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Berardo C, Calcaterra V, Mauri A, Carelli S, Messa L, Destro F, Rey F, Cordaro E, Pelizzo G, Zuccotti G, Cereda C. Subcutaneous Adipose Tissue Transcriptome Highlights Specific Expression Profiles in Severe Pediatric Obesity: A Pilot Study. Cells 2023; 12:cells12081105. [PMID: 37190014 DOI: 10.3390/cells12081105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/05/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
The prevalence of pediatric obesity is rising rapidly worldwide, and "omic" approaches are helpful in investigating the molecular pathophysiology of obesity. This work aims to identify transcriptional differences in the subcutaneous adipose tissue (scAT) of children with overweight (OW), obesity (OB), or severe obesity (SV) compared with those of normal weight (NW). Periumbilical scAT biopsies were collected from 20 male children aged 1-12 years. The children were stratified into the following four groups according to their BMI z-scores: SV, OB, OW, and NW. scAT RNA-Seq analyses were performed, and a differential expression analysis was conducted using the DESeq2 R package. A pathways analysis was performed to gain biological insights into gene expression. Our data highlight the significant deregulation in both coding and non-coding transcripts in the SV group when compared with the NW, OW, and OB groups. A KEGG pathway analysis showed that coding transcripts were mainly involved in lipid metabolism. A GSEA analysis revealed the upregulation of lipid degradation and metabolism in SV vs. OB and SV vs. OW. Bioenergetic processes and the catabolism of branched-chain amino acids were upregulated in SV compared with OB, OW, and NW. In conclusion, we report for the first time that a significant transcriptional deregulation occurs in the periumbilical scAT of children with severe obesity compared with those of normal weight or those with overweight or mild obesity.
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Affiliation(s)
- Clarissa Berardo
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Science, University of Milan, 20157 Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Valeria Calcaterra
- Pediatric and Adolescent Unit, Department of Internal Medicine, University of Pavia, 27100 Pavia, Italy
- Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Alessia Mauri
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Science, University of Milan, 20157 Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Stephana Carelli
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Science, University of Milan, 20157 Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Letizia Messa
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milan, Italy
| | - Francesca Destro
- Surgery Department, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Federica Rey
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Science, University of Milan, 20157 Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Erika Cordaro
- Pediatric and Adolescent Unit, Department of Internal Medicine, University of Pavia, 27100 Pavia, Italy
| | - Gloria Pelizzo
- Surgery Department, Buzzi Children's Hospital, 20154 Milan, Italy
- Department of Biomedical and Clinical Science, University of Milan, 20157 Milan, Italy
| | - Gianvincenzo Zuccotti
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Science, University of Milan, 20157 Milan, Italy
- Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
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2
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Unconventional metabolites in chromatin regulation. Biosci Rep 2022; 42:230604. [PMID: 34988581 PMCID: PMC8777195 DOI: 10.1042/bsr20211558] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Chromatin, the complex of DNA and histone proteins, serves as a main integrator of cellular signals. Increasing evidence links cellular functional to chromatin state. Indeed, different metabolites are emerging as modulators of chromatin function and structure. Alterations in chromatin state are decisive for regulating all aspects of genome function and ultimately have the potential to produce phenotypic changes. Several metabolites such as acetyl-CoA, S-adenosylmethionine (SAM) or adenosine triphosphate (ATP) have now been well characterized as main substrates or cofactors of chromatin-modifying enzymes. However, there are other metabolites that can directly interact with chromatin influencing its state or that modulate the properties of chromatin regulatory factors. Also, there is a growing list of atypical enzymatic and nonenzymatic chromatin modifications that originate from different cellular pathways that have not been in the limelight of chromatin research. Here, we summarize different properties and functions of uncommon regulatory molecules originating from intermediate metabolism of lipids, carbohydrates and amino acids. Based on the various modes of action on chromatin and the plethora of putative, so far not described chromatin-regulating metabolites, we propose that there are more links between cellular functional state and chromatin regulation to be discovered. We hypothesize that these connections could provide interesting starting points for interfering with cellular epigenetic states at a molecular level.
