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Occean JR, Yang N, Sun Y, Dawkins MS, Munk R, Belair C, Dar S, Anerillas C, Wang L, Shi C, Dunn C, Bernier M, Price NL, Kim JS, Cui CY, Fan J, Bhattacharyya M, De S, Maragkakis M, deCabo R, Sidoli S, Sen P. Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528714. [PMID: 36824863 PMCID: PMC9949049 DOI: 10.1101/2023.02.15.528714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
DNA hydroxymethylation (5hmC) is the most abundant oxidative derivative of DNA methylation (5mC) and is typically enriched at enhancers and gene bodies of transcriptionally active and tissue-specific genes. Although aberrant genomic 5hmC has been implicated in many age-related diseases, the functional role of the modification in aging remains largely unknown. Here, we report that 5hmC is stably enriched in multiple aged organs. Using the liver and cerebellum as model organs, we show that 5hmC accumulates in gene bodies associated with tissue-specific function and thereby restricts the magnitude of gene expression changes during aging. Mechanistically, we found that 5hmC decreases binding affinity of splicing factors compared to unmodified cytosine and 5mC, and is correlated with age-related alternative splicing events, suggesting RNA splicing as a potential mediator of 5hmC's transcriptionally restrictive function. Furthermore, we show that various age-related contexts, such as prolonged quiescence and senescence, are partially responsible for driving the accumulation of 5hmC with age. We provide evidence that this age-related function is conserved in mouse and human tissues, and further show that the modification is altered by regimens known to modulate lifespan. Our findings reveal that 5hmC is a regulator of tissue-specific function and may play a role in regulating longevity.
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Affiliation(s)
- James R Occean
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Yan Sun
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY
| | - Marshall S Dawkins
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Showkat Dar
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Lin Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Changyou Shi
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Christopher Dunn
- Flow Cytometry Unit, National Institute on Aging, NIH, Baltimore, MD
| | - Michel Bernier
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD
| | - Nathan L Price
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD
| | - Julie S Kim
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY
| | - Chang-Yi Cui
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Jinshui Fan
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | | | - Supriyo De
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
| | - Rafael deCabo
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD
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GLIS1-3: Links to Primary Cilium, Reprogramming, Stem Cell Renewal, and Disease. Cells 2022; 11:cells11111833. [PMID: 35681527 PMCID: PMC9180737 DOI: 10.3390/cells11111833] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/27/2022] [Accepted: 06/02/2022] [Indexed: 12/10/2022] Open
Abstract
The GLI-Similar 1-3 (GLIS1-3) genes, in addition to encoding GLIS1-3 Krüppel-like zinc finger transcription factors, also generate circular GLIS (circGLIS) RNAs. GLIS1-3 regulate gene transcription by binding to GLIS binding sites in target genes, whereas circGLIS RNAs largely act as miRNA sponges. GLIS1-3 play a critical role in the regulation of many biological processes and have been implicated in various pathologies. GLIS protein activities appear to be regulated by primary cilium-dependent and -independent signaling pathways that via post-translational modifications may cause changes in the subcellular localization, proteolytic processing, and protein interactions. These modifications can affect the transcriptional activity of GLIS proteins and, consequently, the biological functions they regulate as well as their roles in disease. Recent studies have implicated GLIS1-3 proteins and circGLIS RNAs in the regulation of stemness, self-renewal, epithelial-mesenchymal transition (EMT), cell reprogramming, lineage determination, and differentiation. These biological processes are interconnected and play a critical role in embryonic development, tissue homeostasis, and cell plasticity. Dysregulation of these processes are part of many pathologies. This review provides an update on our current knowledge of the roles GLIS proteins and circGLIS RNAs in the control of these biological processes in relation to their regulation of normal physiological functions and disease.
