatzilygeroudi
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (T.C.); (N.S.N.)
| | - Nour Sabiha Naji
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (T.C.); (N.S.N.)
| | - Theodoros Karantanos
- Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (P.F.); (N.W.)
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (T.C.); (N.S.N.)
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Ruocco MR, Gisonna A, Acampora V, D’Agostino A, Carrese B, Santoro J, Venuta A, Nasso R, Rocco N, Russo D, Cavaliere A, Altobelli GG, Masone S, Avagliano A, Arcucci A, Fiume G. Guardians and Mediators of Metastasis: Exploring T Lymphocytes, Myeloid-Derived Suppressor Cells, and Tumor-Associated Macrophages in the Breast Cancer Microenvironment. Int J Mol Sci 2024; 25:6224. [PMID: 38892411 PMCID: PMC11172575 DOI: 10.3390/ijms25116224] [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: 02/20/2024] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
Breast cancers (BCs) are solid tumors composed of heterogeneous tissues consisting of cancer cells and an ever-changing tumor microenvironment (TME). The TME includes, among other non-cancer cell types, immune cells influencing the immune context of cancer tissues. In particular, the cross talk of immune cells and their interactions with cancer cells dramatically influence BC dissemination, immunoediting, and the outcomes of cancer therapies. Tumor-infiltrating lymphocytes (TILs), tumor-associated macrophages (TAMs), and myeloid-derived suppressor cells (MDSCs) represent prominent immune cell populations of breast TMEs, and they have important roles in cancer immunoescape and dissemination. Therefore, in this article we review the features of TILs, TAMs, and MDSCs in BCs. Moreover, we highlight the mechanisms by which these immune cells remodel the immune TME and lead to breast cancer metastasis.
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Affiliation(s)
- Maria Rosaria Ruocco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.R.R.); (A.G.)
| | - Armando Gisonna
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.R.R.); (A.G.)
| | - Vittoria Acampora
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (V.A.); (A.V.); (A.A.)
| | - Anna D’Agostino
- IRCCS SYNLAB SDN, Via Emanuele Gianturco 113, 80143 Naples, Italy; (A.D.); (B.C.); (J.S.)
| | - Barbara Carrese
- IRCCS SYNLAB SDN, Via Emanuele Gianturco 113, 80143 Naples, Italy; (A.D.); (B.C.); (J.S.)
| | - Jessie Santoro
- IRCCS SYNLAB SDN, Via Emanuele Gianturco 113, 80143 Naples, Italy; (A.D.); (B.C.); (J.S.)
| | - Alessandro Venuta
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (V.A.); (A.V.); (A.A.)
| | - Rosarita Nasso
- Department of Movement Sciences and Wellness, University of Naples “Parthenope”, 80133 Naples, Italy;
| | - Nicola Rocco
- Department of Advanced Biomedical Science, University of Naples Federico II, 80131 Naples, Italy; (N.R.); (D.R.); (G.G.A.)
| | - Daniela Russo
- Department of Advanced Biomedical Science, University of Naples Federico II, 80131 Naples, Italy; (N.R.); (D.R.); (G.G.A.)
| | | | - Giovanna Giuseppina Altobelli
- Department of Advanced Biomedical Science, University of Naples Federico II, 80131 Naples, Italy; (N.R.); (D.R.); (G.G.A.)
| | - Stefania Masone
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy;
| | - Angelica Avagliano
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (V.A.); (A.V.); (A.A.)
| | - Alessandro Arcucci
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (V.A.); (A.V.); (A.A.)
| | - Giuseppe Fiume
- Department of Experimental and Clinical Medicine, University of Catanzaro “Magna Graecia”, 88100 Catanzaro, Italy;
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Etayo-Urtasun P, Sáez de Asteasu ML, Izquierdo M. Effects of Exercise on DNA Methylation: A Systematic Review of Randomized Controlled Trials. Sports Med 2024:10.1007/s40279-024-02033-0. [PMID: 38839665 DOI: 10.1007/s40279-024-02033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Regular exercise reduces chronic disease risk and extends a healthy lifespan, but the underlying molecular mechanisms remain unclear. DNA methylation is implicated in this process, potentially altering gene expression without changing DNA sequence. However, previous findings appear partly contradictory. OBJECTIVE This review aimed to elucidate exercise effects on DNA methylation patterns. METHODS PubMed, Scopus and Web of Science databases were searched following PRISMA 2020 guidelines. All articles published up to November 2023 were considered for inclusion and assessed for eligibility using the PICOS (Population, Intervention, Comparison, Outcomes and Study) framework. Randomized controlled trials that assessed the impact of exercise interventions on DNA methylation in previously inactive adults were included. We evaluated the methodological quality of trials using the PEDro scale. RESULTS A total of 852 results were identified, of which 12 articles met the inclusion criteria. A total of 827 subjects were included in the studies. Intervention lengths varied from 6 weeks to 12 months. Most trials indicated that exercise interventions can significantly alter the DNA methylation of specific genes and global DNA methylation patterns. CONCLUSIONS The heterogeneity of results may arise from differences in participant demographics, intervention factors, measurement techniques, and the genomic contexts examined. Future research should analyze the influences of activity type, intensity, and duration, as well as the physical fitness outcomes on DNA methylation. Characterizing such dose-response relationships and identifying genes responsive to exercise are crucial for understanding the molecular mechanisms of exercise, unlocking its full potential for disease prevention and treatment.