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4
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Fernandes V, Teles K, Ribeiro C, Treptow W, Santos G. Fat nucleosome: Role of lipids on chromatin. Prog Lipid Res 2018; 70:29-34. [PMID: 29678609 DOI: 10.1016/j.plipres.2018.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/18/2018] [Accepted: 04/16/2018] [Indexed: 01/01/2023]
Abstract
Structural changes in chromatin regulate gene expression and define phenotypic outcomes. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Most recently, the formation of condensed chromatin regions based on phase-separation in the cell, a basic physical mechanism, was proposed. Increased understanding of the mechanisms of interaction between chromatin and lipids suggest that small lipid molecules, such as cholesterol and short-chain fatty acids, can regulate important nuclear functions. New biophysical data has suggested that cholesterol interacts with nucleosome through multiple binding sites and affects chromatin structure in vitro. Regardless of the mechanism of how lipids bind to chromatin, there is currently little awareness that lipids may be stored in chromatin and influence its state. Focusing on lipids that bind to nuclear receptors, clinically relevant transcription factors, we discuss the potential interactions of the nucleosome with steroid hormones, bile acids and fatty acids, which suggest that other lipid chemotypes may also impact chromatin structure through binding to common sites on the nucleosome. Herein, we review the main impacts of lipids on the nuclear environment, emphasizing its role on chromatin architecture. We postulate that lipids that bind to nucleosomes and affect chromatin states are likely to be worth investigating as tools to modify disease phenotypes at a molecular level.
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Affiliation(s)
- Vinicius Fernandes
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília 70919-970, Brazil; Laboratório de Biologia Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, DF 70910-900, Brasília, Brazil
| | - Kaian Teles
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília 70919-970, Brazil
| | - Camyla Ribeiro
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília 70919-970, Brazil
| | - Werner Treptow
- Laboratório de Biologia Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, DF 70910-900, Brasília, Brazil
| | - Guilherme Santos
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília 70919-970, Brazil.
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5
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Silva ITG, Fernandes V, Souza C, Treptow W, Santos GM. Biophysical studies of cholesterol effects on chromatin. J Lipid Res 2017; 58:934-940. [PMID: 28331000 PMCID: PMC5408612 DOI: 10.1194/jlr.m074997] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/20/2017] [Indexed: 11/20/2022] Open
Abstract
Changes in chromatin structure regulate gene expression and genome maintenance. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Previous work indicated that cholesterol, a ubiquitous cellular lipid, may bind to chromatin in vivo, suggesting a potential function for lipids in modulating chromatin architecture. However, the molecular mechanisms of cholesterol’s action on chromatin structure have remained unclear. Here, we explored the biophysical impact of cholesterol on nucleosome and chromatin fibers reconstituted in vitro and characterized in silico the cholesterol binding to the nucleosome. Our findings support that cholesterol assists 10 and 30 nm chromatin formation and induces folding of long chromatin fibers as a result of direct interaction of the cholesterol to six nucleosomal binding sites.