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Liang J, Xia L, Oyang L, Lin J, Tan S, Yi P, Han Y, Luo X, Wang H, Tang L, Pan Q, Tian Y, Rao S, Su M, Shi Y, Cao D, Zhou Y, Liao Q. The functions and mechanisms of prefoldin complex and prefoldin-subunits. Cell Biosci 2020; 10:87. [PMID: 32699605 PMCID: PMC7370476 DOI: 10.1186/s13578-020-00446-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/15/2020] [Indexed: 12/26/2022] Open
Abstract
The correct folding is a key process for a protein to acquire its functional structure and conformation. Prefoldin is a well-known chaperone protein that regulates the correct folding of proteins. Prefoldin plays a crucial role in the pathogenesis of common neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, and Huntington's disease). The important role of prefoldin in emerging fields (such as nanoparticles, biomaterials) and tumors has attracted widespread attention. Also, each of the prefoldin subunits has different and independent functions from the prefoldin complex. It has abnormal expression in different tumors and plays an important role in tumorigenesis and development, especially c-Myc binding protein MM-1. MM-1 can inhibit the activity of c-Myc through various mechanisms to regulate tumor growth. Therefore, an in-depth analysis of the complex functions of prefoldin and their subunits is helpful to understand the mechanisms of protein misfolding and the pathogenesis of diseases caused by misfolded aggregation.
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Affiliation(s)
- Jiaxin Liang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Longzheng Xia
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Linda Oyang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Jinguan Lin
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Shiming Tan
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Pin Yi
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Yaqian Han
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Xia Luo
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Hui Wang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Lu Tang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
- Department of Medical Microbiology Immunology & Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, 913 N. Rutledge Street, Springfield, IL 62794 USA
| | - Qing Pan
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
- Department of Medical Microbiology Immunology & Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, 913 N. Rutledge Street, Springfield, IL 62794 USA
| | - Yutong Tian
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
- Department of Medical Microbiology Immunology & Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, 913 N. Rutledge Street, Springfield, IL 62794 USA
| | - Shan Rao
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Min Su
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Yingrui Shi
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Deliang Cao
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
- Department of Medical Microbiology Immunology & Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, 913 N. Rutledge Street, Springfield, IL 62794 USA
| | - Yujuan Zhou
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Qianjin Liao
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
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HMGA Genes and Proteins in Development and Evolution. Int J Mol Sci 2020; 21:ijms21020654. [PMID: 31963852 PMCID: PMC7013770 DOI: 10.3390/ijms21020654] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
HMGA (high mobility group A) (HMGA1 and HMGA2) are small non-histone proteins that can bind DNA and modify chromatin state, thus modulating the accessibility of regulatory factors to the DNA and contributing to the overall panorama of gene expression tuning. In general, they are abundantly expressed during embryogenesis, but are downregulated in the adult differentiated tissues. In the present review, we summarize some aspects of their role during development, also dealing with relevant studies that have shed light on their functioning in cell biology and with emerging possible involvement of HMGA1 and HMGA2 in evolutionary biology.
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Zhang Q, Liu W, Liu C, Lin SY, Guo AY. SEGtool: a specifically expressed gene detection tool and applications in human tissue and single-cell sequencing data. Brief Bioinform 2019; 19:1325-1336. [PMID: 28981576 DOI: 10.1093/bib/bbx074] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 12/20/2022] Open
Abstract
Different tissues and diseases have distinct transcriptional profilings with specifically expressed genes (SEGs). So, the identification of SEGs is an important issue in the studies of gene function, biological development, disease mechanism and biomarker discovery. However, few accurate and easy-to-use tools are available for RNA sequencing (RNA-seq) data to detect SEGs. Here, we presented SEGtool, a tool based on fuzzy c-means, Jaccard index and greedy annealing method for SEG detection automatically and self-adaptively ignoring data distribution. Testing result showed that our SEGtool outperforms the existing tools, which was mainly developed for microarray data. By applying SEGtool to Genotype-Tissue Expression (GTEx) human tissue data set, we detected 3181 SEGs with tissue-related functions. Regulatory networks reveal tissue-specific transcription factors regulating many SEGs, such as ETV2 in testis, HNF4A in liver and NEUROD1 in brain. Applied to a case study of single-cell sequencing (SCS) data from embryo cells, we identified many SEGs in specific stages of human embryogenesis. Notably, SEGtool is suitable for RNA-seq data and even SCS data with high specificity and accuracy. An implementation of SEGtool R package is freely available at http://bioinfo.life.hust.edu.cn/SEGtool/.
