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Hu C, Zhang K, Jiang F, Wang H, Shao Q. Epigenetic modifications in thymic epithelial cells: an evolutionary perspective for thymus atrophy. Clin Epigenetics 2021; 13:210. [PMID: 34819170 PMCID: PMC8612001 DOI: 10.1186/s13148-021-01197-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/08/2021] [Indexed: 02/06/2023] Open
Abstract
Background The thymic microenvironment is mainly comprised of thymic epithelial cells, the cytokines, exosomes, surface molecules, and hormones from the cells, and plays a vital role in the development, differentiation, maturation and homeostasis of T lymphocytes. However, the thymus begins to degenerate as early as the second year of life and continues through aging in human beings, leading to a decreased output of naïve T cells, the limited TCR diversity and an expansion of monoclonal memory T cells in the periphery organs. These alternations will reduce the adaptive immune response to tumors and emerging infectious diseases, such as COVID-19, also it is easier to suffer from autoimmune diseases in older people. In the context of global aging, it is important to investigate and clarify the causes and mechanisms of thymus involution. Main body Epigenetics include histone modification, DNA methylation, non-coding RNA effects, and chromatin remodeling. In this review, we discuss how senescent thymic epithelial cells determine and control age-related thymic atrophy, how this process is altered by epigenetic modification. How the thymus adipose influences the dysfunctions of the thymic epithelial cells, and the prospects of targeting thymic epithelial cells for the treatment of thymus atrophy. Conclusion Epigenetic modifications are emerging as key regulators in governing the development and senescence of thymic epithelial cells. It is beneficial to re-establish effective thymopoiesis, identify the potential therapeutic strategy and rejuvenate the immune function in the elderly.
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Affiliation(s)
- Cexun Hu
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China.,Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, No. 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Keyu Zhang
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China.,Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, No. 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Feng Jiang
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China.,Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, No. 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Hui Wang
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China. .,Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, No. 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China.
| | - Qixiang Shao
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China. .,Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, No. 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China. .,Jiangsu College of Nursing, School of Medical Science and Laboratory Medicine, Huai'an, 223002, Jiangsu, People's Republic of China.
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Guan ZX, Li SH, Zhang ZM, Zhang D, Yang H, Ding H. A Brief Survey for MicroRNA Precursor Identification Using Machine Learning Methods. Curr Genomics 2020; 21:11-25. [PMID: 32655294 PMCID: PMC7324890 DOI: 10.2174/1389202921666200214125102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 11/22/2022] Open
Abstract
MicroRNAs, a group of short non-coding RNA molecules, could regulate gene expression. Many diseases are associated with abnormal expression of miRNAs. Therefore, accurate identification of miRNA precursors is necessary. In the past 10 years, experimental methods, comparative genomics methods, and artificial intelligence methods have been used to identify pre-miRNAs. However, experimental methods and comparative genomics methods have their disadvantages, such as time-consuming. In contrast, machine learning-based method is a better choice. Therefore, the review summarizes the current advances in pre-miRNA recognition based on computational methods, including the construction of benchmark datasets, feature extraction methods, prediction algorithms, and the results of the models. And we also provide valid information about the predictors currently available. Finally, we give the future perspectives on the identification of pre-miRNAs. The review provides scholars with a whole background of pre-miRNA identification by using machine learning methods, which can help researchers have a clear understanding of progress of the research in this field.
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Affiliation(s)
- Zheng-Xing Guan
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu610054, China
| | - Shi-Hao Li
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu610054, China
| | - Zi-Mei Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu610054, China
| | - Dan Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu610054, China
| | - Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu610054, China
| | - Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu610054, China
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Yang Z, Liu S, Wang Y, Chen Y, Zhang P, Liu Y, Zhang H, Zhang P, Tao Z, Xiong K. High expression of KITLG is a new hallmark activating the MAPK pathway in type A and AB thymoma. Thorac Cancer 2020; 11:1944-1954. [PMID: 32463597 PMCID: PMC7327682 DOI: 10.1111/1759-7714.13486] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/14/2022] Open
Abstract
Background KIT proto‐oncogene ligand (KITLG) is a pleiotropic factor which is found in diverse cancers and is involved in cell proliferation, differentiation, and survival. However, the value of KITLG in thymoma remains unclear. Methods A total of 121 thymoma samples from The Cancer Genome Atlas Thymoma (TCGA‐THYM) dataset were used to analyze KITLG related genome‐wide expression profiles, and microRNA profiles and methylation alterations and a GEO dataset‐GSE29695, including 37 samples was used as verification. For cell‐based studies, specific small interfering RNA targeting KITLG or a KITLG overexpression vector were used to clarify the changes of the MAPK pathway in an AB thymoma cell line Thy0517. Results Both datasets showed that high expression of KITLG was significantly associated with type A and AB thymoma. Through multiomic analysis of the TCGA‐THYM, it was found that with the high expression of KITLG, there were 220 upregulated and 72 downregulated genes at the mRNA level, 79 positive and 78 negative miRNAs, 28 hypermethylation and 163 hypomethylation regions. In the thymoma cell line Thy0517, it was found that the expression of GRB2 and the phosphorylation levels of BRAF, MEK1/2, and ERK1/2 in the MAPK pathway were positively correlated with the change in KITLG. Conclusions High expression of KITLG is a new hallmark of WHO type A and AB thymomas in which it might play a critical role through the activation of the MAPK signaling pathway. Additionally, it is hoped that KITLG will become a potential target for the diagnosis of type A and AB thymoma through further research in the future. Key points Significant findings of the study KIT proto‐oncogene ligand (KITLG) is a new hallmark of type A and AB thymomas which induce a series of aberrant alteration of mRNA, miRNA and DNA methylation. The expression of KITLG is significantly higher in type A and AB than other subtypes of thymoma. What this study adds KITLG activated the MAPK signaling pathway to promote type A and AB thymoma which might be a potential diagnostic biomarker or target.