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Affiliation(s)
- Isabel T G Silva
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília, Brazil
| | - Vinícius Fernandes
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília, Brazil.,Laboratório de Biologia Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Caio Souza
- Laboratório de Biologia Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Werner Treptow
- Laboratório de Biologia Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Guilherme M Santos
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília, Brazil
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6
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Waterland RA, Rached MT. Developmental establishment of epigenotype: a role for dietary fatty acids? SCANDINAVIAN JOURNAL OF FOOD & NUTRITION 2016. [DOI: 10.1080/17482970601066488] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Robert A. Waterland
- Departments of Pediatrics and Molecular and Human GeneticsBaylor College of Medicine, USDA Children's Nutrition Research CenterHoustonTexasUSA
| | - Marie-Therese Rached
- Departments of Pediatrics and Molecular and Human GeneticsBaylor College of Medicine, USDA Children's Nutrition Research CenterHoustonTexasUSA
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7
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Massart R, Mignon V, Stanic J, Munoz-Tello P, Becker JAJ, Kieffer BL, Darmon M, Sokoloff P, Diaz J. Developmental and adult expression patterns of the G-protein-coupled receptor GPR88 in the rat: Establishment of a dual nuclear-cytoplasmic localization. J Comp Neurol 2016; 524:2776-802. [PMID: 26918661 DOI: 10.1002/cne.23991] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 01/31/2023]
Abstract
GPR88 is a neuronal cerebral orphan G-protein-coupled receptor (GPCR) that has been linked to various psychiatric disorders. However, no extensive description of its localization has been provided so far. Here, we investigate the spatiotemporal expression of the GPR88 in prenatal and postnatal rat tissues by using in situ hybridization and immunohistochemistry. GPR88 protein was initially detected at embryonic day 16 (E16) in the striatal primordium. From E16-E20 to adulthood, the highest expression levels of both protein and mRNA were observed in striatum, olfactory tubercle, nucleus accumbens, amygdala, and neocortex, whereas in spinal cord, pons, and medulla GPR88 expression remains discrete. We observed an intracellular redistribution of GPR88 during cortical lamination. In the cortical plate of the developing cortex, GPR88 presents a classical GPCR plasma membrane/cytoplasmic localization that shifts, on the day of birth, to nuclei of neurons progressively settling in layers V to II. This intranuclear localization remains throughout adulthood and was also detected in monkey and human cortex as well as in the amygdala and hypothalamus of rats. Apart from the central nervous system, GPR88 was transiently expressed at high levels in peripheral tissues, including adrenal cortex (E16-E21) and cochlear ganglia (E19-P3), and also at moderate levels in retina (E18-E19) and spleen (E21-P7). The description of the GPR88 anatomical expression pattern may provide precious functional insights into this novel receptor. Furthermore, the GRP88 nuclear localization suggests nonclassical GPCR modes of action of the protein that could be relevant for cortical development and psychiatric disorders. J. Comp. Neurol. 524:2776-2802, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Renaud Massart
- INSERM UMR894, Centre de Psychiatrie et Neurosciences, Université Paris Descartes, 75014, Paris, France.,Neurology-Psychiatry Department, Pierre Fabre Research Institute, 81100, Castres, France
| | - Virginie Mignon
- INSERM UMR894, Centre de Psychiatrie et Neurosciences, Université Paris Descartes, 75014, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
| | - Jennifer Stanic
- INSERM UMR894, Centre de Psychiatrie et Neurosciences, Université Paris Descartes, 75014, Paris, France
| | - Paola Munoz-Tello
- INSERM UMR894, Centre de Psychiatrie et Neurosciences, Université Paris Descartes, 75014, Paris, France
| | - Jerôme A J Becker
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, CNRS, INSERM, 67400, Illkirch-Graffenstaden, France
| | - Brigitte L Kieffer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, CNRS, INSERM, 67400, Illkirch-Graffenstaden, France
| | - Michèle Darmon
- INSERM UMR894, Centre de Psychiatrie et Neurosciences, Université Paris Descartes, 75014, Paris, France
| | - Pierre Sokoloff
- Neurology-Psychiatry Department, Pierre Fabre Research Institute, 81100, Castres, France
| | - Jorge Diaz
- INSERM UMR894, Centre de Psychiatrie et Neurosciences, Université Paris Descartes, 75014, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
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8
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Ibeagha-Awemu EM, Zhao X. Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs. Front Genet 2015; 6:302. [PMID: 26442116 PMCID: PMC4585011 DOI: 10.3389/fgene.2015.00302] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 09/11/2015] [Indexed: 12/30/2022] Open
Abstract
Improvement in animal productivity has been achieved over the years through careful breeding and selection programs. Today, variations in the genome are gaining increasing importance in livestock improvement strategies. Genomic information alone, however, explains only a part of the phenotypic variance in traits. It is likely that a portion of the unaccounted variance is embedded in the epigenome. The epigenome encompasses epigenetic marks such as DNA methylation, histone tail modifications, chromatin remodeling, and other molecules that can transmit epigenetic information such as non-coding RNA species. Epigenetic factors respond to external or internal environmental cues such as nutrition, pathogens, and climate, and have the ability to change gene expression leading to emergence of specific phenotypes. Accumulating evidence shows that epigenetic marks influence gene expression and phenotypic outcome in livestock species. This review examines available evidence of the influence of epigenetic marks on livestock (cattle, sheep, goat, and pig) traits and discusses the potential for consideration of epigenetic markers in livestock improvement programs. However, epigenetic research activities on farm animal species are currently limited partly due to lack of recognition, funding and a global network of researchers. Therefore, considerable less attention has been given to epigenetic research in livestock species in comparison to extensive work in humans and model organisms. Elucidating therefore the epigenetic determinants of animal diseases and complex traits may represent one of the principal challenges to use epigenetic markers for further improvement of animal productivity.
