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Jueraitetibaike K, Tang T, Ma R, Zhao S, Wu R, Yang Y, Huang X, Cheng X, Zhou C, Zhang H, Zheng L, Ge X, Chen L, Yao B. MiR-425-5p suppression of Crebzf regulates oocyte aging via chromatin modification. GeroScience 2024; 46:3723-3742. [PMID: 37532927 DOI: 10.1007/s11357-023-00875-6] [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: 03/20/2023] [Accepted: 07/12/2023] [Indexed: 08/04/2023] Open
Abstract
Female infertility due to declining oocyte quality with age remains a significant challenge for patients and physicians, despite extensive research efforts. Recent studies suggest that microRNAs (miRNAs), which respond to various stressors in the aging process, may provide a promising solution. With the approval of small RNA drugs for clinical use, miRNA-based treatment of oocyte aging appears to be a viable option. Through high-throughput sequencing, miR-425-5p was identified as the only miRNA elevated under natural aging and oxidative stress. Microinjection of inhibitors to inhibit miR-425-5p effectively improved compromised phenotypes of old oocytes in vitro. Further investigation revealed that Crebzf acts as a mediator of miR-425-5p's age-related functions in old oocytes. In vivo treatment with miR-425-5p antagomirs significantly improved impaired oocyte development in reproductively old females by targeting Crebzf. Single-cell RNA sequencing revealed that Crebzf plays a vital role in regulating mRNAs targeting histone H3, trimethylated lysine 4 (H3K4me3), a crucial marker for transcriptional silencing. Overexpression of miR-425-5p could hinder oocyte maturation by downregulating Crebzf expression and disrupting transcriptional regulation. Our findings provide new insights into the potential of miR-425-5p antagomirs as a treatment for female infertility and highlight an elegant mechanism by which miR-425-5p inhibition of Crebzf inhibits a developmental switch in GV oocytes by regulating a group of histone methyltransferase mRNAs.
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Affiliation(s)
- Kadiliya Jueraitetibaike
- Department of Reproductive Medicine, Nanjing Jinling Hospital: East Region Military Command General Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China
| | - Ting Tang
- Department of Reproductive Medicine, Nanjing Jinling Hospital: East Region Military Command General Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, People's Republic of China
| | - Rujun Ma
- Department of Reproductive Medicine, Nanjing Jinling Hospital: East Region Military Command General Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China
| | - Shanmeizi Zhao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210002, People's Republic of China
| | - Ronghua Wu
- Department of Reproductive Medicine, Nanjing Jinling Hospital: East Region Military Command General Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China
| | - Yang Yang
- Basic Medical Laboratory, Institute of Clinical Laboratory Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China
| | - Xuan Huang
- Department of Reproductive Medicine, Nanjing Jinling Hospital: East Region Military Command General Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China
| | - Xi Cheng
- Department of Reproductive Medicine, Nanjing Jinling Hospital: East Region Military Command General Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China
| | - Cheng Zhou
- Department of Reproductive Medicine, Nanjing Jinling Hospital: East Region Military Command General Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China
| | - Hong Zhang
- Department of Reproductive Medicine, Nanjing Jinling Hospital: East Region Military Command General Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China
| | - Lu Zheng
- Department of Reproductive Medicine, Nanjing Jinling Hospital: East Region Military Command General Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China
| | - Xie Ge
- Department of Reproductive Medicine, Nanjing Jinling Hospital: East Region Military Command General Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China
| | - Li Chen
- Department of Reproductive Medicine, Nanjing Jinling Hospital: East Region Military Command General Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China.
| | - Bing Yao
- Department of Reproductive Medicine, Nanjing Jinling Hospital: East Region Military Command General Hospital, Medical School of Nanjing University, Nanjing, 210002, People's Republic of China.
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, People's Republic of China.
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2
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Zhou H, Gui J, Zhu L, Mi Y. The Role and Mechanism of the Histone Methyltransferase G9a in Tumors: Update. Onco Targets Ther 2024; 17:449-462. [PMID: 38832355 PMCID: PMC11146345 DOI: 10.2147/ott.s451108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 04/30/2024] [Indexed: 06/05/2024] Open
Abstract
Methylation-mediated gene silencing is closely related to the occurrence and development of human tumors. The euchromatic histone lysine methyltransferase 2 (EHMT2, also known as G9a) is highly expressed in many tumors and is generally considered to be an oncogene, which is associated with the poor outcome of many tumors. Combined immunotherapy and immune checkpoint blockade therapy also have good efficacy and certain safety. However, there are still many difficulties in the drugs targeting G9a, and the combined effect and safety of G9a with many drugs is still under study. This article aims to summarize the role and mechanism of G9a and its inhibitors in tumors in the past two years, and to understand the application prospect of G9a from the perspective of diagnosis and treatment.