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Affiliation(s)
- Zhaoyu Yang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Shinan Liu
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yuanguo Wang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yuan Chen
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Peng Zhang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yimei Liu
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Hui Zhang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Peng Zhang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Ziyou Tao
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Kai Xiong
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
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Yahaya T, Shemishere U. Association between Bioactive Molecules in Breast Milk and Type 1 Diabetes Mellitus. Sultan Qaboos Univ Med J 2020; 20:e5-e12. [PMID: 32190364 PMCID: PMC7065699 DOI: 10.18295/squmj.2020.20.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/23/2019] [Accepted: 11/03/2019] [Indexed: 02/05/2023] Open
Abstract
The association between breastfeeding and type 1 diabetes mellitus (T1DM) is controversial. However, several recent studies have established a link between these two factors, necessitating a need to review this subject to raise public awareness. Current research indicates that breast milk contains a variety of bioactive substances including immunoglobulins, oligosaccharides, insulin, lactoferrin, lysozyme, cytokines, epidermal growth factors, leukocytes, nucleotides, beneficial bacteria and vitamins. Such substances strengthen the breastfeeding infant's immune system, both directly, by increasing gut microbiota diversity and attacking harmful bacteria and pro-inflammatory molecules, and indirectly, by increasing thymus performance. Accordingly, a lack of or inadequate breastfeeding may predispose infants to several autoimmune disorders, including T1DM. Nursing mothers and caregivers are therefore advised to follow optimal breastfeeding practices prior to introducing complementary foods.
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Affiliation(s)
- Tajudeen Yahaya
- Department of Biology, Federal University Birnin Kebbi, Birnin Kebbi, Nigeria
| | - Ufuoma Shemishere
- Department of Biochemistry & Molecular Biology, Federal University Birnin Kebbi, Birnin Kebbi, Nigeria
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Xu M, Gan T, Ning H, Wang L. MicroRNA Functions in Thymic Biology: Thymic Development and Involution. Front Immunol 2018; 9:2063. [PMID: 30254640 PMCID: PMC6141719 DOI: 10.3389/fimmu.2018.02063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 08/21/2018] [Indexed: 01/02/2023] Open
Abstract
During the entire processes of thymus organogenesis, maturation, and involution, gene regulation occurs post-transcriptionally via recently discovered microRNA (miRNA) transcripts. Numerous reports indicate that miRNAs may be involved in the construction of a normal thymic microenvironment, which constitutes a critical component to support T lymphocyte development. MiRNAs are also expressed in thymic stromal cells including thymic epithelial cells (TECs) during maturation and senescence. This review focuses on the function of miRNAs in thymic development and involution. A better understanding of these processes will provide new insights into the regulatory network of TECs and further comprehension of how genes control TECs to maintain the thymic microenvironment during thymus development and aging, thus supporting a normal cellular immune system.
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Affiliation(s)
- Minwen Xu
- First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Tao Gan
- Department of Biotechnology, Gannan Medical University, Ganzhou, China
| | - Huiting Ning
- Department of Biotechnology, Gannan Medical University, Ganzhou, China
| | - Liefeng Wang
- Department of Biotechnology, Gannan Medical University, Ganzhou, China
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Abstract
Breast feeding has been associated with improved infant outcomes in multiple aspects, including immune outcomes such as infections and potentially atopy and autoimmunity. However associations do not necessarily implicate cause and effect and at this point, exactly how breast feeding and components of breast milk may modulate the infant's immune compartment remains unclear, especially in humans. Some lines of evidence suggest that breastfeeding affects the development of the infant's thymus, a critical organ for T cell development. This may be a direct effect mediated by breast milk components or alternatively, a secondary effect from the impact of breast feeding on the infant's gut microbiome. Here we discuss the potential mechanisms and impact of this association between breast feeding and thymic development.
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Affiliation(s)
- Peter S Hsu
- Allergy and Immunology, Kids Research, The Children's Hospital at Westmead, Sydney, NSW, Australia.,Discipline of Child and Adolescent Health, The University of Sydney, Sydney, NSW, Australia
| | - Ralph Nanan
- Charles Perkins Centre Nepean, University of Sydney, Sydney, NSW, Australia
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