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Ren C, Carrillo ND, Cryns VL, Anderson RA, Chen M. Environmental pollutants and phosphoinositide signaling in autoimmunity. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133080. [PMID: 38091799 PMCID: PMC10923067 DOI: 10.1016/j.jhazmat.2023.133080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 02/08/2024]
Abstract
Environmental pollution stands as one of the most critical challenges affecting human health, with an estimated mortality rate linked to pollution-induced non-communicable diseases projected to range from 20% to 25%. These pollutants not only disrupt immune responses but can also trigger immunotoxicity. Phosphoinositide signaling, a pivotal regulator of immune responses, plays a central role in the development of autoimmune diseases and exhibits high sensitivity to environmental stressors. Among these stressors, environmental pollutants have become increasingly prevalent in our society, contributing to the initiation and exacerbation of autoimmune conditions. In this review, we summarize the intricate interplay between phosphoinositide signaling and autoimmune diseases within the context of environmental pollutants and contaminants. We provide an up-to-date overview of stress-induced phosphoinositide signaling, discuss 14 selected examples categorized into three groups of environmental pollutants and their connections to immune diseases, and shed light on the associated phosphoinositide signaling pathways. Through these discussions, this review advances our understanding of how phosphoinositide signaling influences the coordinated immune response to environmental stressors at a biological level. Furthermore, it offers valuable insights into potential research directions and therapeutic targets aimed at mitigating the impact of environmental pollutants on the pathogenesis of autoimmune diseases. SYNOPSIS: Phosphoinositide signaling at the intersection of environmental pollutants and autoimmunity provides novel insights for managing autoimmune diseases aggravated by pollutants.
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Affiliation(s)
- Chang Ren
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Noah D Carrillo
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Vincent L Cryns
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; University of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Richard A Anderson
- University of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Mo Chen
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China.
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2
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Mu J, Lam SM, Shui G. Emerging roles and therapeutic potentials of sphingolipids in pathophysiology: emphasis on fatty acyl heterogeneity. J Genet Genomics 2024; 51:268-278. [PMID: 37364711 DOI: 10.1016/j.jgg.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/29/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023]
Abstract
Sphingolipids not only exert structural roles in cellular membranes, but also act as signaling molecules in various physiological and pathological processes. A myriad of studies have shown that abnormal levels of sphingolipids and their metabolic enzymes are associated with a variety of human diseases. Moreover, blood sphingolipids can also be used as biomarkers for disease diagnosis. This review summarizes the biosynthesis, metabolism, and pathological roles of sphingolipids, with emphasis on the biosynthesis of ceramide, the precursor for the biosynthesis of complex sphingolipids with different fatty acyl chains. The possibility of using sphingolipids for disease prediction, diagnosis, and treatment is also discussed. Targeting endogenous ceramides and complex sphingolipids along with their specific fatty acyl chain to promote future drug development will also be discussed.
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Affiliation(s)
- Jinming Mu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Lipidall Technologies Company Limited, Changzhou, Jiangsu 213000, China.
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China.
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3
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Luan Y, Zhu X, Jiao Y, Liu H, Huang Z, Pei J, Xu Y, Yang Y, Ren K. Cardiac cell senescence: molecular mechanisms, key proteins and therapeutic targets. Cell Death Discov 2024; 10:78. [PMID: 38355681 PMCID: PMC10866973 DOI: 10.1038/s41420-023-01792-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 02/16/2024] Open
Abstract
Cardiac aging, particularly cardiac cell senescence, is a natural process that occurs as we age. Heart function gradually declines in old age, leading to continuous heart failure, even in people without a prior history of heart disease. To address this issue and improve cardiac cell function, it is crucial to investigate the molecular mechanisms underlying cardiac senescence. This review summarizes the main mechanisms and key proteins involved in cardiac cell senescence. This review further discusses the molecular modulators of cellular senescence in aging hearts. Furthermore, the discussion will encompass comprehensive descriptions of the key drugs, modes of action and potential targets for intervention in cardiac senescence. By offering a fresh perspective and comprehensive insights into the molecular mechanisms of cardiac senescence, this review seeks to provide a fresh perspective and important theoretical foundations for the development of drugs targeting this condition.
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Affiliation(s)
- Yi Luan
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
| | - Xiaofan Zhu
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
| | - Yuxue Jiao
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
| | - Hui Liu
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Zhen Huang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Jinyan Pei
- Quality Management Department, Henan No.3 Provincial People's Hospital, Zhengzhou, 450052, P. R. China
| | - Yawei Xu
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China.
| | - Yang Yang
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China.
| | - Kaidi Ren
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China.
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, P. R. China.
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Crochemore C, Chica C, Garagnani P, Lattanzi G, Horvath S, Sarasin A, Franceschi C, Bacalini MG, Ricchetti M. Epigenomic signature of accelerated ageing in progeroid Cockayne syndrome. Aging Cell 2023; 22:e13959. [PMID: 37688320 PMCID: PMC10577576 DOI: 10.1111/acel.13959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/16/2023] [Accepted: 07/31/2023] [Indexed: 09/10/2023] Open
Abstract
Cockayne syndrome (CS) and UV-sensitive syndrome (UVSS) are rare genetic disorders caused by mutation of the DNA repair and multifunctional CSA or CSB protein, but only CS patients display a progeroid and neurodegenerative phenotype, providing a unique conceptual and experimental paradigm. As DNA methylation (DNAm) remodelling is a major ageing marker, we performed genome-wide analysis of DNAm of fibroblasts from healthy, UVSS and CS individuals. Differential analysis highlighted a CS-specific epigenomic signature (progeroid-related; not present in UVSS) enriched in three categories: developmental transcription factors, ion/neurotransmitter membrane transporters and synaptic neuro-developmental genes. A large fraction of CS-specific DNAm changes were associated with expression changes in CS samples, including in previously reported post-mortem cerebella. The progeroid phenotype of CS was further supported by epigenomic hallmarks of ageing: the prediction of DNAm of repetitive elements suggested an hypomethylation of Alu sequences in CS, and the epigenetic clock returned a marked increase in CS biological age respect to healthy and UVSS cells. The epigenomic remodelling of accelerated ageing in CS displayed both commonalities and differences with other progeroid diseases and regular ageing. CS shared DNAm changes with normal ageing more than other progeroid diseases do, and included genes functionally validated for regular ageing. Collectively, our results support the existence of an epigenomic basis of accelerated ageing in CS and unveil new genes and pathways that are potentially associated with the progeroid/degenerative phenotype.