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Affiliation(s)
- Eveline M. Ibeagha-Awemu
- Dairy and Swine Research and Development Centre, Agriculture and Agri-Food CanadaSherbrooke, QC, Canada
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-De-BellevueQC, Canada
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9
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Maghbooli Z, Larijani B, Emamgholipour S, Amini M, Keshtkar A, Pasalar P. Aberrant DNA methylation patterns in diabetic nephropathy. J Diabetes Metab Disord 2014; 13:69. [PMID: 25028646 PMCID: PMC4099150 DOI: 10.1186/2251-6581-13-69] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 06/11/2014] [Indexed: 12/18/2022]
Abstract
Background The aim of this study was to evaluate whether global levels of DNA methylation status were associated with albuminuria and progression of diabetic nephropathy in a case-control study of 123 patients with type 2 diabetes- 53 patients with albuminuria and 70 patients without albuminuria. Methods The 5-methyl cytosine content was assessed by reverse phase high pressure liquid chromatography (RP-HPLC) of peripheral blood mononuclear cells to determine individual global DNA methylation status in two groups. Results Global DNA methylation levels were significantly higher in patients with albuminuria compared with those in normal range of albuminuria (p = 0.01). There were significant differences in global levels of DNA methylation in relation to albuminuria (p = 0.028) and an interesting pattern of increasing global levels of DNA methylation in terms of albuminuria severity. In patients with micro- and macro albuminuria, we found no significant correlations between global DNA methylation levels and duration of diabetes (p > 0.05). In both sub groups, there were not significant differences between global DNA methylation levels with good and poor glycaemic control (p > 0.05). In addition, in patients with albuminuria, no differences in DNA methylation levels were observed between patients with and without other risk factors including age, gender, hypertension, dyslipidaemia and obesity. Conclusions These data may be helpful in further studies to develop novel biomarkers and new strategies for clinical care of patients at risk of diabetic nephropathy.
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Affiliation(s)
- Zhila Maghbooli
- Endocrinology and Metabolism Clinical Sciences Institute of Tehran University of medical sciences, EMRI, 5th floor, Shariati Hospital, North Karegar Avenue, P.O Box: 1411413137, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Clinical Sciences Institute of Tehran University of medical sciences, EMRI, 5th floor, Shariati Hospital, North Karegar Avenue, P.O Box: 1411413137, Tehran, Iran
| | - Solaleh Emamgholipour
- Clinical Biochemistry Department, School of Medicine, Faculty of Medicine Tehran University of medical sciences, EMRI, 5th floor, Shariati Hospital, North Karegar Avenue, P.O Box: 1411413137, Tehran, Iran
| | - Manochehr Amini
- Nephrology Department, Shariati Hospital, Tehran University of Medical Sciences, EMRI, 5th floor, Shariati Hospital, North Karegar Avenue, P.O Box: 1411413137, Tehran, Iran
| | - Abbasali Keshtkar
- Endocrinology and Metabolism Clinical Sciences Institute of Tehran University of medical sciences, EMRI, 5th floor, Shariati Hospital, North Karegar Avenue, P.O Box: 1411413137, Tehran, Iran
| | - Parvin Pasalar
- Clinical Biochemistry Department, School of Medicine, Faculty of Medicine Tehran University of medical sciences, EMRI, 5th floor, Shariati Hospital, North Karegar Avenue, P.O Box: 1411413137, Tehran, Iran
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10
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Principles of electrostatic interactions and self-assembly in lipid/peptide/DNA systems: applications to gene delivery. Adv Colloid Interface Sci 2014; 205:221-9. [PMID: 24055029 DOI: 10.1016/j.cis.2013.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/23/2013] [Accepted: 08/23/2013] [Indexed: 11/22/2022]
Abstract
Recently, great progress has been achieved in development of a wide variety of formulations for gene delivery in vitro and in vivo, which include lipids, peptides and DNA (LPD). Additionally, application of natural histone-DNA complexes (chromatin) in combination with transfection lipids has been suggested as a potential route for gene delivery (chromofection). However, the thermodynamic mechanisms responsible for formation of the ternary lipid-peptide-DNA supramolecular structures have rarely been analyzed. Using recent experimental studies on LPD complexes (including mixtures of chromatin with cationic lipids) and general polyelectrolyte theory, we review and analyze the major determinants defining the internal structure, particle composition and size, surface charge and ultimately, transfection properties of the LPD formulations.