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Affiliation(s)
| | - Mikel L Sáez de Asteasu
- Navarrabiomed, Pamplona, Spain
- Department of Health Sciences, Hospital Universitario de Navarra (HUN)-Universidad Pública de Navarra (UPNA), IdiSNA, Av. De Barañain s/n, 31008, Pamplona, Navarra, Spain
- CIBER of Frailty and Healthy Aging (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
| | - Mikel Izquierdo
- Navarrabiomed, Pamplona, Spain.
- Department of Health Sciences, Hospital Universitario de Navarra (HUN)-Universidad Pública de Navarra (UPNA), IdiSNA, Av. De Barañain s/n, 31008, Pamplona, Navarra, Spain.
- CIBER of Frailty and Healthy Aging (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain.
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Morgan RK, Wang K, Svoboda LK, Rygiel CA, Lalancette C, Cavalcante R, Bartolomei MS, Prasasya R, Neier K, Perera BP, Jones TR, Colacino JA, Sartor MA, Dolinoy DC. Effects of Developmental Lead and Phthalate Exposures on DNA Methylation in Adult Mouse Blood, Brain, and Liver: A Focus on Genomic Imprinting by Tissue and Sex. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:67003. [PMID: 38833407 PMCID: PMC11166413 DOI: 10.1289/ehp14074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Maternal exposure to environmental chemicals can cause adverse health effects in offspring. Mounting evidence supports that these effects are influenced, at least in part, by epigenetic modifications. It is unknown whether epigenetic changes in surrogate tissues such as the blood are reflective of similar changes in target tissues such as cortex or liver. OBJECTIVE We examined tissue- and sex-specific changes in DNA methylation (DNAm) associated with human-relevant lead (Pb) and di(2-ethylhexyl) phthalate (DEHP) exposure during perinatal development in cerebral cortex, blood, and liver. METHODS Female mice were exposed to human relevant doses of either Pb (32 ppm ) via drinking water or DEHP (5 mg / kg-day ) via chow for 2 weeks prior to mating through offspring weaning. Whole genome bisulfite sequencing (WGBS) was utilized to examine DNAm changes in offspring cortex, blood, and liver at 5 months of age. Metilene and methylSig were used to identify differentially methylated regions (DMRs). Annotatr and ChIP-enrich were used for genomic annotations and gene set enrichment tests of DMRs, respectively. RESULTS The cortex contained the majority of DMRs associated with Pb (66%) and DEHP (57%) exposure. The cortex also contained the greatest degree of overlap in DMR signatures between sexes (n = 13 and 8 DMRs with Pb and DEHP exposure, respectively) and exposure types (n = 55 and 39 DMRs in males and females, respectively). In all tissues, detected DMRs were preferentially found at genomic regions associated with gene expression regulation (e.g., CpG islands and shores, 5' UTRs, promoters, and exons). An analysis of GO terms associated with DMR-containing genes identified imprinted genes to be impacted by both Pb and DEHP exposure. Of these, Gnas and Grb10 contained DMRs across tissues, sexes, and exposures, with some signatures replicated between target and surrogate tissues. DMRs were enriched in the imprinting control regions (ICRs) of Gnas and Grb10, and we again observed a replication of DMR signatures between blood and target tissues. Specifically, we observed hypermethylation of the Grb10 ICR in both blood and liver of Pb-exposed male animals. CONCLUSIONS These data provide preliminary evidence that imprinted genes may be viable candidates in the search for epigenetic biomarkers of toxicant exposure in target tissues. Additional research is needed on allele- and developmental stage-specific effects, as well as whether other imprinted genes provide additional examples of this relationship. https://doi.org/10.1289/EHP14074.
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Affiliation(s)
- Rachel K. Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Christine A. Rygiel
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Claudia Lalancette
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Raymond Cavalcante
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rexxi Prasasya
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kari Neier
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Bambarendage P.U. Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Tamara R. Jones
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
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Liu X, Huang W, Bishir M, Hodgkinson C, Goldman D, Chang SL. Sex-dependent responses to high concentration of binge ethanol in spleen of adolescent F344 rats. ALCOHOL, CLINICAL & EXPERIMENTAL RESEARCH 2024; 48:1063-1075. [PMID: 38627206 DOI: 10.1111/acer.15328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/25/2024] [Accepted: 04/01/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND We previously reported that binge ethanol induces atrophy of the spleen, a key immune organ, in adolescent male F344 rats. Because there are significant sex effects in immune function, we investigated whether binge ethanol exerts sex-dependent effects on the spleen, including producing splenic atrophy. METHODS We gave F344 rats ethanol (4.8 g/kg/day; 52% w/v; i.g.) on postnatal days [PND] 36 ~ 38 and sacrificed them on PND 39 for spleen collection. We performed immunophenotyping analysis of splenic cells and examined the expression of 158 genes related to alcohol metabolism, epigenetic modification, and immune regulation in the spleens of adolescent (PND 39) male and female rats. RESULTS Following a 3-day ethanol exposure, a loss of body weight, and absolute and relative spleen weight, was seen only in male adolescent rats. Ethanol altered the relative proportions of lymphocyte subtypes in both sexes with different patterns. We also found that 3-day ethanol exposure induced sex-dependent gene expression changes in spleen. Among the 158 genes studied, the expression of only three genes was significantly increased in female rats. However, the expression of 30 genes was significantly increased/decreased in male rats. Female rats had greater expression of alcohol metabolizing enzyme genes in the spleen under physiological conditions and when stimulated by binge ethanol. The genes are involved in epigenetic modification were differentially expressed in a sex-dependent manner. CONCLUSION We found that male adolescent rats were more sensitive to binge ethanol than female rats. Differential expression of the genes related to alcohol metabolism and epigenetic modification (of DNA methyltransferase and histone deacetylases) between the sexes could account for the observed sex-dependent responses to binge ethanol in adolescent rats.
