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Lim TB, Foo SYR, Chen CK. The Role of Epigenetics in Congenital Heart Disease. Genes (Basel) 2021; 12:genes12030390. [PMID: 33803261 PMCID: PMC7998561 DOI: 10.3390/genes12030390] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/23/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023] Open
Abstract
Congenital heart disease (CHD) is the most common birth defect among newborns worldwide and contributes to significant infant morbidity and mortality. Owing to major advances in medical and surgical management, as well as improved prenatal diagnosis, the outcomes for these children with CHD have improved tremendously so much so that there are now more adults living with CHD than children. Advances in genomic technologies have discovered the genetic causes of a significant fraction of CHD, while at the same time pointing to remarkable complexity in CHD genetics. For this reason, the complex process of cardiogenesis, which is governed by multiple interlinked and dose-dependent pathways, is a well investigated process. In addition to the sequence of the genome, the contribution of epigenetics to cardiogenesis is increasingly recognized. Significant progress has been made dissecting the epigenome of the heart and identified associations with cardiovascular diseases. The role of epigenetic regulation in cardiac development/cardiogenesis, using tissue and animal models, has been well reviewed. Here, we curate the current literature based on studies in humans, which have revealed associated and/or causative epigenetic factors implicated in CHD. We sought to summarize the current knowledge on the functional role of epigenetics in cardiogenesis as well as in distinct CHDs, with an aim to provide scientists and clinicians an overview of the abnormal cardiogenic pathways affected by epigenetic mechanisms, for a better understanding of their impact on the developing fetal heart, particularly for readers interested in CHD research.
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Affiliation(s)
- Tingsen Benson Lim
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Sik Yin Roger Foo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Ching Kit Chen
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Division of Cardiology, Department of Paediatrics, Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore 119228, Singapore
- Correspondence:
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Skol AD, Jung SC, Sokovic AM, Chen S, Fazal S, Sosina O, Borkar PP, Lin A, Sverdlov M, Cao D, Swaroop A, Bebu I, Stranger BE, Grassi MA. Integration of genomics and transcriptomics predicts diabetic retinopathy susceptibility genes. eLife 2020; 9:59980. [PMID: 33164750 PMCID: PMC7728435 DOI: 10.7554/elife.59980] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
We determined differential gene expression in response to high glucose in lymphoblastoid cell lines derived from matched individuals with type 1 diabetes with and without retinopathy. Those genes exhibiting the largest difference in glucose response were assessed for association with diabetic retinopathy in a genome-wide association study meta-analysis. Expression quantitative trait loci (eQTLs) of the glucose response genes were tested for association with diabetic retinopathy. We detected an enrichment of the eQTLs from the glucose response genes among small association p-values and identified folliculin (FLCN) as a susceptibility gene for diabetic retinopathy. Expression of FLCN in response to glucose was greater in individuals with diabetic retinopathy. Independent cohorts of individuals with diabetes revealed an association of FLCN eQTLs with diabetic retinopathy. Mendelian randomization confirmed a direct positive effect of increased FLCN expression on retinopathy. Integrating genetic association with gene expression implicated FLCN as a disease gene for diabetic retinopathy. One of the side effects of diabetes is loss of vision from diabetic retinopathy, which is caused by injury to the light sensing tissue in the eye, the retina. Almost all individuals with diabetes develop diabetic retinopathy to some extent, and it is the leading cause of irreversible vision loss in working-age adults in the United States. How long a person has been living with diabetes, the extent of increased blood sugars and genetics all contribute to the risk and severity of diabetic retinopathy. Unfortunately, virtually no genes associated with diabetic retinopathy have yet been identified. When a gene is activated, it produces messenger molecules known as mRNA that are used by cells as instructions to produce proteins. The analysis of mRNA molecules, as well as genes themselves, can reveal the role of certain genes in disease. The studies of all genes and their associated mRNAs are respectively called genomics and transcriptomics. Genomics reveals what genes are present, while transcriptomics shows how active genes are in different cells. Skol et al. developed methods to study genomics and transcriptomics together to help discover genes that cause diabetic retinopathy. Genes involved in how cells respond to high blood sugar were first identified using cells grown in the lab. By comparing the activity of these genes in people with and without retinopathy the study identified genes associated with an increased risk of retinopathy in diabetes. In people with retinopathy, the activity of the folliculin gene (FLCN) increased more in response to high blood sugar. This was further verified with independent groups of people and using computer models to estimate the effect of different versions of the folliculin gene. The methods used here could be applied to understand complex genetics in other diseases. The results provide new understanding of the effects of diabetes. They may also help in the development of new treatments for diabetic retinopathy, which are likely to improve on the current approach of using laser surgery or injections into the eye.
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Affiliation(s)
- Andrew D Skol
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, United States
| | - Segun C Jung
- Research and Development, NeoGenomics Laboratories, Aliso Viejo, United States
| | | | - Siquan Chen
- Cellular Screening Center, Office of Shared Research Facilities, The University of Chicago, Chicago, United States
| | - Sarah Fazal
- Cellular Screening Center, Office of Shared Research Facilities, The University of Chicago, Chicago, United States
| | - Olukayode Sosina
- Department of Biostatistics, Johns Hopkins University, Baltimore, United States.,National Eye Institute, National Institutes of Health (NIH), Bethesda, United States
| | | | - Amy Lin
- University of Illinois at Chicago, Chicago, United States
| | - Maria Sverdlov
- University of Illinois at Chicago, Chicago, United States
| | - Dingcai Cao
- University of Illinois at Chicago, Chicago, United States
| | - Anand Swaroop
- National Eye Institute, National Institutes of Health (NIH), Bethesda, United States
| | - Ionut Bebu
- The George Washington University, Biostatistics Center, Rockville, United States
| | | | - Barbara E Stranger
- Department of Pharmacology, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States
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Reading between the (Genetic) Lines: How Epigenetics is Unlocking Novel Therapies for Type 1 Diabetes. Cells 2020; 9:cells9112403. [PMID: 33153010 PMCID: PMC7692667 DOI: 10.3390/cells9112403] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 12/19/2022] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune condition where the body’s immune cells destroy their insulin-producing pancreatic beta cells leading to dysregulated glycaemia. Individuals with T1D control their blood glucose through exogenous insulin replacement therapy, often using multiple daily injections or pumps. However, failure to accurately mimic intrinsic glucose regulation results in glucose fluctuations and long-term complications impacting key organs such as the heart, kidneys, and/or the eyes. It is well established that genetic and environmental factors contribute to the initiation and progression of T1D, but recent studies show that epigenetic modifications are also important. Here, we discuss key epigenetic modifications associated with T1D pathogenesis and discuss how recent research is finding ways to harness epigenetic mechanisms to prevent, reverse, or manage T1D.