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Affiliation(s)
- Clément Crochemore
- Institut Pasteur, Université Paris Cité, Molecular Mechanisms of Pathological and Physiological Ageing Unit, UMR3738 CNRSParisFrance
- Institut Pasteur, Team Stability of Nuclear and Mitochondrial DNA, Stem Cells and Development, UMR3738 CNRSParisFrance
- Sup'BiotechVillejuifFrance
| | - Claudia Chica
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HubParisFrance
| | - Paolo Garagnani
- IRCCS Azienda Ospedaliero‐Universitaria di BolognaBolognaItaly
- Department of Medical and Surgical Sciences (DIMEC)University of BolognaBolognaItaly
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli‐Sforza”, Unit of BolognaBolognaItaly
- IRCCS Istituto Ortopedico RizzoliBolognaItaly
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of MedicineUniversity of CaliforniaLos AngelesUSA
- Department of Biostatistics Fielding School of Public HealthUniversity of CaliforniaLos AngelesUSA
| | - Alain Sarasin
- Laboratory of Genetic Stability and Oncogenesis, Institut de Cancérologie Gustave RoussyUniversity Paris‐SudVillejuifFrance
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and MechanicsLobachevsky UniversityNizhniy NovgorodRussia
| | | | - Miria Ricchetti
- Institut Pasteur, Université Paris Cité, Molecular Mechanisms of Pathological and Physiological Ageing Unit, UMR3738 CNRSParisFrance
- Institut Pasteur, Team Stability of Nuclear and Mitochondrial DNA, Stem Cells and Development, UMR3738 CNRSParisFrance
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Mei X, Blanchard J, Luellen C, Conboy MJ, Conboy IM. Fail-tests of DNA methylation clocks, and development of a noise barometer for measuring epigenetic pressure of aging and disease. Aging (Albany NY) 2023; 15:8552-8575. [PMID: 37702598 PMCID: PMC10522373 DOI: 10.18632/aging.205046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/20/2023] [Indexed: 09/14/2023]
Abstract
This study shows that Elastic Net (EN) DNA methylation (DNAme) clocks have low accuracy of predictions for individuals of the same age and a low resolution between healthy and disease cohorts; caveats inherent in applying linear model to non-linear processes. We found that change in methylation of cytosines with age is, interestingly, not the determinant for their selection into the clocks. Moreover, an EN clock's selected cytosines change when non-clock cytosines are removed from the training data; as expected from optimization in a machine learning (ML) context, but inconsistently with the identification of health markers in a biological context. To address these limitations, we moved from predictions to measurement of biological age, focusing on the cytosines that on average remain invariable in their methylation through lifespan, postulated to be homeostatically vital. We established that dysregulation of such cytosines, measured as the sums of standard deviations of their methylation values, quantifies biological noise, which in our hypothesis is a biomarker of aging and disease. We term this approach a "noise barometer" - the pressure of aging and disease on an organism. These noise-detecting cytosines are particularly important as sums of SD on the entire 450K DNAme array data yield a random pattern through chronology. Testing how many cytosines of the 450K arrays become noisier with age, we found that the paradigm of DNAme noise as a biomarker of aging and disease remarkably manifests in ~1/4 of the total. In that large set even the cytosines that have on average constant methylation through age show increased SDs and can be used as noise detectors of the barometer.
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Affiliation(s)
- Xiaoyue Mei
- Department of Bioengineering and QB3, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joshua Blanchard
- Department of Bioengineering and QB3, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Connor Luellen
- Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael J. Conboy
- Department of Bioengineering and QB3, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Irina M. Conboy
- Department of Bioengineering and QB3, University of California, Berkeley, Berkeley, CA 94720, USA
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Kim JE, Jo MJ, Cho E, Ahn SY, Kwon YJ, Gim JA, Ko GJ. The Effect of DNA Methylation in the Development and Progression of Chronic Kidney Disease in the General Population: An Epigenome-Wide Association Study Using the Korean Genome and Epidemiology Study Database. Genes (Basel) 2023; 14:1489. [PMID: 37510393 PMCID: PMC10379047 DOI: 10.3390/genes14071489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Although knowledge of the genetic factors influencing kidney disease is increasing, epigenetic profiles, which are associated with chronic kidney disease (CKD), have not been fully elucidated. We sought to identify the DNA methylation status of CpG sites associated with reduced kidney function and examine whether the identified CpG sites are associated with CKD development. METHOD We analyzed DNA methylation patterns of 440 participants in the Korean Genome and Epidemiology Study (KoGES) with estimated glomerular filtration rates (eGFRs) ≥ 60 mL/min/1.73 m2 at baseline. CKD development was defined as a decrease in the eGFR of <60 at any time during an 8-year follow-up period ("CKD prediction" analysis). In addition, among the 440 participants, 49 participants who underwent a second methylation profiling were assessed for an association between a decline in kidney function and changes in the degree of methylation of CpG sites during the 8 years ("kidney function slope" analysis). RESULTS In the CKD prediction analysis, methylation profiles of a total of 403,129 CpG sites were evaluated at baseline in 440 participants, and increased and decreased methylation of 268 and 189 CpG sites, respectively, were significantly correlated with the development of CKD in multivariable logistic regression. During kidney function slope analysis using follow-up methylation profiles of 49 participants, the percent methylation changes in 913 CpG sites showed a linear relationship with the percent change in eGFR during 8 years. During functional enrichment analyses for significant CpG sites found in the CKD prediction and kidney function slope analyses, we found that those CpG sites represented MAPK, PI3K/Akt, and Rap1 pathways. In addition, three CpG sites from three genes, NPHS2, CHCHD4, and AHR, were found to be significant in the CKD prediction analysis and related to a decline in kidney function. CONCLUSION It is suggested that DNA methylation on specific genes is associated with the development of CKD and the deterioration of kidney function.