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Affiliation(s)
- Qiong Zhang
- Huazhong University of Science and Technology, China
| | - Wei Liu
- Huazhong University of Science and Technology, China
| | - Chunjie Liu
- Huazhong University of Science and Technology, China
| | - Sheng-Yan Lin
- Huazhong University of Science and Technology, China
| | - An-Yuan Guo
- Huazhong University of Science and Technology, China
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Low Expression of GLIS2 Gene Might Associate with Radiosensitivity of Gastric Cancer. JOURNAL OF ONCOLOGY 2019; 2019:2934925. [PMID: 31281358 PMCID: PMC6590498 DOI: 10.1155/2019/2934925] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/30/2019] [Accepted: 05/20/2019] [Indexed: 01/05/2023]
Abstract
Human gene GLIS family zinc finger 2 (GLIS2) is a member of GLI-similar zinc finger protein family. Previous studies indicated GLIS2 gene involved in tumorigenesis mechanisms. However, the association between GLIS2 expression and radiosensitivity of gastric cancer has not been well understood. In this study, we used the gastric cancer database in TCGA, and significant association was observed between the low expression of GLIS2 and radiosensitivity of patients with gastric cancer. The adjusted HR values for radiotherapy were 0.162(0.035-0.756) and 0.089(0.014-0.564), with p values 0.021 and 0.010, respectively, in training and testing data, for these patients with low expression of GLIS2, while for patients with high expression of GLIS2, there was no significant survival difference between radiotherapy and nonradiotherapy groups. The adjusted HR were 0.676(0.288-1.586) and 0.508(0.178-1.450), with p values 0.368 and 0.206 in training and testing data, respectively. Further study showed that, for low expression patients, radiotherapy did not significantly increase new tumor event rate and disease progression rate, which partially supported our assumption. These results suggested that low expression of GLIS2 might significantly associate with the radiosensitivity of patients with gastric cancer. The GLIS2 gene might be a potential effective molecular marker of gastric cancer for precise radiotherapy.
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Neganova I, Cotts L, Banks P, Gassner K, Shukurov A, Armstrong L, Ladds G, Lako M. Endothelial Differentiation G Protein-Coupled Receptor 5 Plays an Important Role in Induction and Maintenance of Pluripotency. Stem Cells 2019; 37:318-331. [PMID: 30512203 PMCID: PMC6446721 DOI: 10.1002/stem.2954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/08/2018] [Accepted: 10/25/2018] [Indexed: 02/03/2023]
Abstract
Direct reprogramming of human somatic cells toward induced pluripotent stem cells holds great promise for regenerative medicine and basic biology. We used a high-throughput small interfering RNA screening assay in the initiation phase of reprogramming for 784 genes belonging to kinase and phosphatase families and identified 68 repressors and 22 effectors. Six new candidates belonging to the family of the G protein-coupled receptors (GPCRs) were identified, suggesting an important role for this key signaling pathway during somatic cell-induced reprogramming. Downregulation of one of the key GPCR effectors, endothelial differentiation GPCR5 (EDG5), impacted the maintenance of pluripotency, actin cytoskeleton organization, colony integrity, and focal adhesions in human embryonic stem cells, which were associated with the alteration in the RhoA-ROCK-Cofilin-PAXILLIN-actin signaling pathway. Similarly, downregulation of EDG5 during the initiation stage of somatic cell-induced reprogramming resulted in alteration of cytoskeleton, loss of human-induced pluripotent stem cell colony integrity, and a significant reduction in partially and fully reprogrammed cells as well as the number of alkaline phosphatase positive colonies at the end of the reprogramming process. Together, these data point to an important role of EDG5 in the maintenance and acquisition of pluripotency. Stem Cells 2019;37:318-331.