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Affiliation(s)
- Hangsheng Zhou
- Wuxi Medical College, Jiangnan University, Wuxi, Jiangsu Province, 214122, People’s Republic of China
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu Province, 214122, People’s Republic of China
| | - Jiandong Gui
- Wuxi Medical College, Jiangnan University, Wuxi, Jiangsu Province, 214122, People’s Republic of China
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu Province, 214122, People’s Republic of China
| | - Lijie Zhu
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu Province, 214122, People’s Republic of China
| | - Yuanyuan Mi
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu Province, 214122, People’s Republic of China
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3
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Abolghasemi Fard A, Mahmoodzadeh A. Unraveling the Progression of Colon Cancer Pathogenesis Through Epigenetic Alterations and Genetic Pathways. Cureus 2024; 16:e59503. [PMID: 38826873 PMCID: PMC11143495 DOI: 10.7759/cureus.59503] [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] [Accepted: 05/02/2024] [Indexed: 06/04/2024] Open
Abstract
In the modern age, colon cancer has attained a widespread status, affecting a considerable number of people. It develops due to the progressive accumulation of genetic and epigenetic alterations. While genetic mutations have been extensively studied in the context of colon cancer, emerging evidence highlights the pivotal role of epigenetic alterations in its pathogenesis. These alterations ultimately result in the transformation of normal colonic epithelium into colon adenocarcinoma. Key mechanisms of epigenetic modifications include DNA methylation, histone modification, and nucleosome positioning. Research findings have linked these modifications to the development, progression, or metastasis of tumors. Through the assessment of the colon cancer epigenome, it has been discovered that practically all colorectal cancers (CRCs) display gene methylation abnormalities and changes in miRNA expression. Advancements in this area indicate that epigenetic modifications will likely be commonly used in the near future to direct the prevention and treatment of CRC. The maintenance of genome stability is essential for preserving cellular integrity. The development of CRC is primarily influenced by the loss of genomic stability, which allows for the emergence of new mutations contributing to tumor characteristics. Although genetic mutations have been extensively researched in the realm of colon cancer, recent evidence underscores the pivotal role of epigenetic changes in its pathogenesis. The following types of genomic instability will be discussed: chromosomal instability, microsatellite instability, CpG island methylation phenotype, and aberrant DNA methylation.
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Affiliation(s)
- Asal Abolghasemi Fard
- Department of Cellular and Molecular Biology, Faculty of Modern Science and Technologies, Tehran Medical Sciences, Islamic Azad University, Tehran, IRN
| | - Afshin Mahmoodzadeh
- Department of Biology, Roudehen Branch, Islamic Azad University, Tehran, IRN
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4
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Saraswat SK, Mahmood BS, Ajila F, Kareem DS, Alwan M, Athab ZH, Shaier JB, Hosseinifard SR. Deciphering the oncogenic landscape: Unveiling the molecular machinery and clinical significance of LncRNA TMPO-AS1 in human cancers. Pathol Res Pract 2024; 255:155190. [PMID: 38330619 DOI: 10.1016/j.prp.2024.155190] [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: 01/14/2024] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
The in-depth exploration of long non-coding RNAs (lncRNAs) reveals their pivotal and diverse roles in various disorders, particularly cancer. Within this intricate landscape, thymopoietin-antisense RNA-1 (TMPO-AS1) emerges as a noteworthy instigator of oncogenesis in humans. This exhaustive review seeks to intricately unravel the present understanding of TMPO-AS1, emphasizing its molecular foundations and highlighting its clinical applications in the realm of cancer research. TMPO-AS1 consistently exhibits heightened expression across a spectrum of cancer types, encompassing lung, colorectal, breast, cervical, bladder, pancreatic, hepatocellular, gastric, ovarian, and osteosarcoma. Elevated levels of TMPO-AS1 are intricately linked to unfavorable prognoses, accompanied by distinctive clinical and pathological characteristics. Functionally, TMPO-AS1 showcases its prowess in enhancing cancer cell migration, invasion, proliferation, and orchestrating epithelial-mesenchymal transition (EMT) through a myriad of molecular mechanisms. These mechanisms entail intricate interactions with proteins, microRNAs, and intricate signaling pathways. Furthermore, TMPO-AS1 is intricately involved in regulating critical cellular processes, including apoptosis and the cell cycle. The mounting evidence converges towards the potential of TMPO-AS1 serving as a diagnostic and prognostic biomarker, further entwined with its potential role in influencing chemoresistance in cancer. This potential is underscored by its consistent associations with clinical outcomes and treatment responses. This comprehensive investigation not only consolidates our existing knowledge of TMPO-AS1's multifaceted roles but also sheds illuminating insights on its profound significance in the intricate landscape of cancer biology, paving the way for potential applications in clinical practice.