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Liu P, Zhu Y, Li Q, Cheng B. Comprehensive Analysis of Differentially Expressed miRNAs and mRNAs Reveals That miR-181a-5p Plays a Key Role in Diabetic Dermal Fibroblasts. J Diabetes Res 2020; 2020:4581954. [PMID: 33102604 PMCID: PMC7568154 DOI: 10.1155/2020/4581954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/05/2020] [Indexed: 12/16/2022] Open
Abstract
A diabetic nonhealing wound causes heavy economic burden and compromised quality of life in patients. The human dermal fibroblast (HDF), which is an important kind of effector cell in the wound healing process, represents different biological behaviors in the normal and diabetic skins. Given this, we attempt to explore functional changes in diabetic skin-derived HDFs and try to find out the "hub" genes that modulate diabetic HDFs and may be the potential therapeutic targets of diabetic wound healing. We searched the GEO database for related miRNA (GSE68185, GSE84971) and mRNA (GSE49566, GSE78891) profiles. After eliminating batch effects and identifying differentially expressed genes (DEGs), we applied enrichment analyses and found that 3 miRNAs and 30 mRNAs were differentially expressed in diabetic HDFs. Enrichment analyses showed that these genes are closely related to wound healing, for example, extracellular matrix (ECM) organization, angiogenesis, cell proliferation, and migration. Subsequently, we constructed the gene correlation network of DEGs to identify hub genes by merging the protein-protein interaction network, weighted gene coexpression network, and predicted miRNA-mRNA regulatory network. Based on the gene correlation network, we identified the top 3 hub genes: miR-181a-5p, POSTN, and CDH11. Among these, POSTN is a predicted target of miR-181a-5p and is supposed to work together with CDH11 as a functional group. Finally, we verified the expression pattern of the hub genes by in vitro quantification experiments in glucose-cultured HDFs. Our study suggested that miR-181a-5p possibly plays a key role in modulation of HDF behaviors during the diabetic state. However, the effects and mechanisms of miR-181a-5p in high glucose-cultured HDFs remain to be explored in the future.
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Affiliation(s)
- Peng Liu
- Department of Burn & Plastic Surgery, General Hospital of Southern Theatre Command of PLA, 111 Guangzhou Liuhua Road, Guangzhou 510010, China
- Huabo Post-Doctoral Research Center, Biological Pharmaceutical Research Institute, 111 Guangzhou Liuhua Road, Guangzhou 510010, China
| | - Yi Zhu
- Department of Anesthesiology, General Hospital of Southern Theatre Command of PLA, 111 Guangzhou Liuhua Road, Guangzhou 510010, China
| | - Qin Li
- Department of Burn & Plastic Surgery, General Hospital of Southern Theatre Command of PLA, 111 Guangzhou Liuhua Road, Guangzhou 510010, China
| | - Biao Cheng
- Department of Burn & Plastic Surgery, General Hospital of Southern Theatre Command of PLA, 111 Guangzhou Liuhua Road, Guangzhou 510010, China
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Palmieri B, Vadalà M, Laurino C. Review of the molecular mechanisms in wound healing: new therapeutic targets? J Wound Care 2019; 26:765-775. [PMID: 29244975 DOI: 10.12968/jowc.2017.26.12.765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The restoration of the skin barrier in acute and chronic wounds is controlled by several molecular mechanisms that synergistically regulate cell kinetics, enzymatic functions, and neurovascular activation. These pathways include genetic and epigenetic activation, which modulate physiological wound healing. Our review describes the genetic background of skin repair, namely transcription-independent diffusible damage signals, individual variability, epigenetic mechanism, controlled qualitative traits, post-translational mechanisms, antioxidants, nutrients, DNA modifications, bacteria activation, mitochondrial activity, and oxidative stress. The DNA background modulating skin restoration could be used to plan new diagnostics and therapeutics.
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Affiliation(s)
- B Palmieri
- Associated Professor, Dipartimento Chirurgico, Medico, Odontoiatrico e di Scienze Morfologiche con Interesse Trapiantologico, Oncologico e di Medicina Rigenerativa, Università degli Studi di Modena e Reggio Emilia, Modena, Italy; Network del Secondo Parere, Modena (MO), Italy
| | - M Vadalà
- Biologist Researcher, Dipartimento Chirurgico, Medico, Odontoiatrico e di Scienze Morfologiche con Interesse Trapiantologico, Oncologico e di Medicina Rigenerativa, Università degli Studi di Modena e Reggio Emilia, Modena, Italy; Network del Secondo Parere, Modena (MO), Italy
| | - C Laurino
- Biologist Researcher, Dipartimento Chirurgico, Medico, Odontoiatrico e di Scienze Morfologiche con Interesse Trapiantologico, Oncologico e di Medicina Rigenerativa, Università degli Studi di Modena e Reggio Emilia, Modena, Italy; Network del Secondo Parere, Modena (MO), Italy
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Lyu G, Zhang C, Ling T, Liu R, Zong L, Guan Y, Huang X, Sun L, Zhang L, Li C, Nie Y, Tao W. Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease. BMC Genomics 2018; 19:428. [PMID: 29866040 PMCID: PMC5987557 DOI: 10.1186/s12864-018-4814-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 05/22/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is the leading non-infectious cause of death in infants. Monozygotic (MZ) twins share nearly all of their genetic variants before and after birth. Nevertheless, MZ twins are sometimes discordant for common complex diseases. The goal of this study is to identify genomic and epigenomic differences between a pair of twins discordant for a form of congenital heart disease, double outlet right ventricle (DORV). RESULTS A monoamniotic monozygotic (MZ) twin pair discordant for DORV were subjected to genome-wide sequencing and methylation analysis. We identified few genomic differences but 1566 differentially methylated regions (DMRs) between the MZ twins. Twenty percent (312/1566) of the DMRs are located within 2 kb upstream of transcription start sites (TSS), containing 121 binding sites of transcription factors. Particularly, ZIC3 and NR2F2 are found to have hypermethylated promoters in both the diseased twin and additional patients suffering from DORV. CONCLUSIONS The results showed a high correlation between hypermethylated promoters at ZIC3 and NR2F2 and down-regulated gene expression levels of these two genes in patients with DORV compared to normal controls, providing new insight into the potential mechanism of this rare form of CHD.