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11
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Pliss A, Kuzmin AN, Kachynski AV, Jiang H, Hu Z, Ren Y, Feng J, Prasad PN. Nucleolar Molecular Signature of Pluripotent Stem Cells. Anal Chem 2013; 85:3545-52. [DOI: 10.1021/ac303806j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Artem Pliss
- Institute for Lasers,
Photonics
and Biophotonics, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
| | - Andrey N. Kuzmin
- Institute for Lasers,
Photonics
and Biophotonics, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
| | - Aliaksandr V. Kachynski
- Institute for Lasers,
Photonics
and Biophotonics, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
| | - Houbo Jiang
- Department of Physiology and
Biophysics, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Zhixing Hu
- Department of Physiology and
Biophysics, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Yong Ren
- Department of Physiology and
Biophysics, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Jian Feng
- Department of Physiology and
Biophysics, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Paras N. Prasad
- Institute for Lasers,
Photonics
and Biophotonics, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
- Department of Chemistry, University
at Buffalo, State University of New York, Buffalo, New York 14260, United States
- Department of Chemistry, Korea University, Seoul, 136-701, Korea
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12
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Berezhnoy NV, Lundberg D, Korolev N, Lu C, Yan J, Miguel M, Lindman B, Nordenskiöld L. Supramolecular Organization in Self-Assembly of Chromatin and Cationic Lipid Bilayers is Controlled by Membrane Charge Density. Biomacromolecules 2012; 13:4146-57. [DOI: 10.1021/bm301436x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Nikolay V. Berezhnoy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| | - Dan Lundberg
- Department
of Chemistry, University of Coimbra, Rua
Larga, 3004-535 Coimbra,
Portugal
- Department of Physical
Chemistry,
Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| | - Chenning Lu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| | - Jiang Yan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| | - Maria Miguel
- Department
of Chemistry, University of Coimbra, Rua
Larga, 3004-535 Coimbra,
Portugal
| | - Björn Lindman
- Department
of Chemistry, University of Coimbra, Rua
Larga, 3004-535 Coimbra,
Portugal
- Department of Physical
Chemistry,
Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
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McGuinness D, McGlynn LM, Johnson PCD, MacIntyre A, Batty GD, Burns H, Cavanagh J, Deans KA, Ford I, McConnachie A, McGinty A, McLean JS, Millar K, Packard CJ, Sattar NA, Tannahill C, Velupillai YN, Shiels PG. Socio-economic status is associated with epigenetic differences in the pSoBid cohort. Int J Epidemiol 2012; 41:151-60. [PMID: 22253320 DOI: 10.1093/ije/dyr215] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Epigenetic programming and epigenetic mechanisms driven by environmental factors are thought to play an important role in human health and ageing. Global DNA methylation has been postulated as an epigenetic marker for epidemiological studies as it is reflective of changes in gene expression linked to disease. How epigenetic mechanisms are affected by psychological, sociological and biological determinants of health still remains unclear. The aim of this study was to investigate the relationship between socio-economic and lifestyle factors and epigenetic status, as measured by global DNA methylation content, in the pSoBid cohort, which is characterized by an extreme socio-economic and health gradient. METHODS DNA was extracted from peripheral blood leukocytes using the Maxwell® 16 System and Maxwell® 16 Blood DNA Purification kit (Promega, UK). Global DNA methylation was assessed using Methylamp™ Global DNA Methylation Quantification Ultra kit (Epigentek, USA). Associations between global DNA methylation and socio-economic and lifestyle factors were investigated in linear regression models. RESULTS Global DNA hypomethylation was observed in the most socio-economically deprived subjects. Job status demonstrated a similar relationship, with manual workers having 24% lower DNA methylation content than non-manual. Additionally, associations were found between global DNA methylation content and biomarkers of cardiovascular disease (CVD) and inflammation, including fibrinogen and interleukin-6 (IL-6), after adjustment for socio-economic factors. CONCLUSIONS This study has indicated an association between epigenetic status and socio-economic status (SES). This relationship has direct implications for population health and is reflected in further associations between global DNA methylation content and emerging biomarkers of CVD.