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Affiliation(s)
| | | | - Freddy Ajila
- Facultad de Informática y Electrónica, Escuela Superior Politécnica de Chimborazo (ESPOCH), Sede Orellana, El Coca 220001, Ecuador.
| | | | - Mariem Alwan
- Medical Technical College, Al-Farahidi University, Iraq
| | - Zainab H Athab
- Department of Pharmacy, Al-Zahrawi University College, Karbala, Iraq
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5
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Housini M, Dariya B, Ahmed N, Stevens A, Fiadjoe H, Nagaraju GP, Basha R. Colorectal cancer: Genetic alterations, novel biomarkers, current therapeutic strategies and clinical trials. Gene 2024; 892:147857. [PMID: 37783294 DOI: 10.1016/j.gene.2023.147857] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/04/2023]
Abstract
Colorectal cancer (CRC) is the third most commonly detected cancer with a serious global health issue. The rates for incidence and mortality for CRC are alarming, especially since the prognosis is abysmal when the CRC is diagnosed at an advanced or metastatic stage. Both type of (modifiable/ non-modifiable) types of risk factors are established for CRC. Despite the advances in recent technology and sophisticated research, the survival rate is still meager due to delays in diagnosis. Therefore, there is urgently required to identify critical biomarkers aiming at early diagnosis and improving effective therapeutic strategies. Additionally, a complete understanding of the dysregulated pathways like PI3K/Akt, Notch, and Wnt associated with CRC progression and metastasis is very beneficial in designing a therapeutic regimen. This review article focused on the dysregulated signaling pathways, genetics and epigenetics alterations, and crucial biomarkers of CRC. This review also provided the list of clinical trials targeting signaling cascades and therapies involving small molecules. This review discusses up-to-date information on novel diagnostic and therapeutic strategies alongside specific clinical trials.
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Affiliation(s)
- Mohammad Housini
- Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX 76107, United States
| | - Begum Dariya
- Center for Drug Design, University of Minnesota, Minneapolis, MN 5545, United States
| | - Nadia Ahmed
- Department of Diagnostic Radiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Alyssa Stevens
- Missouri Southern State University, Joplin, MO 64801, United States
| | - Hope Fiadjoe
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, United States
| | - Ganji Purnachandra Nagaraju
- Division of Hematology & Oncology, The University of Alabama at Birmingham, Birmingham, AL 35233, United States.
| | - Riyaz Basha
- Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX 76107, United States; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, United States.
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6
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Bure IV, Nemtsova MV. Mutual Regulation of ncRNAs and Chromatin Remodeling Complexes in Normal and Pathological Conditions. Int J Mol Sci 2023; 24:ijms24097848. [PMID: 37175555 PMCID: PMC10178202 DOI: 10.3390/ijms24097848] [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: 03/23/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Chromatin remodeling is the one of the main epigenetic mechanisms of gene expression regulation both in normal cells and in pathological conditions. In recent years, a growing number of investigations have confirmed that epigenetic regulators are tightly connected and form a comprehensive network of regulatory pathways and feedback loops. Genes encoding protein subunits of chromatin remodeling complexes are often mutated and change their expression in diseases, as well as non-coding RNAs (ncRNAs). Moreover, different mechanisms of their mutual regulation have already been described. Further understanding of these processes may help apply their clinical potential for establishment of the diagnosis, prognosis, and treatment of the diseases. The therapeutic targeting of the chromatin structure has many limitations because of the complexity of its regulation, with the involvement of a large number of genes, proteins, non-coding transcripts, and other intermediary molecules. However, several successful strategies have been proposed to target subunits of chromatin remodeling complexes and genes encoding them, as well as the ncRNAs that regulate the operation of these complexes and direct them to the target gene regions. In our review, we focus on chromatin remodeling complexes and ncRNAs, their mutual regulation, role in cellular processes and potential clinical application.