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Affiliation(s)
- Ji-Eun Kim
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Min-Jee Jo
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Eunjung Cho
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Shin-Young Ahn
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Young-Joo Kwon
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Jeong-An Gim
- Medical Science Research Center, Korea University College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Gang-Jee Ko
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
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Di Risi T, Cuomo M, Vinciguerra R, Ferraro S, Della Monica R, Costabile D, Buonaiuto M, Trio F, Capoluongo E, Visconti R, Riccio E, Pisani A, Chiariotti L. Methylome Profiling in Fabry Disease in Clinical Practice: A Proof of Concept. Int J Mol Sci 2022; 23:ijms232012110. [PMID: 36292965 PMCID: PMC9602470 DOI: 10.3390/ijms232012110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Anderson−Fabry disease (FD) is an X-linked disease caused by a functional deficit of the α-galactosidase A enzyme. FD diagnosis relies on the clinical manifestations and research of GLA gene mutations. However, because of the lack of a clear genotype/phenotype correlation, FD diagnosis can be challenging. Recently, several studies have highlighted the importance of investigating DNA methylation patterns for confirming the correct diagnosis of different rare Mendelian diseases, but to date, no such studies have been reported for FD. Thus, in the present investigation, we analyzed for the first time the genome-wide methylation profile of a well-characterized cohort of patients with Fabry disease. We profiled the methylation status of about 850,000 CpG sites in 5 FD patients, all carrying the same mutation in the GLA gene (exon 6 c.901C>G) and presenting comparable low levels of α-Gal A activity. We found that, although the whole methylome profile did not discriminate the FD group from the unaffected one, several genes were significantly differentially methylated in Fabry patients. Thus, we provide here a proof of concept, to be tested in patients with different mutations and in a larger cohort, that the methylation state of specific genes can potentially identify Fabry patients and possibly predict organ involvement and disease evolution.
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Affiliation(s)
- Teodolinda Di Risi
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Public Health, University Federico II, 80131 Naples, Italy
| | - Mariella Cuomo
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
| | | | - Sara Ferraro
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
| | - Rosa Della Monica
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
| | - Davide Costabile
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- SEMM-European School of Molecular Medicine, University Federico II, 80145 Naples, Italy
| | - Michela Buonaiuto
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
| | - Federica Trio
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
| | - Ettore Capoluongo
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
- Department of Clinical Pathology and Genomics, Azienda Ospedaliera per L’Emergenza Cannizzaro, 95126 Catania, Italy
| | - Roberta Visconti
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Institute for the Experimental Endocrinology and Oncology, Italian National Council of Research, 80131 Naples, Italy
| | - Eleonora Riccio
- Institute for Biomedical Research and Innovation, Italian National Research Council, 90146 Palermo, Italy
| | - Antonio Pisani
- Department of Public Health, University Federico II, 80131 Naples, Italy
| | - Lorenzo Chiariotti
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
- Correspondence:
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Zhang TP, Li HM, Huang Q, Wang L, Li XM. Vitamin D Metabolic Pathway Genes Polymorphisms and Their Methylation Levels in Association With Rheumatoid Arthritis. Front Immunol 2021; 12:731565. [PMID: 34925313 PMCID: PMC8677352 DOI: 10.3389/fimmu.2021.731565] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/02/2021] [Indexed: 01/12/2023] Open
Abstract
Abnormal vitamin D metabolism is involved in the pathogenesis of rheumatoid arthritis (RA). In this study, we evaluated the association of single nucleotide polymorphisms (SNPs) and methylation levels in vitamin D metabolic pathway genes with RA susceptibility. Ten SNPs in vitamin D metabolic pathway genes (CYP2R1, CYP24A1, VDR, CYP27B1) were genotyped in 477 RA patients and 496 controls by improved multiple ligase detection reaction (iMLDR). The methylation levels of the promoter regions of these genes were detected in 122 RA patients and 123 controls using Illumina Hiseq platform. We found that the CYP2R1 rs1993116 GA genotype, CYP27B1 rs4646536 GA genotype, rs4646536 A allele frequencies were significantly increased in RA patients when compared to controls. The decreased risk of rs1993116, rs4646536 was found under the dominant mode in RA patients. However, no significant association was found between CYP2R1 rs7936142, rs12794714, CYP24A1 rs2762934, rs6068816, rs2296239, rs2296241, VDR rs11574129, rs3847987 polymorphism, and RA susceptibility. The VDR, CYP27B1 methylation levels in RA patients were significantly lower than those in controls, while CYP2R1, CYP24A1 methylation levels were not associated with RA. There were no statistical associations between CYP2R1, CYP24A1, VDR, CYP27B1 methylation levels and their respective genotype in RA patients. In addition, plasma 25OHD level in RA patients was significantly lower than that in healthy controls. In summary, our results showed that CYP2R1, CYP27B1 genetic variations were associated with the genetic background of RA, while altered VDR, CYP27B1 methylation levels were related to the risk of RA.