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Affiliation(s)
- Guoliang Lyu
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Chao Zhang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Te Ling
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Rui Liu
- Department of Cardiovascular Surgery, Center for Cardiovascular Regenerative Medicine, Fuwai Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100871 China
| | - Le Zong
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yiting Guan
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Xiaoke Huang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Lei Sun
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Lijun Zhang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yu Nie
- Department of Cardiovascular Surgery, Center for Cardiovascular Regenerative Medicine, Fuwai Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100871 China
| | - Wei Tao
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
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7
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Jones IV AR, Coleman EL, Husni NR, Deeney JT, Raval F, Steenkamp D, Dooms H, Nikolajczyk BS, Corkey BE. Type 1 diabetes alters lipid handling and metabolism in human fibroblasts and peripheral blood mononuclear cells. PLoS One 2017; 12:e0188474. [PMID: 29206239 PMCID: PMC5714353 DOI: 10.1371/journal.pone.0188474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023] Open
Abstract
Triggers of the autoimmune response that leads to type 1 diabetes (T1D) remain poorly understood. A possibility is that parallel changes in both T cells and target cells provoke autoimmune attack. We previously documented greater Ca2+ transients in fibroblasts from T1D subjects than non-T1D after exposure to fatty acids (FA) and tumor necrosis factor α (TNFα). These data indicate that metabolic and signal transduction defects present in T1D can be elicited ex vivo in isolated cells. Changes that precede T1D, including inflammation, may activate atypical responses in people that are genetically predisposed to T1D. To identify such cellular differences in T1D, we quantified a panel of metabolic responses in fibroblasts and peripheral blood cells (PBMCs) from age-matched T1D and non-T1D subjects, as models for non-immune and immune cells, respectively. Fibroblasts from T1D subjects accumulated more lipid, had higher LC-CoA levels and converted more FA to CO2, with less mitochondrial proton leak in response to oleate alone or with TNFα, using the latter as a model of inflammation. T1D-PBMCs contained and also accumulated more lipid following FA exposure. In addition, they formed more peroxidized lipid than controls following FA exposure. We conclude that both immune and non-immune cells in T1D subjects differ from controls in terms of responses to FA and TNFα. Our results suggest a differential sensitivity to inflammatory insults and FA that may precede and contribute to T1D by priming both immune cells and their targets for autoimmune reactions.
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Affiliation(s)
- Albert R. Jones IV
- Obesity Research Center, Evans Department of Medicine, Boston University School of Medicine, Boston, MA, United States of America
| | - Emily L. Coleman
- Yale University School of Medicine, New Haven, CT, United States of America
| | - Nicholas R. Husni
- Obesity Research Center, Evans Department of Medicine, Boston University School of Medicine, Boston, MA, United States of America
| | - Jude T. Deeney
- Obesity Research Center, Evans Department of Medicine, Boston University School of Medicine, Boston, MA, United States of America
| | - Forum Raval
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Devin Steenkamp
- Endocrinology Section, Evans Department of Medicine, Boston University School of Medicine, Boston, MA, United States of America
| | - Hans Dooms
- Rheumatology Section, Evans Department of Medicine, Boston University School of Medicine, Boston, MA, United States of America
| | - Barbara S. Nikolajczyk
- Department of Translational Research in Diabetes, University of Kentucky School of Medicine, Lexington, KY, United States of America
- Department of Pharmacology and Nutritional Sciences, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Barbara E. Corkey
- Obesity Research Center, Evans Department of Medicine, Boston University School of Medicine, Boston, MA, United States of America
- * E-mail:
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Chernikov AA, Severina AS, Shamhalova MS, Shestakova MV. The role of «metabolic memory» mechanisms in the development and progression of vascular complications of diabetes mellitus. DIABETES MELLITUS 2017. [DOI: 10.14341/7674] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The study of diabetes mellitus (DM), its complications and related pathologies has been continuously performed for many years; however, despite the substantial work and outstanding achievements in studying the mechanisms of DM development and the success of new medicinal products for controlling glycaemia, the problems associated with the late complications of DM continue to increase. The importance of glycaemic control in the early stages of DM for the development of complications is seen only after a sufficiently long period of observation. Such a delayed effect of primary good or unsatisfactory metabolic control, which shapes the patients clinical fate to a greater extent, is termed metabolic memory. The disorders developed under the influence of hyperglycaemia persist for long periods after the normalisation of carbohydrate metabolism; moreover, the effect of previous hyperglycaemia extends over the next 20 and even 30 years. Current research is focused on the possible mechanisms of metabolic memory development, including oxidative stress, advanced glycation end products and epigenetic mechanisms. This research will provide insight into potential markers for the early development and progression of vascular complications and new therapeutic possibilities for the future. However, determining the probable point of no return is more important, which implies that a point exists; after this point is crossed, the progression of vascular complications associated with DM cannot be prevented or reversed. The results of numerous experimental studies demonstrate that the prerequisite components of metabolic memory can be used as potential markers of the progression of DM complications, and may be potential therapeutic targets.