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Affiliation(s)
- Irina V Bure
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Marina V Nemtsova
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
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7
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Molderings GJ. Systemic mast cell activation disease variants and certain genetically determined comorbidities may be consequences of a common underlying epigenetic disease. Med Hypotheses 2022. [DOI: 10.1016/j.mehy.2022.110862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Ghai M, Kader F. A Review on Epigenetic Inheritance of Experiences in Humans. Biochem Genet 2021; 60:1107-1140. [PMID: 34792705 DOI: 10.1007/s10528-021-10155-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022]
Abstract
If genetics defines the inheritance of DNA, epigenetics aims to regulate and make it adaptable. Epigenetic alterations include DNA methylation, chromatin remodelling, post-translational modifications of histone proteins and activity of non-coding RNAs. Several studies, especially in animal models, have reported transgenerational inheritance of epigenetic marks. However, evidence of transgenerational inheritance in humans via germline in the absence of any direct exposure to the driving external stimulus remains controversial. Most of the epimutations exist in relation with genetic variants. The present review looks at intergenerational and transgenerational inheritance in humans, (both father and mother) in response to diet, exposure to chemicals, stress, exercise, and disease status. If not transgenerational, at least intergenerational human studies could help to understand early processes of inheritance. In humans, female and male germline development follow separate paths of epigenetic events and both oocyte and sperm possess their own unique epigenomes. While DNA methylation alterations are reset during epigenetic reprogramming, non-coding RNAs via human sperm provide evidence of being reliable carriers for transgenerational inheritance. Human studies reveal that one mechanism of epigenetic inheritance cannot be applied to the complete human genome. Multiple factors including time, type, and tissue of exposure determine if the modified epigenetic mark could be transmissible and till which generation. Population-specific differences should also be taken into consideration while associating inheritance to an environmental exposure. A longitudinal study targeting one environmental factor, but different population groups should be conducted at a specific geographical location to pinpoint heritable epigenetic changes.
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Affiliation(s)
- Meenu Ghai
- Discipline of Genetics, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, KwaZulu Natal, South Africa.
| | - Farzeen Kader
- Discipline of Genetics, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, KwaZulu Natal, South Africa
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9
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Dzobo K. Coronavirus Disease 19 and Future Ecological Crises: Hopes from Epigenomics and Unraveling Genome Regulation in Humans and Infectious Agents. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:269-278. [PMID: 33904782 DOI: 10.1089/omi.2021.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
With coronavirus disease 19 (COVID-19), we have witnessed a shift from public health to planetary health and a growing recognition of the importance of systems science in developing effective solutions against pandemics in the 21st century. COVID-19 and the history of frequent infectious outbreaks in the last two decades suggest that COVID-19 is likely a dry run for future ecological crises. Now is the right time to plan ahead and deploy the armamentarium of systems science scholarship for planetary health. The science of epigenomics, which investigates both genetic and nongenetic traits regarding heritable phenotypic alterations, and new approaches to understanding genome regulation in humans and pathogens offer veritable prospects to boost the global scientific capacities to innovate therapeutics and diagnostics against novel and existing infectious agents. Several reversible epigenetic alterations, such as chromatin remodeling and histone methylation, control and influence gene expression. COVID-19 lethality is linked, in part, to the cytokine storm, age, and status of the immune system in a given person. Additionally, due to reduced human mobility and daily activities, effects of the pandemic on the environment have been both positive and negative. For example, reduction in environmental pollution and lesser extraction from nature have potential positive corollaries on water and air quality. Negative effects include pollution as plastics and other materials were disposed in unconventional places and spaces in the course of the pandemic. I discuss the opportunities and challenges associated with the science of epigenomics, specifically with an eye to inform and prevent future ecological crises and pandemics that are looming on the horizon in the 21st century. In particular, this article underscores that epigenetics of both viruses and the host may influence virus infectivity and severity of attendant disease.
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Affiliation(s)
- Kevin Dzobo
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, South Africa.,Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Mossink B, Negwer M, Schubert D, Nadif Kasri N. The emerging role of chromatin remodelers in neurodevelopmental disorders: a developmental perspective. Cell Mol Life Sci 2021; 78:2517-2563. [PMID: 33263776 PMCID: PMC8004494 DOI: 10.1007/s00018-020-03714-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022]
Abstract
Neurodevelopmental disorders (NDDs), including intellectual disability (ID) and autism spectrum disorders (ASD), are a large group of disorders in which early insults during brain development result in a wide and heterogeneous spectrum of clinical diagnoses. Mutations in genes coding for chromatin remodelers are overrepresented in NDD cohorts, pointing towards epigenetics as a convergent pathogenic pathway between these disorders. In this review we detail the role of NDD-associated chromatin remodelers during the developmental continuum of progenitor expansion, differentiation, cell-type specification, migration and maturation. We discuss how defects in chromatin remodelling during these early developmental time points compound over time and result in impaired brain circuit establishment. In particular, we focus on their role in the three largest cell populations: glutamatergic neurons, GABAergic neurons, and glia cells. An in-depth understanding of the spatiotemporal role of chromatin remodelers during neurodevelopment can contribute to the identification of molecular targets for treatment strategies.