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Affiliation(s)
- Tian-Ping Zhang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Hong-Miao Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Anhui Provincial Laboratory of Inflammatory and Immune Diseases, Hefei, China
| | - Qian Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Anhui Provincial Laboratory of Inflammatory and Immune Diseases, Hefei, China
| | - Li Wang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiao-Mei Li
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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Kim JL, Mestre B, Shin SH, Futerman AH. Ceramide synthases: Reflections on the impact of Dr. Lina M. Obeid. Cell Signal 2021; 82:109958. [PMID: 33607256 DOI: 10.1016/j.cellsig.2021.109958] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/12/2021] [Accepted: 02/12/2021] [Indexed: 12/16/2022]
Abstract
Sphingolipids are a family of lipids that are critical to cell function and survival. Much of the recent work done on sphingolipids has been performed by a closely-knit family of sphingolipid researchers, which including our colleague, Dr. Lina Obeid, who recently passed away. We now briefly review where the sphingolipid field stands today, focusing in particular on areas of sphingolipid research to which Dr. Obeid made valued contributions. These include the 'many-worlds' view of ceramides and the role of a key enzyme in the sphingolipid biosynthetic pathway, namely the ceramide synthases (CerS). The CerS contain a number of functional domains and also interact with a number of other proteins in lipid metabolic pathways, fulfilling Dr. Obeid's prophecy that ceramides, and the enzymes that generate ceramides, form the critical hub of the sphingolipid metabolic pathway.
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Affiliation(s)
- Jiyoon L Kim
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Beatriz Mestre
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sun-Hye Shin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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Detection of a DNA Methylation Signature for the Intellectual Developmental Disorder, X-Linked, Syndromic, Armfield Type. Int J Mol Sci 2021; 22:ijms22031111. [PMID: 33498634 PMCID: PMC7865843 DOI: 10.3390/ijms22031111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/19/2022] Open
Abstract
A growing number of genetic neurodevelopmental disorders are known to be associated with unique genomic DNA methylation patterns, called episignatures, which are detectable in peripheral blood. The intellectual developmental disorder, X-linked, syndromic, Armfield type (MRXSA) is caused by missense variants in FAM50A. Functional studies revealed the pathogenesis to be a spliceosomopathy that is characterized by atypical mRNA processing during development. In this study, we assessed the peripheral blood specimens in a cohort of individuals with MRXSA and detected a unique and highly specific DNA methylation episignature associated with this disorder. We used this episignature to construct a support vector machine model capable of sensitive and specific identification of individuals with pathogenic variants in FAM50A. This study contributes to the expanding number of genetic neurodevelopmental disorders with defined DNA methylation episignatures, provides an additional understanding of the associated molecular mechanisms, and further enhances our ability to diagnose patients with rare disorders.
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12
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Haghshenas S, Bhai P, Aref-Eshghi E, Sadikovic B. Diagnostic Utility of Genome-Wide DNA Methylation Analysis in Mendelian Neurodevelopmental Disorders. Int J Mol Sci 2020; 21:ijms21239303. [PMID: 33291301 PMCID: PMC7730976 DOI: 10.3390/ijms21239303] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
Mendelian neurodevelopmental disorders customarily present with complex and overlapping symptoms, complicating the clinical diagnosis. Individuals with a growing number of the so-called rare disorders exhibit unique, disorder-specific DNA methylation patterns, consequent to the underlying gene defects. Besides providing insights to the pathophysiology and molecular biology of these disorders, we can use these epigenetic patterns as functional biomarkers for the screening and diagnosis of these conditions. This review summarizes our current understanding of DNA methylation episignatures in rare disorders and describes the underlying technology and analytical approaches. We discuss the computational parameters, including statistical and machine learning methods, used for the screening and classification of genetic variants of uncertain clinical significance. Describing the rationale and principles applied to the specific computational models that are used to develop and adapt the DNA methylation episignatures for the diagnosis of rare disorders, we highlight the opportunities and challenges in this emerging branch of diagnostic medicine.
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Affiliation(s)
- Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
| | - Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
- Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- Correspondence:
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13
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Wang J, Zhang J, Ma D, Li X. The Potential Role of CERS1 in Autophagy Through PI3K/AKT Signaling Pathway in Hypophysoma. Technol Cancer Res Treat 2020; 19:1533033820977536. [PMID: 33267708 PMCID: PMC7720334 DOI: 10.1177/1533033820977536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
To explore the role and mechanism of CERS1 in hypophysoma and investigate whether CERS1 overexpression can change the autophagy process of hypophysoma, and then to explore whether CERS1’s effect was regulated by the PI3K/AKT signaling pathway. Western blot and RT-PCR were used to analyze the expression or mRNA level of CERS1 at different tissues or cell lines. Afterwards, the occurrence and development of hypophysoma in vivo and in vitro, respectively, was observed by using CERS1 overexpression by lentivirus. Finally, MK-2206 and LY294002 were applied to discuss whether the role of CERS1 was regulated by the PI3K/AKT signaling pathway. Results show that the CERS1 expression and mRNA level in tumor or AtT-20 cells were decreased. CERS1 over-expressed by lentivirus could inhibit hypophysoma development in vivo and in vitro by reducing tumor volume and weight, weakening tumor proliferation and invasion, and enhancing apoptosis. In addition, shCERS1 could reverse the process. The above results indicate that CERS1 is possibly able to enhance autophagy in hypophysoma through the PI3K/AKT signaling pathway.