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Microenvironmental Gene Expression Plasticity Among Individual Drosophila melanogaster. G3-GENES GENOMES GENETICS 2016; 6:4197-4210. [PMID: 27770026 PMCID: PMC5144987 DOI: 10.1534/g3.116.035444] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Differences in phenotype among genetically identical individuals exposed to the same environmental condition are often noted in genetic studies. Despite this commonplace observation, little is known about the causes of this variability, which has been termed microenvironmental plasticity. One possibility is that stochastic or technical sources of variance produce these differences. A second possibility is that this variation has a genetic component. We have explored gene expression robustness in the transcriptomes of 730 individual Drosophila melanogaster of 16 fixed genotypes, nine of which are infected with Wolbachia. Three replicates of flies were grown, controlling for food, day/night cycles, humidity, temperature, sex, mating status, social exposure, and circadian timing of RNA extraction. Despite the use of inbred genotypes, and carefully controlled experimental conditions, thousands of genes were differentially expressed, revealing a unique and dynamic transcriptional signature for each individual fly. We found that 23% of the transcriptome was differentially expressed among individuals, and that the variability in gene expression among individuals is influenced by genotype. This transcriptional variation originated from specific gene pathways, suggesting a plastic response to the microenvironment; but there was also evidence of gene expression differences due to stochastic fluctuations. These observations reveal previously unappreciated genetic sources of variability in gene expression among individuals, which has implications for complex trait genetics and precision medicine.
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Jhamb S, Vangaveti VN, Malabu UH. Genetic and molecular basis of diabetic foot ulcers: Clinical review. J Tissue Viability 2016; 25:229-236. [DOI: 10.1016/j.jtv.2016.06.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 05/10/2016] [Accepted: 06/21/2016] [Indexed: 12/19/2022]
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Grassi MA, Rao VR, Chen S, Cao D, Gao X, Cleary PA, Huang RS, Paterson AD, Natarajan R, Rehman J, Kern TS. Lymphoblastoid Cell Lines as a Tool to Study Inter-Individual Differences in the Response to Glucose. PLoS One 2016; 11:e0160504. [PMID: 27509144 PMCID: PMC4979894 DOI: 10.1371/journal.pone.0160504] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/20/2016] [Indexed: 01/15/2023] Open
Abstract
Background White blood cells have been shown in animal studies to play a central role in the pathogenesis of diabetic retinopathy. Lymphoblastoid cells are immortalized EBV-transformed primary B-cell leukocytes that have been extensively used as a model for conditions in which white blood cells play a primary role. The purpose of this study was to investigate whether lymphoblastoid cell lines, by retaining many of the key features of primary leukocytes, can be induced with glucose to demonstrate relevant biological responses to those found in diabetic retinopathy. Methods Lymphoblastoid cell lines were obtained from twenty-three human subjects. Differences between high and standard glucose conditions were assessed for expression, endothelial adhesion, and reactive oxygen species. Results Collectively, stimulation of the lymphoblastoid cell lines with high glucose demonstrated corresponding changes on molecular, cellular and functional levels. Lymphoblastoid cell lines up-regulated expression of a panel of genes associated with the leukocyte-mediated inflammation found in diabetic retinopathy that include: a cytokine (IL-1B fold change = 2.11, p-value = 0.02), an enzyme (PKCB fold change = 2.30, p-value = 0.01), transcription factors (NFKB-p50 fold change = 2.05, p-value = 0.01), (NFKB-p65 fold change = 2.82, p-value = 0.003), and an adhesion molecule (CD18 fold change = 2.59, 0.02). Protein expression of CD18 was also increased (p-value = 2.14x10-5). The lymphoblastoid cell lines demonstrated increased adhesiveness to endothelial cells (p = 1.28x10-5). Reactive oxygen species were increased (p = 2.56x10-6). Significant inter-individual variation among the lymphoblastoid cell lines in these responses was evident (F = 18.70, p < 0.0001). Conclusions Exposure of lymphoblastoid cell lines derived from different human subjects to high glucose demonstrated differential and heterogeneous gene expression, adhesion, and cellular effects that recapitulated features found in the diabetic state. Lymphoblastoid cells may represent a useful tool to guide an individualized understanding of the development and potential treatment of diabetic complications like retinopathy.
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Affiliation(s)
- Michael A. Grassi
- Department of Ophthalmology & Visual Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Vidhya R. Rao
- Department of Ophthalmology & Visual Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Siquan Chen
- Cellular Screening Center, Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Dingcai Cao
- Department of Ophthalmology & Visual Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Xiaoyu Gao
- The Biostatistics Center, George Washington University, Rockville, Maryland, United States of America
| | - Patricia A. Cleary
- The Biostatistics Center, George Washington University, Rockville, Maryland, United States of America
| | - R. Stephanie Huang
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, United States of America
| | - Andrew D. Paterson
- Genetics and Genome Biology Research Institute, Sickkids, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
| | - Jalees Rehman
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Timothy S. Kern
- Departments of Medicine and Pharmacology Case Western Reserve University, Cleveland, Ohio, United States of America, and the Veterans Administration Medical Center Research Service 151, Cleveland, Ohio, United States of America
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12
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Park LK, Maione AG, Smith A, Gerami-Naini B, Iyer LK, Mooney DJ, Veves A, Garlick JA. Genome-wide DNA methylation analysis identifies a metabolic memory profile in patient-derived diabetic foot ulcer fibroblasts. Epigenetics 2015; 9:1339-49. [PMID: 25437049 PMCID: PMC4622843 DOI: 10.4161/15592294.2014.967584] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Diabetic foot ulcers (DFUs) are a serious complication of diabetes. Previous exposure to hyperglycemic conditions accelerates a decline in cellular function through metabolic memory despite normalization of glycemic control. Persistent, hyperglycemia-induced epigenetic patterns are considered a central mechanism that activates metabolic memory; however, this has not been investigated in patient-derived fibroblasts from DFUs. We generated a cohort of patient-derived lines from DFU fibroblasts (DFUF), and site- and age-matched diabetic foot fibroblasts (DFF) and non-diabetic foot fibroblasts (NFF) to investigate global and genome-wide DNA methylation patterns using liquid chromatography/mass spectrometry and the Illumina Infinium HumanMethylation450K array. DFFs and DFUFs demonstrated significantly lower global DNA methylation compared to NFFs (p = 0.03). Hierarchical clustering of differentially methylated probes (DMPs, p = 0.05) showed that DFFs and DFUFs cluster together and separately from NFFs. Twenty-five percent of the same probes were identified as DMPs when individually comparing DFF and DFUF to NFF. Functional annotation identified enrichment of DMPs associated with genes critical to wound repair, including angiogenesis (p = 0.07) and extracellular matrix assembly (p = 0.035). Identification of sustained DNA methylation patterns in patient-derived fibroblasts after prolonged passage in normoglycemic conditions demonstrates persistent metabolic memory. These findings suggest that epigenetic-related metabolic memory may also underlie differences in wound healing phenotypes and can potentially identify therapeutic targets.