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Affiliation(s)
- Irina Neganova
- International Centre for Life, Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
| | - Lewis Cotts
- International Centre for Life, Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
| | - Peter Banks
- High Throughput Screening Facility, Medical School, Newcastle, United Kingdom
| | - Katja Gassner
- International Centre for Life, Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
| | - Anvar Shukurov
- School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lyle Armstrong
- International Centre for Life, Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Majlinda Lako
- International Centre for Life, Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
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Koutsouraki E, Pells S, De Sousa PA. Sufficiency of hypoxia-inducible 2-oxoglutarate dioxygenases to block chemical oxidative stress-induced differentiation of human embryonic stem cells. Stem Cell Res 2018; 34:101358. [PMID: 30640062 DOI: 10.1016/j.scr.2018.11.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/18/2018] [Accepted: 11/27/2018] [Indexed: 11/18/2022] Open
Abstract
Hypoxia benefits undifferentiated pluripotent stem cell renewal, and 2-oxoglutarate (2OG) dioxygenases have been implicated in pluripotent stem cell induction and renewal. We show in human embryonic stem cells (hESC) that an ambient oxygen-induced oxidative stress response elicited by culture in a hypoxic atmosphere (0.5% O2) correlates with the expression of 2OG dioxygenases, which oxidise DNA (TET1, 2, 3) and histone H3 (KDM4C), the former reflected by elevation in genomic 5-hydroxymethylcytosine (5hmC). siRNA-mediated targeting of KDM4C and TET1-3 induces hESC differentiation. Under ambient atmospheric oxygen (21% O2), exposure to a low inhibitory concentration of sodium arsenite (NaAsO2, IC10), as a model of chemically-induced oxidative stress, suppresses antioxidant gene expression, reduces mitochondrial membrane potential and induces hESC differentiation. Co-administration of the antioxidant N-acetyl-L-cysteine promoted anti-oxidant, pluripotency and 2OG dioxygenase gene expression, elevated genomic hydroxymethylation and blocked induction of differentiation. Transient ectopic expression of KDM4C or TET1 in ambient atmospheric oxygen achieved the same. Our study substantiates a role for 2OG-dependent dioxygenases in hypoxia's promotion of undifferentiated hESC self-renewal.
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Affiliation(s)
- Eirini Koutsouraki
- Centre for Clinical Brain Sciences, Chancellors Building, 49 Little France Crescent, University of Edinburgh, Edinburgh EH16 4SB, UK; MRC Centre for Regenerative Medicine, Scottish Centre for Regenerative Medicine, 5 Little France Dr, Edinburgh EH16 4UU, UK
| | - Steve Pells
- Centre for Clinical Brain Sciences, Chancellors Building, 49 Little France Crescent, University of Edinburgh, Edinburgh EH16 4SB, UK; MRC Centre for Regenerative Medicine, Scottish Centre for Regenerative Medicine, 5 Little France Dr, Edinburgh EH16 4UU, UK
| | - Paul A De Sousa
- Centre for Clinical Brain Sciences, Chancellors Building, 49 Little France Crescent, University of Edinburgh, Edinburgh EH16 4SB, UK; MRC Centre for Regenerative Medicine, Scottish Centre for Regenerative Medicine, 5 Little France Dr, Edinburgh EH16 4UU, UK.