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Affiliation(s)
- Jingtao Wang
- Third Department of Neurosurgery, Affiliated Hospital of Hebei University of Engineering, Handan, Hebei, People's Republic of China
| | - Jimin Zhang
- Third Department of Neurosurgery, Affiliated Hospital of Hebei University of Engineering, Handan, Hebei, People's Republic of China
| | - Dongzhou Ma
- Third Department of Neurosurgery, Affiliated Hospital of Hebei University of Engineering, Handan, Hebei, People's Republic of China
| | - Xiushan Li
- Third Department of Neurosurgery, Affiliated Hospital of Hebei University of Engineering, Handan, Hebei, People's Republic of China
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14
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Hu X, Tang L, Wang L, Wu FX, Li M. MADA: a web service for analysing DNA methylation array data. BMC Bioinformatics 2020; 21:403. [PMID: 33203349 PMCID: PMC7672854 DOI: 10.1186/s12859-020-03734-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 09/03/2020] [Indexed: 11/15/2022] Open
Abstract
Background DNA methylation in the human genome is acknowledged to be widely associated with biological processes and complex diseases. The Illumina Infinium methylation arrays have been approved as one of the most efficient and universal technologies to investigate the whole genome changes of methylation patterns. As methylation arrays may still be the dominant method for detecting methylation in the anticipated future, it is crucial to develop a reliable workflow to analysis methylation array data. Results In this study, we develop a web service MADA for the whole process of methylation arrays data analysis, which includes the steps of a comprehensive differential methylation analysis pipeline: pre-processing (data loading, quality control, data filtering, and normalization), batch effect correction, differential methylation analysis, and downstream analysis. In addition, we provide the visualization of pre-processing, differentially methylated probes or regions, gene ontology, pathway and cluster analysis results. Moreover, a customization function for users to define their own workflow is also provided in MADA. Conclusions With the analysis of two case studies, we have shown that MADA can complete the whole procedure of methylation array data analysis. MADA provides a graphical user interface and enables users with no computational skills and limited bioinformatics background to carry on complicated methylation array data analysis. The web server is available at: http://120.24.94.89:8080/MADA
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Affiliation(s)
- Xinyu Hu
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Li Tang
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Linconghua Wang
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Fang-Xiang Wu
- Division of Biomedical Engineering and Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SKS7N5A9, Canada
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, China.
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15
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16
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Variability in DNA methylation at the serotonin transporter gene promoter: epigenetic mechanism or cell-type artifact? Mol Psychiatry 2020; 25:1906-1909. [PMID: 30082839 PMCID: PMC7473835 DOI: 10.1038/s41380-018-0121-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 04/10/2018] [Accepted: 05/25/2018] [Indexed: 11/09/2022]
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17
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Maierhofer A, Flunkert J, Oshima J, Martin GM, Poot M, Nanda I, Dittrich M, Müller T, Haaf T. Epigenetic signatures of Werner syndrome occur early in life and are distinct from normal epigenetic aging processes. Aging Cell 2019; 18:e12995. [PMID: 31259468 PMCID: PMC6718529 DOI: 10.1111/acel.12995] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/24/2019] [Accepted: 06/05/2019] [Indexed: 12/11/2022] Open
Abstract
Werner Syndrome (WS) is an adult-onset segmental progeroid syndrome. Bisulfite pyrosequencing of repetitive DNA families revealed comparable blood DNA methylation levels between classical (18 WRN-mutant) or atypical WS (3 LMNA-mutant and 3 POLD1-mutant) patients and age- and sex-matched controls. WS was not associated with either age-related accelerated global losses of ALU, LINE1, and α-satellite DNA methylations or gains of rDNA methylation. Single CpG methylation was analyzed with Infinium MethylationEPIC arrays. In a correspondence analysis, atypical WS samples clustered together with the controls and were clearly separated from classical WS, consistent with distinct epigenetic pathologies. In classical WS, we identified 659 differentially methylated regions (DMRs) comprising 3,656 CpG sites and 613 RefSeq genes. The top DMR was located in the HOXA4 promoter. Additional DMR genes included LMNA, POLD1, and 132 genes which have been reported to be differentially expressed in WRN-mutant/depleted cells. DMRs were enriched in genes with molecular functions linked to transcription factor activity and sequence-specific DNA binding to promoters transcribed by RNA polymerase II. We propose that transcriptional misregulation of downstream genes by the absence of WRN protein contributes to the variable premature aging phenotypes of WS. There were no CpG sites showing significant differences in DNA methylation changes with age between WS patients and controls. Genes with both WS- and age-related methylation changes exhibited a constant offset of methylation between WRN-mutant patients and controls across the entire analyzed age range. WS-specific epigenetic signatures occur early in life and do not simply reflect an acceleration of normal epigenetic aging processes.