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Affiliation(s)
- Britt Mossink
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Moritz Negwer
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands.
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11
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Khan MI, Nur SM, Adhami V, Mukhtar H. Epigenetic regulation of RNA sensors: Sentinels of immune response. Semin Cancer Biol 2021; 83:413-421. [PMID: 33484869 DOI: 10.1016/j.semcancer.2020.12.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022]
Abstract
Living host system possess mechanisms like innate immune system to combat against inflammation, stress singling, and cancer. These mechanisms are initiated by PAMP and DAMP mediated recognition by PRR. PRR is consist of variety of nucleic acid sensors like-RNA sensors. They play crucial role in identifying exogenous and endogenous RNA molecules, which subsequently mediate pro/inflammatory cytokine, IFN and ISGs response in traumatized or tumorigenic conditions. The sensors can sensitize wide range of nucleic acid particle in term of size and structure, while each category sensors belongs subclasses with differentially expressed in cell and distinguished functioning mechanisms. They are also able to make comparison between self and non-self-nucleic acid molecules through specific mechanisms. Besides exhibiting anti-inflammatory and anti-tumorigenic responses, RNA sensors cover the broad spectrum of response mechanisms. Transcriptionally RNA sensors undergo with tight epigenetic regulations. In this review study, we will be going to discuss about the details of RNA sensors, their functional mechanisms and epi-transactional regulations.
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Affiliation(s)
- Mohammad Imran Khan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Suza Mohammad Nur
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vaqar Adhami
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Hasan Mukhtar
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, USA.
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12
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Joshi RO, Chellappan S, Kukshal P. Exploring the Role of Maternal Nutritional Epigenetics in Congenital Heart Disease. Curr Dev Nutr 2020; 4:nzaa166. [PMID: 33294766 PMCID: PMC7703391 DOI: 10.1093/cdn/nzaa166] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/17/2022] Open
Abstract
Congenital heart disease (CHD) is one of the major debilitating birth defects resulting in significant impact on neonatal and child mortality globally. The etiology of CHD is complex and multifactorial. Many causative genes responsible for CHDs have been identified from the familial forms previously. Still, the non-Mendelian inheritance and predominant sporadic cases have stimulated research to understand the epigenetic basis and environmental impact on the incidence of CHD. The fetal epigenetic programming affecting cardiac development is susceptible to the availability of key dietary factors during the crucial periconceptional period. This article highlights the need and importance of in-depth research in the new emerging area of maternal nutritional epigenetics and CHD. It summarizes the current research and underlines the limitations in these types of studies. This review will benefit the future research on nutrition as a modifiable environmental factor to decrease the incidence of CHD.
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Affiliation(s)
- Radha O Joshi
- Department of Genomics Research, Sri Sathya Sai Sanjeevani Research Foundation, Palwal, Haryana, India
| | - Subramanian Chellappan
- Department of Anesthesia, Sri Sathya Sai Sanjeevani International Centre for Child Heart Care and Research, Palwal, Haryana, India
| | - Prachi Kukshal
- Department of Genomics Research, Sri Sathya Sai Sanjeevani Research Foundation, Palwal, Haryana, India
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13
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Atlante S, Mongelli A, Barbi V, Martelli F, Farsetti A, Gaetano C. The epigenetic implication in coronavirus infection and therapy. Clin Epigenetics 2020; 12:156. [PMID: 33087172 PMCID: PMC7576975 DOI: 10.1186/s13148-020-00946-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023] Open
Abstract
Epigenetics is a relatively new field of science that studies the genetic and non-genetic aspects related to heritable phenotypic changes, frequently caused by environmental and metabolic factors. In the host, the epigenetic machinery can regulate gene expression through a series of reversible epigenetic modifications, such as histone methylation and acetylation, DNA/RNA methylation, chromatin remodeling, and non-coding RNAs. The coronavirus disease 19 (COVID-19) is a highly transmittable and pathogenic viral infection. The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which emerged in Wuhan, China, and spread worldwide, causes it. COVID-19 severity and consequences largely depend on patient age and health status. In this review, we will summarize and comparatively analyze how viruses regulate the host epigenome. Mainly, we will be focusing on highly pathogenic respiratory RNA virus infections such as coronaviruses. In this context, epigenetic alterations might play an essential role in the onset of coronavirus disease complications. Although many therapeutic approaches are under study, more research is urgently needed to identify effective vaccine or safer chemotherapeutic drugs, including epigenetic drugs, to cope with this viral outbreak and to develop pre- and post-exposure prophylaxis against COVID-19.