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Affiliation(s)
- Dagmara McGuinness
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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14
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Pliss A, Kuzmin AN, Kachynski AV, Prasad PN. Nonlinear optical imaging and Raman microspectrometry of the cell nucleus throughout the cell cycle. Biophys J 2011; 99:3483-91. [PMID: 21081098 DOI: 10.1016/j.bpj.2010.06.069] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 06/28/2010] [Accepted: 06/30/2010] [Indexed: 11/17/2022] Open
Abstract
Fundamental understanding of cellular processes at molecular level is of considerable importance in cell biology as well as in biomedical disciplines for early diagnosis of infection and cancer diseases, and for developing new molecular medicine-based therapies. Modern biophotonics offers exclusive capabilities to obtain information on molecular composition, organization, and dynamics in a cell by utilizing a combination of optical spectroscopy and optical imaging. We introduce here a combination of Raman microspectrometry, together with coherent anti-Stokes Raman scattering (CARS) and two-photon excited fluorescence (TPEF) nonlinear optical microscopy, to study macromolecular organization of the nucleus throughout the cell cycle. Site-specific concentrations of proteins, DNA, RNA, and lipids were determined in nucleoli, nucleoplasmic transcription sites, nuclear speckles, constitutive heterochromatin domains, mitotic chromosomes, and extrachromosomal regions of mitotic cells by quantitative confocal Raman microspectrometry. A surprising finding, obtained in our study, is that the local concentration of proteins does not increase during DNA compaction. We also demonstrate that postmitotic DNA decondensation is a gradual process, continuing for several hours. The quantitative Raman spectroscopic analysis was corroborated with CARS/TPEF multimodal imaging to visualize the distribution of protein, DNA, RNA, and lipid macromolecules throughout the cell cycle.
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Affiliation(s)
- Artem Pliss
- University at Buffalo, State University of New York, Buffalo, NY, USA
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15
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Signaling mechanisms in the restoration of impaired immune function due to diet-induced obesity. Proc Natl Acad Sci U S A 2011; 108:2867-72. [PMID: 21282635 DOI: 10.1073/pnas.1019270108] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Our previous data have linked obesity with immune dysfunction. It is known that physical exercise with dietary control has beneficial effects on immune function and the comorbidities of obesity. However, the mechanisms underlying the improvement of immune function in obesity after physical exercise with dietary control remain unknown. Here we show that moderate daily exercise with dietary control restores the impaired cytokine responses in diet-induced obese (DIO) mice and improves the resolution of Porphyromonas gingivalis-induced periodontitis. This restoration of immune responses is related to the reduction of circulating free fatty acids (FFAs) and TNF. Both FFAs and TNF induce an Akt inhibitor, carboxyl-terminal modulator protein (CTMP). The expression of CTMP is also observed increased in bone marrow-derived macrophages (BMMΦ) from DIO mice and restored after moderate daily exercise with dietary control. Toll-like receptor 2 (TLR2), which increases CTMP induction by FFAs, is inhibited in BMMΦ from DIO mice or after either FFA or TNF treatment, but unexpectedly is not restored by moderate daily exercise with dietary control. Furthermore, BMMΦ from DIO mice display reduced histone H3 (Lys-9) acetylation and NF-κB recruitment to TNF, IL-10, and TLR2 promoters after P. gingivalis infection. However, moderate daily exercise with dietary control restores these defects at promoters for TNF and IL-10, but not for TLR2. Thus, metabolizing FFAs and TNF by moderate daily exercise with dietary control improves innate immune responses to infection in DIO mice via restoration of CTMP and chromatin modification.