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Affiliation(s)
- Anna Maierhofer
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Julia Flunkert
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Junko Oshima
- Department of Pathology University of Washington Seattle Washington USA
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine Chiba University Chiba Japan
| | - George M. Martin
- Department of Pathology University of Washington Seattle Washington USA
| | - Martin Poot
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Indrajit Nanda
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Marcus Dittrich
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
- Department of Bioinformatics Julius Maximilians University Würzburg Germany
| | - Tobias Müller
- Department of Bioinformatics Julius Maximilians University Würzburg Germany
| | - Thomas Haaf
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
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18
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Giuliani C, Garagnani P, Franceschi C. Genetics of Human Longevity Within an Eco-Evolutionary Nature-Nurture Framework. Circ Res 2019; 123:745-772. [PMID: 30355083 DOI: 10.1161/circresaha.118.312562] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Human longevity is a complex trait, and to disentangle its basis has a great theoretical and practical consequences for biomedicine. The genetics of human longevity is still poorly understood despite several investigations that used different strategies and protocols. Here, we argue that such rather disappointing harvest is largely because of the extraordinary complexity of the longevity phenotype in humans. The capability to reach the extreme decades of human lifespan seems to be the result of an intriguing mixture of gene-environment interactions. Accordingly, the genetics of human longevity is here described as a highly context-dependent phenomenon, within a new integrated, ecological, and evolutionary perspective, and is presented as a dynamic process, both historically and individually. The available literature has been scrutinized within this perspective, paying particular attention to factors (sex, individual biography, family, population ancestry, social structure, economic status, and education, among others) that have been relatively neglected. The strength and limitations of the most powerful and used tools, such as genome-wide association study and whole-genome sequencing, have been discussed, focusing on prominently emerged genes and regions, such as apolipoprotein E, Forkhead box O3, interleukin 6, insulin-like growth factor-1, chromosome 9p21, 5q33.3, and somatic mutations among others. The major results of this approach suggest that (1) the genetics of longevity is highly population specific; (2) small-effect alleles, pleiotropy, and the complex allele timing likely play a major role; (3) genetic risk factors are age specific and need to be integrated in the light of the geroscience perspective; (4) a close relationship between genetics of longevity and genetics of age-related diseases (especially cardiovascular diseases) do exist. Finally, the urgent need of a global approach to the largely unexplored interactions between the 3 genetics of human body, that is, nuclear, mitochondrial, and microbiomes, is stressed. We surmise that the comprehensive approach here presented will help in increasing the above-mentioned harvest.
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Affiliation(s)
- Cristina Giuliani
- From the Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology (C.G.), University of Bologna, Italy.,School of Anthropology and Museum Ethnography, University of Oxford, United Kingdom (C.G.).,Interdepartmental Centre 'L. Galvani' (CIG), University of Bologna, Italy (C.G.)
| | - Paolo Garagnani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES) (P.G.), University of Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden (P.G.)
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Sadikovic B, Aref-Eshghi E, Levy MA, Rodenhiser D. DNA methylation signatures in mendelian developmental disorders as a diagnostic bridge between genotype and phenotype. Epigenomics 2019; 11:563-575. [PMID: 30875234 DOI: 10.2217/epi-2018-0192] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Epigenetic and genetic mechanisms regulate the establishment and maintenance of gene expression in its proper context. Recent genome-wide mapping approaches have identified DNA methylation (DNAm) signatures in patients clinically diagnosed with syndromes manifesting as developmental disabilities with intellectual impairments. Here, we review recent studies in which these DNA methylation signatures have enabled highly sensitive and specific screening of such individuals and have clarified ambiguous cases where subjects present with genetic sequence variants of unknown clinical significance (VUS). We propose that these episignatures be considered as echoes and/or legacies of the initiating mutational events within proteins of the so-called epigenetic machinery. As well, we discuss approaches to directly confirm the functional consequences and the implications of these episignatures to patient management and treatment.
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Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - David Rodenhiser
- Departments of Pediatrics, Biochemistry & Oncology, Western University, London, ON, N6A 3K7, Canada.,Children's Health Research Institute & Lawson Health Research Institute, London, ON, N6C 2V5, Canada.,London Regional Cancer Program, Lawson Health Research Institute, London, ON, N6A 5W9, Canada
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20
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Castagna A, Gareri P, Falvo F, Sestito S, Rocca M, Pensabene L, Concolino D, Coppolino G, Ruotolo G. Werner syndrome: a rare mutation. Aging Clin Exp Res 2019; 31:425-429. [PMID: 29876830 DOI: 10.1007/s40520-018-0982-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/30/2018] [Indexed: 10/14/2022]
Affiliation(s)
- Alberto Castagna
- Center for Cognitive Disorders and Dementia, DSS Catanzaro Lido, ASP Catanzaro, Viale Crotone, 88100, Catanzaro, Italy
| | - Pietro Gareri
- Center for Cognitive Disorders and Dementia, DSS Catanzaro Lido, ASP Catanzaro, Viale Crotone, 88100, Catanzaro, Italy.