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Jetten AM. GLIS1-3 transcription factors: critical roles in the regulation of multiple physiological processes and diseases. Cell Mol Life Sci 2018; 75:3473-3494. [PMID: 29779043 PMCID: PMC6123274 DOI: 10.1007/s00018-018-2841-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 12/12/2022]
Abstract
Krüppel-like zinc finger proteins form one of the largest families of transcription factors. They function as key regulators of embryonic development and a wide range of other physiological processes, and are implicated in a variety of pathologies. GLI-similar 1-3 (GLIS1-3) constitute a subfamily of Krüppel-like zinc finger proteins that act either as activators or repressors of gene transcription. GLIS3 plays a critical role in the regulation of multiple biological processes and is a key regulator of pancreatic β cell generation and maturation, insulin gene expression, thyroid hormone biosynthesis, spermatogenesis, and the maintenance of normal kidney functions. Loss of GLIS3 function in humans and mice leads to the development of several pathologies, including neonatal diabetes and congenital hypothyroidism, polycystic kidney disease, and infertility. Single nucleotide polymorphisms in GLIS3 genes have been associated with increased risk of several diseases, including type 1 and type 2 diabetes, glaucoma, and neurological disorders. GLIS2 plays a critical role in the kidney and GLIS2 dysfunction leads to nephronophthisis, an end-stage, cystic renal disease. In addition, GLIS1-3 have regulatory functions in several stem/progenitor cell populations. GLIS1 and GLIS3 greatly enhance reprogramming efficiency of somatic cells into induced embryonic stem cells, while GLIS2 inhibits reprogramming. Recent studies have obtained substantial mechanistic insights into several physiological processes regulated by GLIS2 and GLIS3, while a little is still known about the physiological functions of GLIS1. The localization of some GLIS proteins to the primary cilium suggests that their activity may be regulated by a downstream primary cilium-associated signaling pathway. Insights into the upstream GLIS signaling pathway may provide opportunities for the development of new therapeutic strategies for diabetes, hypothyroidism, and other diseases.
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Affiliation(s)
- Anton M Jetten
- Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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Scoville DW, Kang HS, Jetten AM. GLIS1-3: emerging roles in reprogramming, stem and progenitor cell differentiation and maintenance. Stem Cell Investig 2017; 4:80. [PMID: 29057252 DOI: 10.21037/sci.2017.09.01] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/27/2017] [Indexed: 12/12/2022]
Abstract
Recent studies have provided evidence for a regulatory role of GLI-similar (GLIS) transcription factors in reprogramming, maintenance and differentiation of several stem and progenitor cell populations. GLIS1, in conjunction with several other reprogramming factors, was shown to markedly increase the efficiency of generating induced pluripotent stem cells (iPSC) from somatic cells. GLIS2 has been reported to contribute to the maintenance of the pluripotent state in hPSCs. In addition, GLIS2 has a function in regulating self-renewal of hematopoietic progenitors and megakaryocytic differentiation. GLIS3 plays a critical role during the development of several tissues. GLIS3 is able to promote reprogramming of human fibroblasts into retinal pigmented epithelial (RPE) cells. Moreover, GLIS3 is essential for spermatogonial stem cell renewal and spermatogonial progenitor cell differentiation. During pancreas development, GLIS3 protein is first detectable in bipotent pancreatic progenitors and pro-endocrine progenitors and plays a critical role in the generation of pancreatic beta cells. Here, we review the current status of the roles of GLIS proteins in the maintenance and differentiation of these different stem and progenitor cells.
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Affiliation(s)
- David W Scoville
- Cell Biology Section, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Hong Soon Kang
- Cell Biology Section, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Anton M Jetten
- Cell Biology Section, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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Lee SY, Noh HB, Kim HT, Lee KI, Hwang DY. Glis family proteins are differentially implicated in the cellular reprogramming of human somatic cells. Oncotarget 2017; 8:77041-77049. [PMID: 29100368 PMCID: PMC5652762 DOI: 10.18632/oncotarget.20334] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/19/2017] [Indexed: 11/25/2022] Open
Abstract
The ground-breaking discovery of the reprogramming of somatic cells into pluripotent cells, termed induced pluripotent stem cells (iPSCs), was accomplished by delivering 4 transcription factors, Oct4, Sox2, Klf4, and c-Myc, into fibroblasts. Since then, several efforts have attempted to unveil other factors that are directly implicated in or might enhance reprogramming. Importantly, a number of transcription factors are reported to retain reprogramming activity. A previous study suggested Gli-similar 1 (Glis1) as a factor that enhances the reprogramming of fibroblasts during iPSC generation. However, the implication of other Glis members, including Glis2 and Glis3 (variants 1 and 2), in cellular reprogramming remains unknown. In this study, we investigated the potential involvement of human Glis family proteins, including hGlis1-3, in cellular reprogramming. Our results demonstrate that hGlis1, which is reported to reprogram human fibroblasts, promotes the reprogramming of human adipose-derived stromal cells (hADSCs), indicating that the reprogramming activity of Glis1 is not cell type-specific. Strikingly, hGlis3 promoted the reprogramming of hADSCs as efficiently as hGlis1. On the contrary, hGlis2 showed a strong negative effect on reprogramming. Together, our results reveal clear differences in the cellular reprogramming activity among Glis family members and provide valuable insight into the development of a new reprogramming strategy using Glis family proteins.