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Key Words
- ANOVA, Analysis of Variance
- BMP, Bone Morphogenic Protein
- COL4A1, Collagen 4A1
- DAVID, Database for Annotation, Visualization, and Integrative Discovery
- DCCT, Diabetes Control and Complications Trial
- DFF, Diabetic Foot Fibroblast
- DFU, Diabetic Foot Ulcer
- DFUF, Diabetic Foot Ulcer Fibroblast
- DHS, DNase Hypersensitive Site
- DMP, Differentially Methylated Probe
- DNA methylation
- ECM, Extracellular Matrix
- EDIC, Epidemiology of Diabetes Interventions and Complications
- ENCODE, Encyclopedia of DNA Elements
- FGF1, Fibroblast Growth Factor 1
- HbA1c, Hemoglobin A1c
- NFF, Non-diabetic Foot Fibroblast
- NHLF, Normal Human Lung Fibroblast
- PLAU, Plasminogen Activator Urokinase
- SNP, Single Nucleotide Polymorphism
- TFBS, Transcription Factor Binding Site
- TGFb, Transforming Growth Factor b
- TNFa, Tumor Necrosis Factor a
- TSS, Transcription Start Site
- UTR, Untranslated Region.
- dNTPs, deoxynucleotide
- diabetes
- diabetic foot ulcer
- epigenetics
- fibroblast
- metabolic memory
- wound healing
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Affiliation(s)
- Lara K Park
- a Department of Oral and Maxillofacial Pathology ; Oral Medicine and Craniofacial Pain ; Tufts University School of Dental Medicine ; Boston , MA USA
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Caramori ML, Kim Y, Natarajan R, Moore JH, Rich SS, Mychaleckyj JC, Kuriyama R, Kirkpatrick D, Mauer M. Differential Response to High Glucose in Skin Fibroblasts of Monozygotic Twins Discordant for Type 1 Diabetes. J Clin Endocrinol Metab 2015; 100:E883-9. [PMID: 25901990 PMCID: PMC5393515 DOI: 10.1210/jc.2014-4467] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CONTEXT Most epigenetic studies in diabetes compare normal cells in "high glucose" (HG) to cells in "normal glucose" (NG) and cells returned from HG to NG. Here we challenge this approach. OBJECTIVE The objective was to determine whether there were differences in gene expression in skin fibroblasts of monozygotic twins (MZT) discordant for type 1 diabetes (T1D). DESIGN Skin fibroblasts were grown in NG (5.5 mmol/L) and HG (25 mmol/L) for multiple passages. SETTING This study was conducted at the University of Minnesota. PATIENTS Patients were nine MZT pairs discordant for T1D. MAIN OUTCOME MEASURE(S) Gene expression was assessed by mRNA-Seq, using the Illumina HiSeq 2000 instrument. Pathway analysis tested directionally consistent group differences within the Kyoto Encyclopedia of Genes and Genomes pathways. RESULTS A total of 3308 genes were differentially expressed between NG and HG in T1D MZT vs 889 in non-T1D twins. DNA replication, proteasome, cell cycle, base excision repair, homologous recombination, pyrimidine metabolism, and spliceosome pathways had overrepresented genes with increased expression in T1D twins with P values ranging from 7.21 × 10(-10) to 1.39 × 10(-4). In a companion article, we demonstrate that these pathway changes are related to diabetic nephropathy risk. There were no pathways statistically significant differently expressed in nondiabetic twins in HG vs NG. CONCLUSIONS In vivo exposure to diabetes alters cells in a manner that markedly changes their in vitro responses to HG. These results highlight the importance of using cells directly derived from diabetic patients for studies examining the effects of HG in diabetes.