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Affiliation(s)
- Sandra Atlante
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
| | - Alessia Mongelli
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
| | - Veronica Barbi
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
| | - Fabio Martelli
- Laboratorio di Cardiologia Molecolare, Policlinico San Donato IRCCS, Milan, Italy
| | - Antonella Farsetti
- Institute for Systems Analysis and Computer Science “A. Ruberti” (IASI), National Research Council (CNR), Rome, Italy
| | - Carlo Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
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14
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Cao J, Zhang M, Zhang L, Lou J, Zhou F, Fang M. Non-coding RNA in thyroid cancer - Functions and mechanisms. Cancer Lett 2020; 496:117-126. [PMID: 32949678 DOI: 10.1016/j.canlet.2020.08.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/26/2020] [Accepted: 08/19/2020] [Indexed: 12/29/2022]
Abstract
Thyroid cancer is the most common endocrine malignant tumor, and its incidence has increased significantly in the past few years. A growing number of noncoding RNAs (ncRNAs) have shown abnormal expression patterns in human thyroid cancer in recent studies. Depending on size, ncRNAs are usually subdivided into two categories: short ncRNAs and long ncRNAs (longer than 200 nucleotides). Short ncRNAs include microRNAs (miRNAs), PIWI-interacting RNAs, small nucleolar RNAs, and endogenous small interfering RNAs, which have been extensively studied due to their roles in developmental and tumor biology. Compared to that of short ncRNAs, the involvement of lncRNAs in human cancers, especially in thyroid cancer, is not as well studied. Here, we reviewed the roles and clinical significance of miRNAs, lncRNAs, and circular RNA in thyroid development, tumorigenesis, and metastasis to offer a new approach to thyroid cancer treatment.
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Affiliation(s)
- Jun Cao
- Department of Rare and Head and Neck Oncology, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
| | - Mengdi Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Long Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Jianlin Lou
- Department of Head and Neck Surgery, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, China.
| | - Meiyu Fang
- Department of Rare and Head and Neck Oncology, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China.
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15
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Boukelia A, Boucheham A, Belguidoum M, Batouche M, Zehraoui F, Tahi F. A Novel Integrative Approach for Non-coding RNA Classification Based on Deep Learning. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191105160633] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background:
Molecular biomarkers show new ways to understand many disease
processes. Noncoding RNAs as biomarkers play a crucial role in several cellular activities, which
are highly correlated to many human diseases especially cancer. The classification and the
identification of ncRNAs have become a critical issue due to their application, such as biomarkers
in many human diseases.
Objective:
Most existing computational tools for ncRNA classification are mainly used for
classifying only one type of ncRNA. They are based on structural information or specific known
features. Furthermore, these tools suffer from a lack of significant and validated features.
Therefore, the performance of these methods is not always satisfactory.
Methods:
We propose a novel approach named imCnC for ncRNA classification based on
multisource deep learning, which integrates several data sources such as genomic and epigenomic
data to identify several ncRNA types. Also, we propose an optimization technique to visualize the
extracted features pattern from the multisource CNN model to measure the epigenomics features
of each ncRNA type.
Results:
The computational results using a dataset of 16 human ncRNA classes downloaded from
RFAM show that imCnC outperforms the existing tools. Indeed, imCnC achieved an accuracy of
94,18%. In addition, our method enables to discover new ncRNA features using an optimization
technique to measure and visualize the features pattern of the imCnC classifier.