| | - Francesca Falvo
- Department of Pediatrics, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Simona Sestito
- Department of Pediatrics, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Maurizio Rocca
- Center for Cognitive Disorders and Dementia, DSS Catanzaro Lido, ASP Catanzaro, Viale Crotone, 88100, Catanzaro, Italy
| | - Licia Pensabene
- Department of Pediatrics, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Daniela Concolino
- Department of Pediatrics, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Giuseppe Coppolino
- Nephrology and Dialysis Unit, "Pugliese-Ciaccio" Hospital of Catanzaro, Catanzaro, Italy
| | - Giovanni Ruotolo
- SOC Geriatrics, Azienda Ospedaliera Pugliese-Ciaccio, Catanzaro, Italy
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21
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Franceschi C, Garagnani P, Parini P, Giuliani C, Santoro A. Inflammaging: a new immune-metabolic viewpoint for age-related diseases. Nat Rev Endocrinol 2018; 14:576-590. [PMID: 30046148 DOI: 10.1038/s41574-018-0059-4] [Citation(s) in RCA: 1441] [Impact Index Per Article: 240.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ageing and age-related diseases share some basic mechanistic pillars that largely converge on inflammation. During ageing, chronic, sterile, low-grade inflammation - called inflammaging - develops, which contributes to the pathogenesis of age-related diseases. From an evolutionary perspective, a variety of stimuli sustain inflammaging, including pathogens (non-self), endogenous cell debris and misplaced molecules (self) and nutrients and gut microbiota (quasi-self). A limited number of receptors, whose degeneracy allows them to recognize many signals and to activate the innate immune responses, sense these stimuli. In this situation, metaflammation (the metabolic inflammation accompanying metabolic diseases) is thought to be the form of chronic inflammation that is driven by nutrient excess or overnutrition; metaflammation is characterized by the same mechanisms underpinning inflammaging. The gut microbiota has a central role in both metaflammation and inflammaging owing to its ability to release inflammatory products, contribute to circadian rhythms and crosstalk with other organs and systems. We argue that chronic diseases are not only the result of ageing and inflammaging; these diseases also accelerate the ageing process and can be considered a manifestation of accelerated ageing. Finally, we propose the use of new biomarkers (DNA methylation, glycomics, metabolomics and lipidomics) that are capable of assessing biological versus chronological age in metabolic diseases.
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Affiliation(s)
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
- Laboratory of Cell Biology, Rizzoli Orthopaedic Institute, Bologna, Italy
- CNR Institute of Molecular Genetics, Unit of Bologna, Bologna, Italy
| | - Paolo Parini
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy.
- Interdepartmental Centre 'L. Galvani' (CIG), University of Bologna, Bologna, Italy.
| | - Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Interdepartmental Centre 'L. Galvani' (CIG), University of Bologna, Bologna, Italy
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22
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Wang M, Kong W, He B, Li Z, Song H, Shi P, Wang J. Vitamin D and the promoter methylation of its metabolic pathway genes in association with the risk and prognosis of tuberculosis. Clin Epigenetics 2018; 10:118. [PMID: 30208925 PMCID: PMC6136159 DOI: 10.1186/s13148-018-0552-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/04/2018] [Indexed: 12/24/2022] Open
Abstract
Background A variety of abnormalities in vitamin D metabolism have been reported in patients with active tuberculosis. However, intervention trials have produced inconsistent results. We hypothesized that genetic and epigenetic changes in the key genes of the vitamin D metabolic pathway may partly explain the differences between studies. Methods We performed a case-control study followed by a prospective cohort study. We recruited 122 patients with pulmonary tuberculosis and 118 healthy controls. The serum 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D levels were measured. The methylation of the promoter regions of key genes in the vitamin D metabolic pathway (CYP24A1, CYP27A1, CYP27B1, CYP2R1, and VDR) was detected using the Illumina MiSeq platform. The specific methylation profiles were examined as epigenetic biomarkers. The sensitivity, specificity, and receiver operating characteristic (ROC) curves were used to estimate the predictive value of the biomarkers. Results The baseline serum 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D concentrations in the cases were significantly lower than those in the controls (51.60 ± 27.25 nmol/L vs. 117.50 ± 75.50 nmol/L, Z = − 8.515, P < 0.001; 82.63 ± 51.43 pmol/L vs. 94.02 ± 49.26 pmol/L, Z = − 2.165, P = 0.03). We sequenced 310 CpG sites in five candidate genes. After Bonferroni correction, there were 55 differentially methylated CpG sites between cases and controls; 41.5% were in the CYP27B1 gene, 31.7% were in the CYP24A1 gene, 14.7% were in the VDR gene, and 12.3% were in the CYP27A1 gene. When we designated the CpG sites that remained significant after the Bonferroni correction as the biomarkers, the area under the curve (AUC) for the cumulative methylation was 0.810 (95% CI 0.754–0.866). There was an interaction between CYP27A1 methylation level and 1,25-dihydroxyvitamin D concentration associated with the risk of TB (ORinteraction = 4.11, 95% CI 1.26–13.36, P = 0.019). The serum 1,25-dihydroxyvitamin D concentration at the end of the intensive treatment stage was related to a patient’s prognosis (P = 0.008). There were 23 CpG sites that were individually related to the treatment outcomes, but the relationships were not significant after the Bonferroni correction. Conclusion Both serum vitamin D concentrations and the methylation levels of key genes in the vitamin D metabolic pathway are related to the risk and prognosis of tuberculosis. Electronic supplementary material The online version of this article (10.1186/s13148-018-0552-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, 101 Longmian Ave, Nanjing, 211166, People's Republic of China.,Department of Preventive Health Care, People's Hospital of Suzhou High-tech Zone, Suzhou, People's Republic of China
| | - Weimin Kong
- Department of Nursing, The First People's Hospital of Yancheng City, Yancheng, People's Republic of China
| | - Biyu He
- Department of Epidemiology, School of Public Health, Nanjing Medical University, 101 Longmian Ave, Nanjing, 211166, People's Republic of China
| | - Zhongqi Li
- Department of Epidemiology, School of Public Health, Nanjing Medical University, 101 Longmian Ave, Nanjing, 211166, People's Republic of China
| | - Huan Song
- Department of Epidemiology, School of Public Health, Nanjing Medical University, 101 Longmian Ave, Nanjing, 211166, People's Republic of China
| | - Peiyi Shi
- Department of Epidemiology, School of Public Health, Nanjing Medical University, 101 Longmian Ave, Nanjing, 211166, People's Republic of China
| | - Jianming Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, 101 Longmian Ave, Nanjing, 211166, People's Republic of China. .,Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China.