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Affiliation(s)
- M Luiza Caramori
- Departments of Medicine and Pediatrics (M.L.C., M.M.) and Pediatrics and Laboratory Medicine and Pathology (Y.K.), University of Minnesota, Minneapolis, Minnesota 55455; Department of Diabetes Complications, Obesity and Metabolism (R.N.), Beckman Research Institute, City of Hope, Duarte, California 91010; Department of Genetics (J.H.M.), Dartmouth College, Hanover, New Hampshire 03755; Departments of Public Health Sciences (S.S.R.) and Bioinformatics and Genetics (J.C.M.), University of Virginia, Charlottesville, Virginia 22908; and Department of Genetics, Cell Biology and Development (R.K., D.K.), University of Minnesota, Minneapolis, Minnesota 55455
| | - Youngki Kim
- Departments of Medicine and Pediatrics (M.L.C., M.M.) and Pediatrics and Laboratory Medicine and Pathology (Y.K.), University of Minnesota, Minneapolis, Minnesota 55455; Department of Diabetes Complications, Obesity and Metabolism (R.N.), Beckman Research Institute, City of Hope, Duarte, California 91010; Department of Genetics (J.H.M.), Dartmouth College, Hanover, New Hampshire 03755; Departments of Public Health Sciences (S.S.R.) and Bioinformatics and Genetics (J.C.M.), University of Virginia, Charlottesville, Virginia 22908; and Department of Genetics, Cell Biology and Development (R.K., D.K.), University of Minnesota, Minneapolis, Minnesota 55455
| | - Rama Natarajan
- Departments of Medicine and Pediatrics (M.L.C., M.M.) and Pediatrics and Laboratory Medicine and Pathology (Y.K.), University of Minnesota, Minneapolis, Minnesota 55455; Department of Diabetes Complications, Obesity and Metabolism (R.N.), Beckman Research Institute, City of Hope, Duarte, California 91010; Department of Genetics (J.H.M.), Dartmouth College, Hanover, New Hampshire 03755; Departments of Public Health Sciences (S.S.R.) and Bioinformatics and Genetics (J.C.M.), University of Virginia, Charlottesville, Virginia 22908; and Department of Genetics, Cell Biology and Development (R.K., D.K.), University of Minnesota, Minneapolis, Minnesota 55455
| | - Jason H Moore
- Departments of Medicine and Pediatrics (M.L.C., M.M.) and Pediatrics and Laboratory Medicine and Pathology (Y.K.), University of Minnesota, Minneapolis, Minnesota 55455; Department of Diabetes Complications, Obesity and Metabolism (R.N.), Beckman Research Institute, City of Hope, Duarte, California 91010; Department of Genetics (J.H.M.), Dartmouth College, Hanover, New Hampshire 03755; Departments of Public Health Sciences (S.S.R.) and Bioinformatics and Genetics (J.C.M.), University of Virginia, Charlottesville, Virginia 22908; and Department of Genetics, Cell Biology and Development (R.K., D.K.), University of Minnesota, Minneapolis, Minnesota 55455
| | - Stephen S Rich
- Departments of Medicine and Pediatrics (M.L.C., M.M.) and Pediatrics and Laboratory Medicine and Pathology (Y.K.), University of Minnesota, Minneapolis, Minnesota 55455; Department of Diabetes Complications, Obesity and Metabolism (R.N.), Beckman Research Institute, City of Hope, Duarte, California 91010; Department of Genetics (J.H.M.), Dartmouth College, Hanover, New Hampshire 03755; Departments of Public Health Sciences (S.S.R.) and Bioinformatics and Genetics (J.C.M.), University of Virginia, Charlottesville, Virginia 22908; and Department of Genetics, Cell Biology and Development (R.K., D.K.), University of Minnesota, Minneapolis, Minnesota 55455
| | - Josyf C Mychaleckyj
- Departments of Medicine and Pediatrics (M.L.C., M.M.) and Pediatrics and Laboratory Medicine and Pathology (Y.K.), University of Minnesota, Minneapolis, Minnesota 55455; Department of Diabetes Complications, Obesity and Metabolism (R.N.), Beckman Research Institute, City of Hope, Duarte, California 91010; Department of Genetics (J.H.M.), Dartmouth College, Hanover, New Hampshire 03755; Departments of Public Health Sciences (S.S.R.) and Bioinformatics and Genetics (J.C.M.), University of Virginia, Charlottesville, Virginia 22908; and Department of Genetics, Cell Biology and Development (R.K., D.K.), University of Minnesota, Minneapolis, Minnesota 55455
| | - Ryoko Kuriyama
- Departments of Medicine and Pediatrics (M.L.C., M.M.) and Pediatrics and Laboratory Medicine and Pathology (Y.K.), University of Minnesota, Minneapolis, Minnesota 55455; Department of Diabetes Complications, Obesity and Metabolism (R.N.), Beckman Research Institute, City of Hope, Duarte, California 91010; Department of Genetics (J.H.M.), Dartmouth College, Hanover, New Hampshire 03755; Departments of Public Health Sciences (S.S.R.) and Bioinformatics and Genetics (J.C.M.), University of Virginia, Charlottesville, Virginia 22908; and Department of Genetics, Cell Biology and Development (R.K., D.K.), University of Minnesota, Minneapolis, Minnesota 55455
| | - David Kirkpatrick
- Departments of Medicine and Pediatrics (M.L.C., M.M.) and Pediatrics and Laboratory Medicine and Pathology (Y.K.), University of Minnesota, Minneapolis, Minnesota 55455; Department of Diabetes Complications, Obesity and Metabolism (R.N.), Beckman Research Institute, City of Hope, Duarte, California 91010; Department of Genetics (J.H.M.), Dartmouth College, Hanover, New Hampshire 03755; Departments of Public Health Sciences (S.S.R.) and Bioinformatics and Genetics (J.C.M.), University of Virginia, Charlottesville, Virginia 22908; and Department of Genetics, Cell Biology and Development (R.K., D.K.), University of Minnesota, Minneapolis, Minnesota 55455
| | - Michael Mauer
- Departments of Medicine and Pediatrics (M.L.C., M.M.) and Pediatrics and Laboratory Medicine and Pathology (Y.K.), University of Minnesota, Minneapolis, Minnesota 55455; Department of Diabetes Complications, Obesity and Metabolism (R.N.), Beckman Research Institute, City of Hope, Duarte, California 91010; Department of Genetics (J.H.M.), Dartmouth College, Hanover, New Hampshire 03755; Departments of Public Health Sciences (S.S.R.) and Bioinformatics and Genetics (J.C.M.), University of Virginia, Charlottesville, Virginia 22908; and Department of Genetics, Cell Biology and Development (R.K., D.K.), University of Minnesota, Minneapolis, Minnesota 55455
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Dhliwayo N, Sarras MP, Luczkowski E, Mason SM, Intine RV. Parp inhibition prevents ten-eleven translocase enzyme activation and hyperglycemia-induced DNA demethylation. Diabetes 2014; 63:3069-76. [PMID: 24722243 PMCID: PMC4141369 DOI: 10.2337/db13-1916] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 04/01/2014] [Indexed: 01/24/2023]
Abstract
Studies from human cells, rats, and zebrafish have documented that hyperglycemia (HG) induces the demethylation of specific cytosines throughout the genome. We previously documented that a subset of these changes become permanent and may provide, in part, a mechanism for the persistence of complications referred to as the metabolic memory phenomenon. In this report, we present studies aimed at elucidating the molecular machinery that is responsible for the HG-induced DNA demethylation observed. To this end, RNA expression and enzymatic activity assays indicate that the ten-eleven translocation (Tet) family of enzymes are activated by HG. Furthermore, through the detection of intermediates generated via conversion of 5-methyl-cytosine back to the unmethylated form, the data were consistent with the use of the Tet-dependent iterative oxidation pathway. In addition, evidence is provided that the activity of the poly(ADP-ribose) polymerase (Parp) enzyme is required for activation of Tet activity because the use of a Parp inhibitor prevented demethylation of specific loci and the accumulation of Tet-induced intermediates. Remarkably, this inhibition was accompanied by a complete restoration of the tissue regeneration deficit that is also induced by HG. The ultimate goal of this work is to provide potential new avenues for therapeutic discovery.