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Affiliation(s)
- Abdelbasset Boukelia
- Computer Science Department, Faculty NTIC, University Abdelhamid Mehri Constantine 2, Constantine 25000, Algeria
| | - Anouar Boucheham
- University Salah Boubnider Constantine 3, Constantine 25000, Algeria
| | - Meriem Belguidoum
- Computer Science Department, Faculty NTIC, University Abdelhamid Mehri Constantine 2, Constantine 25000, Algeria
| | - Mohamed Batouche
- IT Department, CCIS - RC, Princess Nourah University, Riyadh, Saudi Arabia
| | - Farida Zehraoui
- IBISC, University Evry, University Paris-Saclay, Evry, France
| | - Fariza Tahi
- IBISC, University Evry, University Paris-Saclay, Evry, France
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16
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Harati-Sadegh M, Kohan L, Teimoori B, Mehrabani M, Salimi S. The effects of placental long noncoding RNA H19 polymorphisms and promoter methylation on H19 expression in association with preeclampsia susceptibility. IUBMB Life 2019; 72:413-425. [PMID: 31769935 DOI: 10.1002/iub.2199] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/28/2019] [Indexed: 12/19/2022]
Abstract
The effect of DNA methylation on gene expression triggered it as a susceptibility factor in various diseases including preeclampsia (PE). The pathogenesis of PE is closely associated with the methylation status and genetic variants of relevant genes. Therefore, the aim of the study was to investigate the possible impacts of the placental DNA methylation and rs3741219, rs217727, and rs2107425 polymorphisms of the H19 gene on the PE susceptibility as well as the its mRNA expression. Moreover, eight haplotypes of three loci in the H19 gene were analyzed. In this case-control study, the placentas of 107 preeclamptic and 113 non-preeclamptic women were collected after delivery. The methylation status was assessed by methylation-specific polymerase chain reaction (PCR). The H19 polymorphisms were genotyped using polymerase chain reaction-restriction fragment length polymorphism or amplification refractory mutation system-polymerase chain reaction methods. The quantitative real time PCR was used for mRNA expression assay. The placental H19 rs3741219 and rs2107425 polymorphisms were not associated with PE. However, H19 rs217727CT and TT genotypes might be associated with a 9.2- and 17.7-fold increased risk of PE, respectively. The Trs3741219 Crs217727 Crs2107425 and Trs3741219 Crs217727 Trs2107425 haplotypes were significantly lower, whereas the Trs3741219 Trs217727 Crs2107425 and Crs3741219 Trs217727 Crs2107425 haplotypes were significantly higher in PE women. Promoter but not upstream region hypermethylation of H19 gene could be led to decreased risk of PE (MM vs. UM + UU). No significant difference was observed in the placental mRNA expression between two groups. The H19 expression was significantly higher in women with unmethylated (UU), compared to methylated promoter (MM). The H19 expression was 17- and 15-fold higher in H19-rs2107425 CC and CT genotypes in PE women. In conclusion, the H19 rs2107425 polymorphism was associated with a higher risk of PE and increased H19 mRNA expression. The promoter hypermethylation of H19 gene was associated with a lower risk of PE and decreased H19 mRNA expression.
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Affiliation(s)
- Mahdiyeh Harati-Sadegh
- Genetic of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Leila Kohan
- Department of Biology, Arsanjan Branch, Islamic Azad University, Arsanjan, Iran
| | - Batool Teimoori
- Department of Obstetrics and Gynecology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mehrnaz Mehrabani
- Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Saeedeh Salimi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.,Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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17
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Silva LBAR, Pinheiro-Castro N, Novaes GM, Pascoal GDFL, Ong TP. Bioactive food compounds, epigenetics and chronic disease prevention: Focus on early-life interventions with polyphenols. Food Res Int 2019; 125:108646. [DOI: 10.1016/j.foodres.2019.108646] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 08/20/2019] [Accepted: 08/23/2019] [Indexed: 12/14/2022]
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18
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Hanly D, Esteller M, Berdasco M. Altered Long Non-coding RNA Expression in Cancer: Potential Biomarkers and Therapeutic Targets? ACTA ACUST UNITED AC 2019. [DOI: 10.1007/7355_2019_83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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19
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Cuevas-Bermúdez A, Garrido-Godino AI, Navarro F. A novel yeast chromatin-enriched fractions purification approach, yChEFs, for the chromatin-associated protein analysis used for chromatin-associated and RNA-dependent chromatin-associated proteome studies from Saccharomyces cerevisiae. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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20
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Potential of epigenetic events in human thyroid cancer. Cancer Genet 2019; 239:13-21. [PMID: 31472323 DOI: 10.1016/j.cancergen.2019.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/27/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022]
Abstract
Thyroid cancer remains the highest prevailing endocrine malignancy, and its incidence rate has progressively increased in the previous years. Above 95% of thyroid tumor are follicular cells types of carcinoma in which are considered invasive type of tumor. The pathogenesis and molecular mechanism of thyroid tumors are yet remains elucidated, in spite of activating RET, RAS and BRAF carcinogenesis have been well introduced. Nemours molecular alterations have been defined and have revealed promise for their diagnostic, prognostic and therapeutic capacity but still need further confirmation. Among different types of mechanisms, the current article reviews the importance of epigenetic modifications in thyroid cancer. Increasing data from previous reports demonstrate that acquired epigenetic abnormalities together with genetic changes plays an important role in alteration of gene expression patterns. Aberrant DNA methylation has been well known in the CpG regions and profile of microRNAs (mi-RNAs) expression also involved in cancer development. In addition, the gene expression through epigenetic control contribution to thyroid cancer is analyzed and it is semi considered in the clinic. However the epigenetic of the thyroid cancer is yet remains in its early stages, and it carries encouraging potential thyroid cancer detections in its early stages, assessment of prognosis and targeted cancer treatment.