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Affiliation(s)
- Xiangqian Liu
- Institute of NeuroImmune Pharmacology, South Orange, New Jersey, USA
- Department of Histology and Embryology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenfei Huang
- Institute of NeuroImmune Pharmacology, South Orange, New Jersey, USA
- Department of Biological Sciences, Seton Hall University, South Orange, New Jersey, USA
| | - Muhammed Bishir
- Institute of NeuroImmune Pharmacology, South Orange, New Jersey, USA
- Department of Biological Sciences, Seton Hall University, South Orange, New Jersey, USA
| | - Colin Hodgkinson
- Laboratory of Neurogenetics, NIAAA, NIH, Rockville, Maryland, USA
| | - David Goldman
- Laboratory of Neurogenetics, NIAAA, NIH, Rockville, Maryland, USA
| | - Sulie L Chang
- Institute of NeuroImmune Pharmacology, South Orange, New Jersey, USA
- Department of Biological Sciences, Seton Hall University, South Orange, New Jersey, USA
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35
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Mabe NW, Perry JA, Malone CF, Stegmaier K. Pharmacological targeting of the cancer epigenome. NATURE CANCER 2024; 5:844-865. [PMID: 38937652 DOI: 10.1038/s43018-024-00777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
Epigenetic dysregulation is increasingly appreciated as a hallmark of cancer, including disease initiation, maintenance and therapy resistance. As a result, there have been advances in the development and evaluation of epigenetic therapies for cancer, revealing substantial promise but also challenges. Three epigenetic inhibitor classes are approved in the USA, and many more are currently undergoing clinical investigation. In this Review, we discuss recent developments for each epigenetic drug class and their implications for therapy, as well as highlight new insights into the role of epigenetics in cancer.
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Affiliation(s)
- Nathaniel W Mabe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jennifer A Perry
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
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36
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Jan Z, Ahmed WS, Biswas KH, Jithesh PV. Identification of a potential DNA methyltransferase (DNMT) inhibitor. J Biomol Struct Dyn 2024; 42:4730-4744. [PMID: 37424222 DOI: 10.1080/07391102.2023.2233637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023]
Abstract
DNA methyltransferases (DNMTs) play an important role in the epigenetic regulation of gene expression through the methylation of DNA. Since hypermethylation and consequent suppression of tumor suppressor genes are associated with cancer development and progression, DNA hypomethylating agents (HMAs) such as DNMT inhibitors have been proposed for cancer therapy. Two nucleoside analogues approved for the treatment of hematological cancers, decitabine and azacytidine, have poor pharmacokinetic properties, and hence there is a critical need for identifying novel HMAs. Virtual screening of a library of ∼40,000 compounds from the ZINC database, followed by molecular docking of 4,000 compounds having potential druggable properties with DNMT1, DNMT3A and DNMT3B were performed. One unique inhibitor (ZINC167686681) was identified that successfully passed through the Lipinski Rule of 5, geometry constraints as well as ADME/Tox filters and having strong binding energy for DNMTs. Further, molecular dynamics simulations of the docked complexes showed detailed structural features critical for its binding with the DNMTs and the stability of their interaction. Our study identified a compound with potential druggable properties and predicted to bind and inhibit DNMTs. Further investigations involving cellular and animal models of ZINC167686681 will help in potentially taking it into clinical trials for the treatment of cancers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zainab Jan
- Division of Genomics and Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Wesam S Ahmed
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Kabir H Biswas
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Puthen Veettil Jithesh
- Division of Genomics and Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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Tang Y, Cui G, Liu H, Han Y, Cai C, Feng Z, Shen H, Zeng S. Converting "cold" to "hot": epigenetics strategies to improve immune therapy effect by regulating tumor-associated immune suppressive cells. Cancer Commun (Lond) 2024; 44:601-636. [PMID: 38715348 PMCID: PMC11194457 DOI: 10.1002/cac2.12546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 06/26/2024] Open
Abstract
Significant developments in cancer treatment have been made since the advent of immune therapies. However, there are still some patients with malignant tumors who do not benefit from immunotherapy. Tumors without immunogenicity are called "cold" tumors which are unresponsive to immunotherapy, and the opposite are "hot" tumors. Immune suppressive cells (ISCs) refer to cells which can inhibit the immune response such as tumor-associated macrophages (TAMs), myeloid-derived suppressor cells (MDSCs), regulatory T (Treg) cells and so on. The more ISCs infiltrated, the weaker the immunogenicity of the tumor, showing the characteristics of "cold" tumor. The dysfunction of ISCs in the tumor microenvironment (TME) may play essential roles in insensitive therapeutic reaction. Previous studies have found that epigenetic mechanisms play an important role in the regulation of ISCs. Regulating ISCs may be a new approach to transforming "cold" tumors into "hot" tumors. Here, we focused on the function of ISCs in the TME and discussed how epigenetics is involved in regulating ISCs. In addition, we summarized the mechanisms by which the epigenetic drugs convert immunotherapy-insensitive tumors into immunotherapy-sensitive tumors which would be an innovative tendency for future immunotherapy in "cold" tumor.