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Affiliation(s)
- Seo-Young Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seongnamsi, Gyeonggido 13488, Korea
| | - Hye Bin Noh
- Department of Biomedical Science, College of Life Science, CHA University, Seongnamsi, Gyeonggido 13488, Korea
| | - Hyeong-Taek Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnamsi, Gyeonggido 13488, Korea
| | - Kang-In Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seongnamsi, Gyeonggido 13488, Korea
| | - Dong-Youn Hwang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnamsi, Gyeonggido 13488, Korea
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Nica D, Popescu C, Draghici G, Privistirescu I, Suciu M, Stöger R. Effect of cadmium on cytosine hydroxymethylation in gastropod hepatopancreas. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:15187-15195. [PMID: 28497329 DOI: 10.1007/s11356-017-9104-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
5-Hydroxymethylcytosine (5hmC) is an important, yet poorly understood epigenetic DNA modification, especially in invertebrates. Aberrant genome-wide 5hmC levels have been associated with cadmium (Cd) exposure in humans, but such information is lacking for invertebrate bioindicators. Here, we aimed to determine whether this epigenetic mark is present in DNA of the hepatopancreas of the land snail Cantareus aspersus and is responsive to Cd exposure. Adult snails were reared under laboratory conditions and exposed to graded amounts of dietary cadmium for 14 days. Weight gain was used as a sublethal endpoint, whereas survival as a lethal endpoint. Our results are the first to provide evidence for the presence of 5hmC in DNA of terrestrial mollusks; 5hmC levels are generally low with the measured values falling below 0.03%. This is also the first study to investigate the interplay of Cd with DNA hydroxymethylation levels in a non-human animal study system. Cadmium retention in the hepatopancreas of C. aspersus increased from a dietary Cd dose of 1 milligram per kilogram dry weight (mg/kg d. wt). For the same treatment, we identified the only significant elevation in percentage of samples with detectable 5hmC levels despite the lack of significant mortalities and changes in weight gain among treatment groups. These findings indicate that 5hmC is an epigenetic mark that may be responsive to Cd exposure, thereby opening a new aspect to invertebrate environmental epigenetics.
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Affiliation(s)
- Dragos Nica
- Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, P-ta Murgu Eftimie 2, RO 300041, Timisoara, Romania.
- Institute of Life Sciences, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, RO 310045, Arad, Romania.