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21
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Cellular Mechanisms and Epigenetic Changes: Role of Nutrition in Livestock. Vet Clin North Am Food Anim Pract 2019; 35:249-263. [PMID: 31103179 DOI: 10.1016/j.cvfa.2018.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the context of physiologic responses that determine the growth, development, and health status of livestock, the role of epigenetics and the underlying cellular mechanisms it affects remain to be fully elucidated. Although recent work has provided evidence that maternal dietary energy level, carbohydrate type, or intestinal supply of methyl donors can elicit molecular changes in tissues of the embryo, fetus, or neonate, there are few data linking epigenetics with biochemical and physiologic outcomes. Therefore, efforts linking the epigenome with physiologic and developmental outcomes offer exciting opportunities for discoveries that can impact efficiency of nutrient use and well-being of livestock.
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22
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Qin J, Wen B, Liang Y, Yu W, Li H. Histone Modifications and their Role in Colorectal Cancer (Review). Pathol Oncol Res 2019; 26:2023-2033. [PMID: 31055775 PMCID: PMC7471167 DOI: 10.1007/s12253-019-00663-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 04/11/2019] [Indexed: 12/11/2022]
Abstract
The development of colorectal cancer is a complex and multistep process mediated by a variety of factors including the dysregulation of genetic and epigenetic under the influence of microenvironment. It is evident that epigenetics that affects gene activity and expression has been recognized as a critical role in the carcinogenesis. Aside from DNA methylation, miRNA level, and genomic imprinting, histone modification is increasingly recognized as an essential mechanism underlying the occurrence and development of colorectal cancer. Aberrant regulation of histone modification like acetylation, methylation and phosphorylation levels on specific residues is implicated in a wide spectrum of cancers, including colorectal cancer. In addition, as this process is reversible and accompanied by a plethora of deregulated enzymes, inhibiting those histone-modifying enzymes activity and regulating its level has been thought of as a potential path for tumor therapy. This review provides insight into the basic information of histone modification and its application in the colorectal cancer treatment, thereby offering new potential targets for treatment of colorectal cancer.
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Affiliation(s)
- Jingchun Qin
- Institute of Spleen and Stomach, Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
| | - Bin Wen
- Institute of Spleen and Stomach, Guangzhou University of Chinese Medicine, Guangzhou, 510000, China.
| | - Yuqi Liang
- Institute of Spleen and Stomach, Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
| | - Weitao Yu
- Lianyungang Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Huixuan Li
- Institute of Spleen and Stomach, Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
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23
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Boon RA. Non-coding RNAs in cardiovascular health and disease. Noncoding RNA Res 2018; 3:99. [PMID: 30175282 PMCID: PMC6114259 DOI: 10.1016/j.ncrna.2018.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 07/31/2018] [Indexed: 11/17/2022] Open
Affiliation(s)
- Reinier A. Boon
- Corresponding author. Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands.
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24
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Abstract
Traffic-related particulate matter (PM) is a major source of outdoor air pollution worldwide. It has been recently hypothesized to cause cardiometabolic syndrome, including cardiovascular dysfunction, obesity, and diabetes. The environmental and toxicological factors involved in the processes, and the detailed mechanisms remain to be explored. The objective of this study is to assess the current scientific evidence of traffic-related PM-induced cardiometabolic syndrome. We conducted a literature review by searching the keywords of “traffic related air pollution”, “particulate matter”, “human health”, and “metabolic syndrome” from 1980 to 2018. This resulted in 25 independent research studies for the final review. Both epidemiological and toxicological findings reveal consistent correlations between traffic-related PM exposure and the measured cardiometabolic health endpoints. Smaller sizes of PM, particularly ultrafine particles, are shown to be more harmful due to their greater concentrations, reactive compositions, longer lung retention, and bioavailability. The active components in traffic-related PM could be attributed to metals, black carbon, elemental carbon, polyaromatic hydrocarbons, and diesel exhaust particles. Existing evidence points out that the development of cardiometabolic symptoms can occur through chronic systemic inflammation and increased oxidative stress. The elderly (especially for women), children, genetically susceptible individuals, and people with pre-existing conditions are identified as vulnerable groups. To advance the characterization of the potential health risks of traffic-related PM, additional research is needed to investigate the detailed chemical compositions of PM constituents, atmospheric transformations, and the mode of action to induce adverse health effects. Furthermore, we recommend that future studies could explore the roles of genetic and epigenetic factors in influencing cardiometabolic health outcomes by integrating multi-omics approaches (e.g., genomics, epigenomics, and transcriptomics) to provide a comprehensive assessment of biological perturbations caused by traffic-related PM.
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