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Affiliation(s)
- Yijia Tang
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Guangzu Cui
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Haicong Liu
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Ying Han
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Changjing Cai
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Ziyang Feng
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Hong Shen
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
- National Clinical Resaerch Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaHunanChina
| | - Shan Zeng
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
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Aguado-Alvaro LP, Garitano N, Pelacho B. Fibroblast Diversity and Epigenetic Regulation in Cardiac Fibrosis. Int J Mol Sci 2024; 25:6004. [PMID: 38892192 PMCID: PMC11172550 DOI: 10.3390/ijms25116004] [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: 05/06/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Cardiac fibrosis, a process characterized by excessive extracellular matrix (ECM) deposition, is a common pathological consequence of many cardiovascular diseases (CVDs) normally resulting in organ failure and death. Cardiac fibroblasts (CFs) play an essential role in deleterious cardiac remodeling and dysfunction. In response to injury, quiescent CFs become activated and adopt a collagen-secreting phenotype highly contributing to cardiac fibrosis. In recent years, studies have been focused on the exploration of molecular and cellular mechanisms implicated in the activation process of CFs, which allow the development of novel therapeutic approaches for the treatment of cardiac fibrosis. Transcriptomic analyses using single-cell RNA sequencing (RNA-seq) have helped to elucidate the high cellular diversity and complex intercellular communication networks that CFs establish in the mammalian heart. Furthermore, a significant body of work supports the critical role of epigenetic regulation on the expression of genes involved in the pathogenesis of cardiac fibrosis. The study of epigenetic mechanisms, including DNA methylation, histone modification, and chromatin remodeling, has provided more insights into CF activation and fibrotic processes. Targeting epigenetic regulators, especially DNA methyltransferases (DNMT), histone acetylases (HAT), or histone deacetylases (HDAC), has emerged as a promising approach for the development of novel anti-fibrotic therapies. This review focuses on recent transcriptomic advances regarding CF diversity and molecular and epigenetic mechanisms that modulate the activation process of CFs and their possible clinical applications for the treatment of cardiac fibrosis.
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Affiliation(s)
- Laura Pilar Aguado-Alvaro
- Department of Biochemistry and Genetics, University of Navarra, 31008 Pamplona, Spain; (L.P.A.-A.); (N.G.)
- Program of Cardiovascular Disease, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Nerea Garitano
- Department of Biochemistry and Genetics, University of Navarra, 31008 Pamplona, Spain; (L.P.A.-A.); (N.G.)
- Program of Cardiovascular Disease, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Beatriz Pelacho
- Department of Biochemistry and Genetics, University of Navarra, 31008 Pamplona, Spain; (L.P.A.-A.); (N.G.)
- Program of Cardiovascular Disease, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
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Di Martino P, Marcozzi V, Bibbò S, Ghinassi B, Di Baldassarre A, Gaggi G, Di Credico A. Unraveling the Epigenetic Landscape: Insights into Parkinson's Disease, Amyotrophic Lateral Sclerosis, and Multiple Sclerosis. Brain Sci 2024; 14:553. [PMID: 38928553 PMCID: PMC11202179 DOI: 10.3390/brainsci14060553] [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: 04/10/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Parkinson's disease (PD), multiple sclerosis (MS), and amyotrophic lateral sclerosis (ALS) are examples of neurodegenerative movement disorders (NMDs), which are defined by a gradual loss of motor function that is frequently accompanied by cognitive decline. Although genetic abnormalities have long been acknowledged as significant factors, new research indicates that epigenetic alterations are crucial for the initiation and development of disease. This review delves into the complex interactions that exist between the pathophysiology of NMDs and epigenetic mechanisms such DNA methylation, histone modifications, and non-coding RNAs. Here, we examine how these epigenetic changes could affect protein aggregation, neuroinflammation, and gene expression patterns, thereby influencing the viability and functionality of neurons. Through the clarification of the epigenetic terrain underpinning neurodegenerative movement disorders, this review seeks to enhance comprehension of the underlying mechanisms of the illness and augment the creation of innovative therapeutic strategies.
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Affiliation(s)
- Pierpaolo Di Martino
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
| | - Valentina Marcozzi
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
| | - Sandra Bibbò
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Barbara Ghinassi
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- UdA-Tech Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Angela Di Baldassarre
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- UdA-Tech Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Giulia Gaggi
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- UdA-Tech Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Andrea Di Credico
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- UdA-Tech Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
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Zhou X, Jiang S, Guo S, Yao S, Sheng Q, Zhang Q, Dong J, Liao L. C/EBPβ-Lin28a positive feedback loop triggered by C/EBPβ hypomethylation enhances the proliferation and migration of vascular smooth muscle cells in restenosis. Chin Med J (Engl) 2024:00029330-990000000-01085. [PMID: 38809089 DOI: 10.1097/cm9.0000000000003110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND The main cause of restenosis after percutaneous transluminal angioplasty (PTA) is the excessive proliferation and migration of vascular smooth muscle cells (VSMCs). Lin28a has been reported to play critical regulatory roles in this process. However, whether CCAAT/enhancer-binding proteins β (C/EBPβ) binds to the Lin28a promoter and drives the progression of restenosis has not been clarified. Therefore, in the present study, we aim to clarify the role of C/EBPβ-Lin28a axis in restenosis. METHODS Restenosis and atherosclerosis rat models of type 2 diabetes (n = 20, for each group) were established by subjecting to PTA. Subsequently, the difference in DNA methylation status and expression of C/EBPβ between the two groups were assessed. EdU, Transwell, and rescue assays were performed to assess the effect of C/EBPβ on the proliferation and migration of VSMCs. DNA methylation status was further assessed using Methyltarget sequencing. The interaction between Lin28a and ten-eleven translocation 1 (TET1) was analysed using co-immunoprecipitation (Co-IP) assay. Student's t-test and one-way analysis of variance were used for statistical analysis. RESULTS C/EBPβ expression was upregulated and accompanied by hypomethylation of its promoter in restenosis when compared with atherosclerosis. In vitroC/EBPβ overexpression facilitated the proliferation and migration of VSMCs and was associated with increased Lin28a expression. Conversely, C/EBPβ knockdown resulted in the opposite effects. Chromatin immunoprecipitation assays further demonstrated that C/EBPβ could directly bind to Lin28a promoter. Increased C/EBPβ expression and enhanced proliferation and migration of VSMCs were observed after decitabine treatment. Further, mechanical stretch promoted C/EBPβ and Lin28a expression accompanied by C/EBPβ hypomethylation. Additionally, Lin28a overexpression reduced C/EBPβ methylation via recruiting TET1 and enhanced C/EBPβ-mediated proliferation and migration of VSMCs. The opposite was noted in Lin28a knockdown cells. CONCLUSION Our findings suggest that the C/EBPβ-Lin28a axis is a driver of restenosis progression, and presents a promising therapeutic target for restenosis.