| | - Cristina Popescu
- Institute of Life Sciences, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, RO 310045, Arad, Romania
- Faculty of Pharmacy, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, RO 310045, Arad, Romania
| | - George Draghici
- Institute of Life Sciences, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, RO 310045, Arad, Romania
| | - Ionela Privistirescu
- Faculty of Medicine, "Victor Babes" University of Medicine and Pharmacy, P-ta Murgu Eftimie 2, RO 300041, Timisoara, Romania
| | - Maria Suciu
- Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, P-ta Murgu Eftimie 2, RO 300041, Timisoara, Romania
- "Babes-Bolyai" University, Str. Mihail Kogalniceanu1, RO 400084, Cluj-Napoca, Romania
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK
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Thirant C, Ignacimouttou C, Lopez CK, Diop M, Le Mouël L, Thiollier C, Siret A, Dessen P, Aid Z, Rivière J, Rameau P, Lefebvre C, Khaled M, Leverger G, Ballerini P, Petit A, Raslova H, Carmichael CL, Kile BT, Soler E, Crispino JD, Wichmann C, Pflumio F, Schwaller J, Vainchenker W, Lobry C, Droin N, Bernard OA, Malinge S, Mercher T. ETO2-GLIS2 Hijacks Transcriptional Complexes to Drive Cellular Identity and Self-Renewal in Pediatric Acute Megakaryoblastic Leukemia. Cancer Cell 2017; 31:452-465. [PMID: 28292442 DOI: 10.1016/j.ccell.2017.02.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 12/22/2016] [Accepted: 02/09/2017] [Indexed: 12/17/2022]
Abstract
Chimeric transcription factors are a hallmark of human leukemia, but the molecular mechanisms by which they block differentiation and promote aberrant self-renewal remain unclear. Here, we demonstrate that the ETO2-GLIS2 fusion oncoprotein, which is found in aggressive acute megakaryoblastic leukemia, confers megakaryocytic identity via the GLIS2 moiety while both ETO2 and GLIS2 domains are required to drive increased self-renewal properties. ETO2-GLIS2 directly binds DNA to control transcription of associated genes by upregulation of expression and interaction with the ETS-related ERG protein at enhancer elements. Importantly, specific interference with ETO2-GLIS2 oligomerization reverses the transcriptional activation at enhancers and promotes megakaryocytic differentiation, providing a relevant interface to target in this poor-prognosis pediatric leukemia.
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Affiliation(s)
- Cécile Thirant
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Cathy Ignacimouttou
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Université Paris Diderot, 75013 Paris, France
| | - Cécile K Lopez
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Université Paris-Sud, 91405 Orsay, France
| | | | - Lou Le Mouël
- Gustave Roussy, 94800 Villejuif, France; Université Paris-Sud, 91405 Orsay, France
| | - Clarisse Thiollier
- Gustave Roussy, 94800 Villejuif, France; Université Paris Diderot, 75013 Paris, France
| | - Aurélie Siret
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Phillipe Dessen
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Zakia Aid
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Julie Rivière
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | | | | | | | | | | | | | - Hana Raslova
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | | | - Benjamin T Kile
- Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia
| | - Eric Soler
- INSERM UMR967, 92265 Fontenay-aux-Roses, France
| | - John D Crispino
- Division of Hematology/Oncology, Northwestern University, Chicago, IL 60611, USA
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilian University Hospital, Munich, Germany
| | | | - Jürg Schwaller
- University Children's Hospital Beider Basel (UKBB), Departement of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - William Vainchenker
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Camille Lobry
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Nathalie Droin
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France; Université Paris-Sud, 91405 Orsay, France; INSERM U523, CNRS UMS3655, Gustave Roussy, 94800 Villejuif, France
| | - Olivier A Bernard
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France; Université Paris-Sud, 91405 Orsay, France
| | - Sébastien Malinge
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Thomas Mercher
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France; Université Paris Diderot, 75013 Paris, France; Université Paris-Sud, 91405 Orsay, France.
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Abstract
Adult diffuse gliomas account for the majority of primary malignant brain tumours, and are in most cases lethal. Current therapies are often only marginally effective, and improved options will almost certainly benefit from further insight into the various processes contributing to gliomagenesis and pathology. While molecular characterization of these tumours classifies them on the basis of genetic alterations and chromosomal abnormalities, DNA methylation patterns are increasingly understood to play a role in glioma pathogenesis. Indeed, a subset of gliomas associated with improved survival is characterized by the glioma CpG island methylator phenotype (G-CIMP), which can be induced by the expression of mutant isocitrate dehydrogenase (IDH1/2). Aberrant methylation of particular genes or regulatory elements, within the context of G-CIMP-positive and/or negative tumours, has also been shown to be associated with differential survival. In this review, we provide an overview of the current knowledge regarding the role of DNA methylation in adult diffuse gliomas. In particular, we discuss IDH mutations and G-CIMP, MGMT promoter methylation, DNA methylation-mediated microRNA regulation and aberrant methylation of specific genes or groups of genes.
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