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Affiliation(s)
- Nyembezi Dhliwayo
- Dr. William M. Scholl College of Podiatric Medicine, Rosalind Franklin University of Medicine and Science, North Chicago, IL
| | - Michael P Sarras
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL
| | - Ernest Luczkowski
- Dr. William M. Scholl College of Podiatric Medicine, Rosalind Franklin University of Medicine and Science, North Chicago, IL
| | - Samantha M Mason
- Dr. William M. Scholl College of Podiatric Medicine, Rosalind Franklin University of Medicine and Science, North Chicago, IL
| | - Robert V Intine
- Dr. William M. Scholl College of Podiatric Medicine, Rosalind Franklin University of Medicine and Science, North Chicago, IL Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL
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Kiyama R, Zhu Y. DNA microarray-based gene expression profiling of estrogenic chemicals. Cell Mol Life Sci 2014; 71:2065-82. [PMID: 24399289 PMCID: PMC11113397 DOI: 10.1007/s00018-013-1544-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/06/2013] [Accepted: 12/16/2013] [Indexed: 12/31/2022]
Abstract
We summarize updated information about DNA microarray-based gene expression profiling by focusing on its application to estrogenic chemicals. First, estrogenic chemicals, including natural/industrial estrogens and phytoestrogens, and the methods for detection and evaluation of estrogenic chemicals were overviewed along with a comprehensive list of estrogenic chemicals of natural or industrial origin. Second, gene expression profiling of chemicals using a focused microarray containing estrogen-responsive genes is summarized. Third, silent estrogens, a new type of estrogenic chemicals characterized by their estrogenic gene expression profiles without growth stimulative or inhibitory effects, have been identified so far exclusively by DNA microarray assay. Lastly, the prospect of a microarray assay is discussed, including issues such as commercialization, future directions of applications and quality control methods.
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Affiliation(s)
- Ryoiti Kiyama
- Signaling Molecules Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan,
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16
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Liu H, Yu S, Zhang H, Xu J. Identification of nitric oxide as an endogenous inhibitor of 26S proteasomes in vascular endothelial cells. PLoS One 2014; 9:e98486. [PMID: 24853093 PMCID: PMC4031199 DOI: 10.1371/journal.pone.0098486] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 05/02/2014] [Indexed: 01/22/2023] Open
Abstract
The 26S proteasome plays a fundamental role in almost all eukaryotic cells, including vascular endothelial cells. However, it remains largely unknown how proteasome functionality is regulated in the vasculature. Endothelial nitric oxide (NO) synthase (eNOS)-derived NO is known to be essential to maintain endothelial homeostasis. The aim of the present study was to establish the connection between endothelial NO and 26S proteasome functionality in vascular endothelial cells. The 26S proteasome reporter protein levels, 26S proteasome activity, and the O-GlcNAcylation of Rpt2, a key subunit of the proteasome regulatory complex, were assayed in 26S proteasome reporter cells, human umbilical vein endothelial cells (HUVEC), and mouse aortic tissues isolated from 26S proteasome reporter and eNOS knockout mice. Like the other selective NO donors, NO derived from activated eNOS (by pharmacological and genetic approach) increased O-GlcNAc modification of Rpt2, reduced proteasome chymotrypsin-like activity, and caused 26S proteasome reporter protein accumulation. Conversely, inactivation of eNOS reversed all the effects. SiRNA knockdown of O-GlcNAc transferase (OGT), the key enzyme that catalyzes protein O-GlcNAcylation, abolished NO-induced effects. Consistently, adenoviral overexpression of O-GlcNAcase (OGA), the enzyme catalyzing the removal of the O-GlcNAc group, mimicked the effects of OGT knockdown. Finally, compared to eNOS wild type aortic tissues, 26S proteasome reporter mice lacking eNOS exhibited elevated 26S proteasome functionality in parallel with decreased Rpt2 O-GlcNAcylation, without changing the levels of Rpt2 protein. In conclusion, the eNOS-derived NO functions as a physiological suppressor of the 26S proteasome in vascular endothelial cells.