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Affiliation(s)
- Xiaojun Zhou
- Department of Endocrinology and Metabology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Shandong Institute of Nephrology, Jinan, Shandong 250014, China
- Department of Endocrinology and Metabology, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250014, China
| | - Shan Jiang
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China
- Department of Endocrinology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Siyi Guo
- Department of Endocrinology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Shuai Yao
- Department of Endocrinology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Qiqi Sheng
- Department of Endocrinology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Qian Zhang
- Department of Pharmacology, Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Jianjun Dong
- Department of Endocrinology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Lin Liao
- Department of Endocrinology and Metabology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Shandong Institute of Nephrology, Jinan, Shandong 250014, China
- Department of Endocrinology and Metabology, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250014, China
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Liu Y, Sun Y, Yang J, Wu D, Yu S, Liu J, Hu T, Luo J, Zhou H. DNMT1-targeting remodeling global DNA hypomethylation for enhanced tumor suppression and circumvented toxicity in oral squamous cell carcinoma. Mol Cancer 2024; 23:104. [PMID: 38755637 PMCID: PMC11097543 DOI: 10.1186/s12943-024-01993-1] [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: 12/19/2023] [Accepted: 04/03/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND The faithful maintenance of DNA methylation homeostasis indispensably requires DNA methyltransferase 1 (DNMT1) in cancer progression. We previously identified DNMT1 as a potential candidate target for oral squamous cell carcinoma (OSCC). However, how the DNMT1- associated global DNA methylation is exploited to regulate OSCC remains unclear. METHODS The shRNA-specific DNMT1 knockdown was employed to target DNMT1 on oral cancer cells in vitro, as was the use of DNMT1 inhibitors. A xenografted OSCC mouse model was established to determine the effect on tumor suppression. High-throughput microarrays of DNA methylation, bulk and single-cell RNA sequencing analysis, multiplex immunohistochemistry, functional sphere formation and protein immunoblotting were utilized to explore the molecular mechanism involved. Analysis of human samples revealed associations between DNMT1 expression, global DNA methylation and collaborative molecular signaling with oral malignant transformation. RESULTS We investigated DNMT1 expression boosted steadily during oral malignant transformation in human samples, and its inhibition considerably minimized the tumorigenicity in vitro and in a xenografted OSCC model. DNMT1 overexpression was accompanied by the accumulation of cancer-specific DNA hypomethylation during oral carcinogenesis; conversely, DNMT1 knockdown caused atypically extensive genome-wide DNA hypomethylation in cancer cells and xenografted tumors. This novel DNMT1-remodeled DNA hypomethylation pattern hampered the dual activation of PI3K-AKT and CDK2-Rb and inactivated GSK3β collaboratively. When treating OSCC mice, targeting DNMT1 achieved greater anticancer efficacy than the PI3K inhibitor, and reduced the toxicity of blood glucose changes caused by the PI3K inhibitor or combination of PI3K and CDK inhibitors as well as adverse insulin feedback. CONCLUSIONS Targeting DNMT1 remodels a novel global DNA hypomethylation pattern to facilitate anticancer efficacy and minimize potential toxic effects via balanced signaling synergia. Our study suggests DNMT1 is a crucial gatekeeper regarding OSCC destiny and treatment outcome.
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Affiliation(s)
- Yangfan Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yu Sun
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- School of Stomatology, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Jin Yang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Deyang Wu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Shuang Yu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Junjiang Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Tao Hu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jingjing Luo
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Hongmei Zhou
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
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Errbii M, Ernst UR, Lajmi A, Privman E, Gadau J, Schrader L. Evolutionary genomics of socially polymorphic populations of Pogonomyrmex californicus. BMC Biol 2024; 22:109. [PMID: 38735942 PMCID: PMC11089791 DOI: 10.1186/s12915-024-01907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/30/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Social insects vary considerably in their social organization both between and within species. In the California harvester ant, Pogonomyrmex californicus (Buckley 1867), colonies are commonly founded and headed by a single queen (haplometrosis, primary monogyny). However, in some populations in California (USA), unrelated queens cooperate not only during founding (pleometrosis) but also throughout the life of the colony (primary polygyny). The genetic architecture and evolutionary dynamics of this complex social niche polymorphism (haplometrosis vs pleometrosis) have remained unknown. RESULTS We provide a first analysis of its genomic basis and evolutionary history using population genomics comparing individuals from a haplometrotic population to those from a pleometrotic population. We discovered a recently evolved (< 200 k years), 8-Mb non-recombining region segregating with the observed social niche polymorphism. This region shares several characteristics with supergenes underlying social polymorphisms in other socially polymorphic ant species. However, we also find remarkable differences from previously described social supergenes. Particularly, four additional genomic regions not in linkage with the supergene show signatures of a selective sweep in the pleometrotic population. Within these regions, we find for example genes crucial for epigenetic regulation via histone modification (chameau) and DNA methylation (Dnmt1). CONCLUSIONS Altogether, our results suggest that social morph in this species is a polygenic trait involving a potential young supergene. Further studies targeting haplo- and pleometrotic individuals from a single population are however required to conclusively resolve whether these genetic differences underlie the alternative social phenotypes or have emerged through genetic drift.