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16
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Abstract
Type 1 and Type 2 diabetes are complex diseases associated with multiple complications, and both genetic and environmental factors have been implicated in these pathologies. While numerous studies have provided a wealth of knowledge regarding the genetics of diabetes, the mechanistic pathways leading to diabetes and its complications remain only partly understood. Studying the role of epigenetics in diabetic complications can provide valuable new insights to clarify the interplay between genes and the environment. DNA methylation and histone modifications in nuclear chromatin can generate epigenetic information as another layer of gene transcriptional regulation sensitive to environmental signals. Recent evidence shows that key biochemical pathways and epigenetic chromatin histone methylation patterns are altered in target cells under diabetic conditions and might also be involved in the metabolic memory phenomenon noted in clinical trials and animal studies. New therapeutic targets and treatment options could be uncovered from an in-depth study of the epigenetic mechanisms that might perpetuate diabetic complications despite glycemic control.
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Affiliation(s)
- Louisa M Villeneuve
- Division of Diabetes, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA-91010, USA
| | - Rama Natarajan
- Author for correspondence: Division of Diabetes, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA-91010, USA, Tel.: +1 626 256 4673 ext. 62289, Fax: +1 626 301 8136,
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Perrotta I, Brunelli E, Sciangula A, Zuccalà V, Donato G, Tripepi S, Martinelli GL, Cassese M. Inducible and endothelial nitric oxide synthase expression in human atherogenesis: an immunohistochemical and ultrastructural study. Cardiovasc Pathol 2009; 18:361-8. [DOI: 10.1016/j.carpath.2008.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 06/25/2008] [Accepted: 08/19/2008] [Indexed: 10/21/2022] Open
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Aggarwal NT, Pfister SL, Campbell WB. Hypercholesterolemia Enhances 15-Lipoxygenase–Mediated Vasorelaxation and Acetylcholine-Induced Hypotension. Arterioscler Thromb Vasc Biol 2008; 28:2209-15. [DOI: 10.1161/atvbaha.108.177113] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Nitin T. Aggarwal
- From the Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee
| | - Sandra L. Pfister
- From the Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee
| | - William B. Campbell
- From the Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee
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Munteanu A, Zingg JM. Cellular, molecular and clinical aspects of vitamin E on atherosclerosis prevention. Mol Aspects Med 2007; 28:538-90. [PMID: 17825403 DOI: 10.1016/j.mam.2007.07.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Accepted: 07/23/2007] [Indexed: 02/07/2023]
Abstract
Randomised clinical trials and epidemiologic studies addressing the preventive effects of vitamin E supplementation against cardiovascular disease reported both positive and negative effects, and recent meta-analyses of the clinical studies were rather disappointing. In contrast to that, many animal studies clearly show a preventive action of vitamin E in several experimental settings, which can be explained by the molecular and cellular effects of vitamin E observed in cell cultures. This review is focusing on the molecular effects of vitamin E on the cells playing a role during atherosclerosis, in particular on the endothelial cells, vascular smooth muscle cells, monocytes/macrophages, T cells, and mast cells. Vitamin E may act by normalizing aberrant signal transduction and gene expression in antioxidant and non-antioxidant manners; in particular, over-expression of scavenger receptors and consequent foam cell formation can be prevented by vitamin E. In addition to that, the cellular effects of alpha-tocopheryl phosphate and of EPC-K1, a composite molecule between alpha-tocopheryl phosphate and l-ascorbic acid, are summarized.
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Affiliation(s)
- Adelina Munteanu
- Physiology Department, Faculty of Medicine, University of Medicine and Pharmacy Bucharest, Romania
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McPherson R, Shepherd J. Peering through the darkened glass: success and disappointment in the management of cardiovascular risk. Curr Opin Lipidol 2006; 17:615-8. [PMID: 17095904 DOI: 10.1097/mol.0b013e32801140ce] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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