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Affiliation(s)
- Hongtao Liu
- Section of Endocrinology, Department of Medicine and Harold Hamm Oklahoma Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Shujie Yu
- Section of Endocrinology, Department of Medicine and Harold Hamm Oklahoma Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Hua Zhang
- Section of Endocrinology, Department of Medicine and Harold Hamm Oklahoma Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Jian Xu
- Section of Endocrinology, Department of Medicine and Harold Hamm Oklahoma Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
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17
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Miao F, Chen Z, Genuth S, Paterson A, Zhang L, Wu X, Li SM, Cleary P, Riggs A, Harlan DM, Lorenzi G, Kolterman O, Sun W, Lachin JM, Natarajan R. Evaluating the role of epigenetic histone modifications in the metabolic memory of type 1 diabetes. Diabetes 2014; 63:1748-62. [PMID: 24458354 PMCID: PMC3994951 DOI: 10.2337/db13-1251] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We assessed whether epigenetic histone posttranslational modifications are associated with the prolonged beneficial effects (metabolic memory) of intensive versus conventional therapy during the Diabetes Control and Complications Trial (DCCT) on the progression of microvascular outcomes in the long-term Epidemiology of Diabetes Interventions and Complications (EDIC) study. We performed chromatin immunoprecipitation linked to promoter tiling arrays to profile H3 lysine-9 acetylation (H3K9Ac), H3 lysine-4 trimethylation (H3K4Me3), and H3K9Me2 in blood monocytes and lymphocytes obtained from 30 DCCT conventional treatment group subjects (case subjects: mean DCCT HbA1c level >9.1% [76 mmol/mol] and progression of retinopathy or nephropathy by EDIC year 10 of follow-up) versus 30 DCCT intensive treatment subjects (control subjects: mean DCCT HbA1c level <7.3% [56 mmol/mol] and without progression of retinopathy or nephropathy). Monocytes from case subjects had statistically greater numbers of promoter regions with enrichment in H3K9Ac (active chromatin mark) compared with control subjects (P = 0.0096). Among the patients in the two groups combined, monocyte H3K9Ac was significantly associated with the mean HbA1c level during the DCCT and EDIC (each P < 2.2E-16). Of note, the top 38 case hyperacetylated promoters (P < 0.05) included >15 genes related to the nuclear factor-κB inflammatory pathway and were enriched in genes related to diabetes complications. These results suggest an association between HbA1c level and H3K9Ac, and a possible epigenetic explanation for metabolic memory in humans.
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Affiliation(s)
- Feng Miao
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA
| | - Zhuo Chen
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA
| | - Saul Genuth
- School of Medicine, Case Western Reserve University, Cleveland, OH
| | - Andrew Paterson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lingxiao Zhang
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA
| | - Xiwei Wu
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA
| | - Sierra Min Li
- Department of Biostatistics, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA
| | - Patricia Cleary
- The Biostatistics Center, George Washington University, Washington, DC
| | - Arthur Riggs
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA
| | - David M. Harlan
- Department of Medicine, University of Massachusetts School of Medicine, Worcester, MA
| | - Gayle Lorenzi
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Orville Kolterman
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Wanjie Sun
- The Biostatistics Center, George Washington University, Washington, DC
| | - John M. Lachin
- The Biostatistics Center, George Washington University, Washington, DC
| | - Rama Natarajan
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA
- Corresponding author: Rama Natarajan,
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Husni NR, Jones IV AR, Simmons AL, Corkey BE. Fibroblasts from type 1 diabetics exhibit enhanced Ca(2+) mobilization after TNF or fat exposure. PLoS One 2014; 9:e87068. [PMID: 24466329 PMCID: PMC3900712 DOI: 10.1371/journal.pone.0087068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 12/24/2013] [Indexed: 01/24/2023] Open
Abstract
The effects of cytokine and fatty acid treatment on signal transduction in dermal fibroblasts from type 1 diabetics and matched controls were compared. Chronic exposure to TNF, accentuated Ca2+ mobilization in response to bradykinin (BK) in cells from both controls and diabetics; responses were three-fold greater in cells from diabetics than in controls. Similarly, with chronic exposure to IL-1β, BK-induced Ca2+ mobilization was accentuated in cells from type 1 diabetics compared to the controls. Pretreatment with the protein synthesis inhibitor cycloheximide or the protein kinase C inhibitor calphostin C prior to the addition of TNF completely abrogated the TNF-induced increment in peak bradykinin response. Ca2+ transients induced by depleting endoplasmic reticulum (ER) Ca2+ with thapsigargin were also greater in TNF treated fibroblasts than in untreated cells, with greater increases in cells from diabetics. Exposing fibroblasts for 48 hours to 2 mM oleate also increased both the peak bradykinin response and the TNF-induced increment in peak response, which were significantly greater in diabetics than controls. These data indicate that cells from diabetic patients acquire elevated ER Ca2+ stores in response to both cytokines and free fatty acids,and thus exhibit greater sensitivity to environmental inflammatory stimuli and elevated lipids.
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Affiliation(s)
- Nicholas R. Husni
- Obesity Research Center, Evans Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Albert R. Jones IV
- Obesity Research Center, Evans Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Amber L. Simmons
- Obesity Research Center, Evans Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Barbara E. Corkey
- Obesity Research Center, Evans Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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Novel Therapeutic Strategy With Hypoxia-Inducible Factors via Reversible Epigenetic Regulation Mechanisms in Progressive Tubulointerstitial Fibrosis. Semin Nephrol 2013; 33:375-82. [DOI: 10.1016/j.semnephrol.2013.05.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Abstract
Recent estimates indicate that diabetes mellitus currently affects more than 10 % of the world's population. Evidence from both the laboratory and large scale clinical trials has revealed that prolonged hyperglycemia induces chronic complications which persist and progress unimpeded even when glycemic control is pharmaceutically achieved via the phenomenon of metabolic memory. The epigenome is comprised of all chromatin modifications including post translational histone modification, expression control via miRNAs and the methylation of cytosine within DNA. Modifications of these epigenetic marks not only allow cells and organisms to quickly respond to changing environmental stimuli but also confer the ability of the cell to "memorize" these encounters. As such, these processes have gained much attention as potential molecular mechanisms underlying metabolic memory and chronic diabetic complications. Here we present a review of the very recent literature published pertaining to this subject.
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Affiliation(s)
- Robert V Intine
- Dr. William M. Scholl College of Podiatric Medicine, Rosalind Franklin University of Medicine and Science, Chicago, IL 60064, USA.
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Abstract
The classical twin study has been a powerful heuristic in biomedical, psychiatric and behavioural research for decades. Twin registries worldwide have collected biological material and longitudinal phenotypic data on tens of thousands of twins, providing a valuable resource for studying complex phenotypes and their underlying biology. In this Review, we consider the continuing value of twin studies in the current era of molecular genetic studies. We conclude that classical twin methods combined with novel technologies represent a powerful approach towards identifying and understanding the molecular pathways that underlie complex traits.
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Gnudi L. Cellular and molecular mechanisms of diabetic glomerulopathy. Nephrol Dial Transplant 2012; 27:2642-9. [DOI: 10.1093/ndt/gfs121] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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