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Affiliation(s)
- Mohammed Errbii
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany
| | - Ulrich R Ernst
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany
- Present Address: Apicultural State Institute, University of Hohenheim, Erna-Hruschka-Weg 6, Stuttgart, DE-70599, Germany
- Center for Biodiversity and Integrative Taxonomy (KomBioTa), University of Hohenheim, Stuttgart, DE-70599, Germany
| | - Aparna Lajmi
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jürgen Gadau
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany.
| | - Lukas Schrader
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany.
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Weng YY, Huang MY. The CpG Island Methylator Phenotype Status in Synchronous and Solitary Primary Colorectal Cancers: Prognosis and Effective Therapeutic Drug Prediction. Int J Mol Sci 2024; 25:5243. [PMID: 38791280 PMCID: PMC11121449 DOI: 10.3390/ijms25105243] [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: 04/04/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Synchronous colorectal cancer (sCRC) is characterized by the occurrence of more than one tumor within six months of detecting the first tumor. Evidence suggests that sCRC might be more common in the serrated neoplasia pathway, marked by the CpG island methylator phenotype (CIMP), than in the chromosomal instability pathway (CIN). An increasing number of studies propose that CIMP could serve as a potential epigenetic predictor or prognostic biomarker of sCRC. Therapeutic drugs already used for treating CIMP-positive colorectal cancers (CRCs) are reviewed and drug selections for sCRC patients are discussed.
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Affiliation(s)
- Yun-Yun Weng
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Ming-Yii Huang
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Radiation Oncology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Oshiro RT, Dunham DT, Seed KD. The vibriophage-encoded inhibitor OrbA abrogates BREX-mediated defense through the ATPase BrxC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593382. [PMID: 38766029 PMCID: PMC11100822 DOI: 10.1101/2024.05.09.593382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Bacteria and phages are locked in a co-evolutionary arms race where each entity evolves mechanisms to restrict the proliferation of the other. Phage-encoded defense inhibitors have proven powerful tools to interrogate how defense systems function. A relatively common defense system is BREX (Bacteriophage exclusion); however, how BREX functions to restrict phage infection remains poorly understood. A BREX system encoded by the SXT integrative and conjugative element, Vch Ind5, was recently identified in Vibrio cholerae , the causative agent of the diarrheal disease cholera. The lytic phage ICP1 that co-circulates with V. cholerae encodes the BREX inhibitor OrbA, but how OrbA inhibits BREX is unclear. Here, we determine that OrbA inhibits BREX using a unique mechanism from known BREX inhibitors by directly binding to the BREX component BrxC. BrxC has a functional ATPase domain that, when mutated, not only disrupts BrxC function but also alters how BrxC multimerizes. Furthermore, we find that OrbA binding disrupts BrxC-BrxC interactions. We determine that OrbA cannot bind BrxC encoded by the distantly related BREX system encoded by the SXT Vch Ban9, and thus fails to inhibit this BREX system that also circulates in epidemic V. cholerae . Lastly, we find that homologs of the Vch Ind5 BrxC are more diverse than the homologs of the Vch Ban9 BrxC. These data provide new insight into the function of the BrxC ATPase and highlight how phage-encoded inhibitors can disrupt phage defense systems using different mechanisms. Importance With renewed interest in phage therapy to combat antibiotic-resistant pathogens, understanding the mechanisms bacteria use to defend themselves against phages and the counter-strategies phages evolve to inhibit defenses is paramount. Bacteriophage exclusion (BREX) is a common defense system with few known inhibitors. Here, we probe how the vibriophage-encoded inhibitor OrbA inhibits the BREX system of Vibrio cholerae , the causative agent of the diarrheal disease cholera. By interrogating OrbA function, we have begun to understand the importance and function of a BREX component. Our results demonstrate the importance of identifying inhibitors against defense systems, as they are powerful tools for dissecting defense activity and can inform strategies to increase the efficacy of some phage therapies.
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Geens B, Goossens S, Li J, Van de Peer Y, Vanden Broeck J. Untangling the gordian knot: The intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects. Mol Cell Endocrinol 2024; 585:112178. [PMID: 38342134 DOI: 10.1016/j.mce.2024.112178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Hormones control developmental and physiological processes, often by regulating the expression of multiple genes simultaneously or sequentially. Crosstalk between hormones and epigenetics is pivotal to dynamically coordinate this process. Hormonal signals can guide the addition and removal of epigenetic marks, steering gene expression. Conversely, DNA methylation, histone modifications and non-coding RNAs can modulate regional chromatin structure and accessibility and regulate the expression of numerous (hormone-related) genes. Here, we provide a review of the interplay between the classical insect hormones, ecdysteroids and juvenile hormones, and epigenetics. We summarize the mode-of-action and roles of these hormones in post-embryonic development, and provide a general overview of epigenetic mechanisms. We then highlight recent advances on the interactions between these hormonal pathways and epigenetics, and their involvement in development. Furthermore, we give an overview of several 'omics techniques employed in the field. Finally, we discuss which questions remain unanswered and possible avenues for future research.