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23
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Chen Z, Gao W, Pu L, Zhang L, Han G, Zuo X, Zhang Y, Li X, Shen H, Wu J, Wang X. PRDM8 exhibits antitumor activities toward hepatocellular carcinoma by targeting NAP1L1. Hepatology 2018; 68:994-1009. [PMID: 29572888 DOI: 10.1002/hep.29890] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/01/2018] [Accepted: 03/18/2018] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma (HCC) is a major leading cause of cancer mortality worldwide. PRDI-BF1 and RIZ homology domain containing 8 (PRDM8) is a key regulator in neural development and testis steroidogenesis; however, its role in liver carcinogenesis remains to be investigated. In this study, PRDM8 was found to be down-regulated in HCC, which was linked with shorter recurrence-free survival. Lentiviral-based overexpression and knockdown approaches showed that PRDM8 inhibited HCC cell proliferation, migration, and invasion. PRDM8 caused G1/S cell cycle arrest and induced apoptosis. An in vivo tumor model confirmed the antitumor role of PRDM8 in HCC growth and metastasis. Mechanistic study showed that PRDM8 suppressed the PI3K/AKT/mTOR signaling cascade through the regulation of nucleosome assembly protein 1-like 1 (NAP1L1). Conclusion: PRDM8 as a functional tumor suppressor is frequently down-regulated in HCC. Through regulating NAP1L1, PRDM8 inhibits PI3K/AKT/mTOR signaling in HCC. PRDM8 is a potential target for therapies of HCC. (Hepatology 2018).
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Affiliation(s)
- Zhiqiang Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Wen Gao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liyong Pu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Long Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Guoyong Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Xueliang Zuo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Yao Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Xiangcheng Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jindao Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xuehao Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
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24
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DNA methylation dynamics in aging: how far are we from understanding the mechanisms? Mech Ageing Dev 2018; 174:3-17. [DOI: 10.1016/j.mad.2017.12.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 02/07/2023]
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25
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Franceschi C, Garagnani P, Morsiani C, Conte M, Santoro A, Grignolio A, Monti D, Capri M, Salvioli S. The Continuum of Aging and Age-Related Diseases: Common Mechanisms but Different Rates. Front Med (Lausanne) 2018; 5:61. [PMID: 29662881 PMCID: PMC5890129 DOI: 10.3389/fmed.2018.00061] [Citation(s) in RCA: 477] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/20/2018] [Indexed: 12/11/2022] Open
Abstract
Geroscience, the new interdisciplinary field that aims to understand the relationship between aging and chronic age-related diseases (ARDs) and geriatric syndromes (GSs), is based on epidemiological evidence and experimental data that aging is the major risk factor for such pathologies and assumes that aging and ARDs/GSs share a common set of basic biological mechanisms. A consequence is that the primary target of medicine is to combat aging instead of any single ARD/GSs one by one, as favored by the fragmentation into hundreds of specialties and sub-specialties. If the same molecular and cellular mechanisms underpin both aging and ARDs/GSs, a major question emerges: which is the difference, if any, between aging and ARDs/GSs? The hypothesis that ARDs and GSs such as frailty can be conceptualized as accelerated aging will be discussed by analyzing in particular frailty, sarcopenia, chronic obstructive pulmonary disease, cancer, neurodegenerative diseases such as Alzheimer and Parkinson as well as Down syndrome as an example of progeroid syndrome. According to this integrated view, aging and ARDs/GSs become part of a continuum where precise boundaries do not exist and the two extremes are represented by centenarians, who largely avoided or postponed most ARDs/GSs and are characterized by decelerated aging, and patients who suffered one or more severe ARDs in their 60s, 70s, and 80s and show signs of accelerated aging, respectively. In between these two extremes, there is a continuum of intermediate trajectories representing a sort of gray area. Thus, clinically different, classical ARDs/GSs are, indeed, the result of peculiar combinations of alterations regarding the same, limited set of basic mechanisms shared with the aging process. Whether an individual will follow a trajectory of accelerated or decelerated aging will depend on his/her genetic background interacting lifelong with environmental and lifestyle factors. If ARDs and GSs are manifestations of accelerated aging, it is urgent to identify markers capable of distinguishing between biological and chronological age to identify subjects at higher risk of developing ARDs and GSs. To this aim, we propose the use of DNA methylation, N-glycans profiling, and gut microbiota composition to complement the available disease-specific markers.
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Affiliation(s)
- Claudio Franceschi
- Institute of Neurological Sciences, University of Bologna, Bellaria Hospital, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden.,Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy.,CNR Institute of Molecular Genetics, Unit of Bologna, Bologna, Italy
| | - Cristina Morsiani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Conte
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.,Interdepartmental Center "L. Galvani" (CIG), University of Bologna, Bologna, Italy
| | - Andrea Grignolio
- Unit and Museum of History of Medicine, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.,Interdepartmental Center "L. Galvani" (CIG), University of Bologna, Bologna, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.,Interdepartmental Center "L. Galvani" (CIG), University of Bologna, Bologna, Italy
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26
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Poot M. Scratching the Surface of Werner Syndrome and Human Ageing. Mol Syndromol 2017; 9:1-4. [PMID: 29456476 PMCID: PMC5803710 DOI: 10.1159/000484424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2017] [Indexed: 11/19/2022] Open
Affiliation(s)
- Martin Poot
- *Martin Poot, Department of Human Genetics, University of Würzburg, Biozentrum, Am Hubland, DE-97074 Würzburg (Germany), E-Mail
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