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Affiliation(s)
- Bart Geens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Stijn Goossens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
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Wang Y, Ren J, Ren S. Larsucosterol: endogenous epigenetic regulator for treating chronic and acute liver diseases. Am J Physiol Endocrinol Metab 2024; 326:E577-E587. [PMID: 38381400 DOI: 10.1152/ajpendo.00406.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 02/22/2024]
Abstract
Larsucosterol, a potent endogenous epigenetic regulator, has been reported to play a significant role in lipid metabolism, inflammatory responses, and cell survival. The administration of larsucosterol has demonstrated a reduction in lipid accumulation within hepatocytes and the attenuation of inflammatory responses induced by lipopolysaccharide (LPS) and TNFα in macrophages, alleviating LPS- and acetaminophen (ATMP)-induced multiple organ injury, and decreasing mortalities in animal models. Results from phase 1 and 2 clinical trials have shown that larsucosterol has potential as a biomedicine for the treatment of acute and chronic liver diseases. Recent evidence suggests that larsucosterol is a promising candidate for treating alcohol-associated hepatitis with positive results from a phase 2a clinical trial, and for metabolic dysfunction-associated steatohepatitis (MASH) from a phase 1b clinical trial. In this review, we present a culmination of our recent research efforts spanning two decades. We summarize the discovery, physiological and pharmacological mechanisms, and clinical applications of larsucosterol. Furthermore, we elucidate the pathophysiological pathways of metabolic dysfunction-associated steatotic liver diseases (MASLD), metabolic dysfunction-associated steatohepatitis (MASH), and acute liver injuries. A central focus of the review is the exploration of the therapeutic potential of larsucosterol in treating life-threatening conditions, including acetaminophen overdose, endotoxin shock, MASLD, MASH, hepatectomy, and alcoholic hepatitis.
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Affiliation(s)
- Yaping Wang
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia, United States
- McGuire Veterans Affairs Medical Center, Richmond, Virginia, United States
| | - Jenna Ren
- Department of Pharmacology, Virginia Commonwealth University, Richmond, Virginia, United States
| | - Shunlin Ren
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia, United States
- McGuire Veterans Affairs Medical Center, Richmond, Virginia, United States
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Santamarina AB, Sertorio MN, Mennitti LV, Souza EAD, Souza DVD, Ribeiro DA, Pisani LP. Hepatic Effects of Low-Carbohydrate Diet Associated with Different Lipid Sources: Insights into Oxidative Stress, Cytotoxicity, and Epigenetic Markers in a mouse Model of Obesity. J Nutr 2024; 154:1517-1531. [PMID: 38484979 DOI: 10.1016/j.tjnut.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/02/2024] [Accepted: 03/08/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND Low-carbohydrate and high-fat diet (LCHF) models have been widely explored as alternatives for treating obesity and promoting weight loss. Their effect is attributed to the change in energy substrate that stimulates ketogenic pathways that can metabolically overload the liver. However, little has been studied about the impact of lipid sources prioritized in the LCHF diet. OBJECTIVES This study aims to evaluate the impact of different fat sources in the LCHF diet on markers of liver injury, oxidative stress, and epigenetics in obesity. METHODS Adult male mice were initially induced to obesity by a high-fat and high-sugar diet for 10 wk. Subsequently, they underwent a weight-loss treatment intervention involving an LCHF diet with various sources of fats, including saturated, omega-3 (ω-3) (n-3), omega-6 (ω-6) (n-6), and omega-9 (ω-9) (n-9). At the end of the treatment, markers of liver injury, oxidative stress, and epigenetics were evaluated. RESULTS The LCHF diet was effective in inducing weight loss. However, unsaturated lipid sources (omegas) exhibited superior outcomes. Specifically, the ω-9 group displayed diminished oxidative stress concentrations and decreased markers of liver injury. The ω-3 group demonstrated efficacy in modulating epigenetic markers, thereby reducing oxidative stress, mutagenicity, and markers of liver injury. Correlation tests demonstrated that there was an interaction between the activity of antioxidants and epigenetic enzymes. CONCLUSIONS Our results suggest that LCHF diets associated with ω-3 and ω-9 have the potential for weight loss and liver health recovery in obesity through antioxidant and epigenetic mechanisms.
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Affiliation(s)
- Aline Boveto Santamarina
- Department of Biosciences, Institute of Health and Society, Federal University of São Paulo (UNIFESP), Santos, São Paulo, Brazil
| | - Marcela Nascimento Sertorio
- Department of Biosciences, Institute of Health and Society, Federal University of São Paulo (UNIFESP), Santos, São Paulo, Brazil
| | - Laís Vales Mennitti
- Department of Biosciences, Institute of Health and Society, Federal University of São Paulo (UNIFESP), Santos, São Paulo, Brazil
| | - Esther Alves de Souza
- Department of Biosciences, Institute of Health and Society, Federal University of São Paulo (UNIFESP), Santos, São Paulo, Brazil
| | - Daniel Vitor de Souza
- Department of Biosciences, Institute of Health and Society, Federal University of São Paulo (UNIFESP), Santos, São Paulo, Brazil
| | - Daniel Araki Ribeiro
- Department of Biosciences, Institute of Health and Society, Federal University of São Paulo (UNIFESP), Santos, São Paulo, Brazil
| | - Luciana Pellegrini Pisani
- Department of Biosciences, Institute of Health and Society, Federal University of São Paulo (UNIFESP), Santos, São Paulo, Brazil.
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Zhao N, Lai C, Wang Y, Dai S, Gu H. Understanding the role of DNA methylation in colorectal cancer: Mechanisms, detection, and clinical significance. Biochim Biophys Acta Rev Cancer 2024; 1879:189096. [PMID: 38499079 DOI: 10.1016/j.bbcan.2024.189096] [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: 10/05/2023] [Revised: 02/18/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
Colorectal cancer (CRC) is one of the deadliest malignancies worldwide, ranking third in incidence and second in mortality. Remarkably, early stage localized CRC has a 5-year survival rate of over 90%; in stark contrast, the corresponding 5-year survival rate for metastatic CRC (mCRC) is only 14%. Compounding this problem is the staggering lack of effective therapeutic strategies. Beyond genetic mutations, which have been identified as critical instigators of CRC initiation and progression, the importance of epigenetic modifications, particularly DNA methylation (DNAm), cannot be underestimated, given that DNAm can be used for diagnosis, treatment monitoring and prognostic evaluation. This review addresses the intricate mechanisms governing aberrant DNAm in CRC and its profound impact on critical oncogenic pathways. In addition, a comprehensive review of the various techniques used to detect DNAm alterations in CRC is provided, along with an exploration of the clinical utility of cancer-specific DNAm alterations.
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Affiliation(s)
- Ningning Zhao
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China
| | - Chuanxi Lai
- Division of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotech. Ltd, Hangzhou 310000, China
| | - Sheng Dai
- Division of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China.
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Cerneckis J, Cai H, Shi Y. Induced pluripotent stem cells (iPSCs): molecular mechanisms of induction and applications. Signal Transduct Target Ther 2024; 9:112. [PMID: 38670977 PMCID: PMC11053163 DOI: 10.1038/s41392-024-01809-0] [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: 07/28/2023] [Revised: 03/09/2024] [Accepted: 03/17/2024] [Indexed: 04/28/2024] Open
Abstract
The induced pluripotent stem cell (iPSC) technology has transformed in vitro research and holds great promise to advance regenerative medicine. iPSCs have the capacity for an almost unlimited expansion, are amenable to genetic engineering, and can be differentiated into most somatic cell types. iPSCs have been widely applied to model human development and diseases, perform drug screening, and develop cell therapies. In this review, we outline key developments in the iPSC field and highlight the immense versatility of the iPSC technology for in vitro modeling and therapeutic applications. We begin by discussing the pivotal discoveries that revealed the potential of a somatic cell nucleus for reprogramming and led to successful generation of iPSCs. We consider the molecular mechanisms and dynamics of somatic cell reprogramming as well as the numerous methods available to induce pluripotency. Subsequently, we discuss various iPSC-based cellular models, from mono-cultures of a single cell type to complex three-dimensional organoids, and how these models can be applied to elucidate the mechanisms of human development and diseases. We use examples of neurological disorders, coronavirus disease 2019 (COVID-19), and cancer to highlight the diversity of disease-specific phenotypes that can be modeled using iPSC-derived cells. We also consider how iPSC-derived cellular models can be used in high-throughput drug screening and drug toxicity studies. Finally, we discuss the process of developing autologous and allogeneic iPSC-based cell therapies and their potential to alleviate human diseases.
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Affiliation(s)
- Jonas Cerneckis
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Hongxia Cai
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
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Haidar L, Georgescu M, Drăghici GA, Bănățean-Dunea I, Nica DV, Șerb AF. DNA Methylation Machinery in Gastropod Mollusks. Life (Basel) 2024; 14:537. [PMID: 38672807 PMCID: PMC11050768 DOI: 10.3390/life14040537] [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: 03/11/2024] [Revised: 04/17/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024] Open
Abstract
The role of DNA methylation in mollusks is just beginning to be understood. This review synthesizes current knowledge on this potent molecular hallmark of epigenetic control in gastropods-the largest class of mollusks and ubiquitous inhabitants of diverse habitats. Their DNA methylation machinery shows a high degree of conservation in CG maintenance methylation mechanisms, driven mainly by DNMT1 homologues, and the presence of MBD2 and MBD2/3 proteins as DNA methylation readers. The mosaic-like DNA methylation landscape occurs mainly in a CG context and is primarily confined to gene bodies and housekeeping genes. DNA methylation emerges as a critical regulator of reproduction, development, and adaptation, with tissue-specific patterns being observed in gonadal structures. Its dynamics also serve as an important regulatory mechanism underlying learning and memory processes. DNA methylation can be affected by various environmental stimuli, including as pathogens and abiotic stresses, potentially impacting phenotypic variation and population diversity. Overall, the features of DNA methylation in gastropods are complex, being an essential part of their epigenome. However, comprehensive studies integrating developmental stages, tissues, and environmental conditions, functional annotation of methylated regions, and integrated genomic-epigenomic analyses are lacking. Addressing these knowledge gaps will advance our understanding of gastropod biology, ecology, and evolution.
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Affiliation(s)
- Laura Haidar
- Department of Functional Sciences, Physiology Discipline, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania;
- Center of Immuno-Physiology and Biotechnologies (CIFBIOTEH), “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
| | - Marius Georgescu
- Department of Functional Sciences, Physiology Discipline, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania;
- Center of Immuno-Physiology and Biotechnologies (CIFBIOTEH), “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
| | - George Andrei Drăghici
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania;
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania
| | - Ioan Bănățean-Dunea
- Biology and Plant Protection Department, Faculty of Agriculture, University of Life Sciences “King Mihai I” from Timișoara, Calea Aradului 119, 300645 Timișoara, Romania;
| | - Dragoș Vasile Nica
- The National Institute of Research—Development for Machines and Installations Designed for Agriculture and Food Industry (INMA), Bulevardul Ion Ionescu de la Brad 6, 077190 București, Romania
| | - Alina-Florina Șerb
- Department of Biochemistry and Pharmacology, Biochemistry Discipline, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania;
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