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Ravaioli F, Bacalini MG, Giuliani C, Pellegrini C, D’Silva C, De Fanti S, Pirazzini C, Giorgi G, Del Re B. Evaluation of DNA Methylation Profiles of LINE-1, Alu and Ribosomal DNA Repeats in Human Cell Lines Exposed to Radiofrequency Radiation. Int J Mol Sci 2023; 24:9380. [PMID: 37298336 PMCID: PMC10253908 DOI: 10.3390/ijms24119380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
A large body of evidence indicates that environmental agents can induce alterations in DNA methylation (DNAm) profiles. Radiofrequency electromagnetic fields (RF-EMFs) are radiations emitted by everyday devices, which have been classified as "possibly carcinogenic"; however, their biological effects are unclear. As aberrant DNAm of genomic repetitive elements (REs) may promote genomic instability, here, we sought to determine whether exposure to RF-EMFs could affect DNAm of different classes of REs, such as long interspersed nuclear elements-1 (LINE-1), Alu short interspersed nuclear elements and ribosomal repeats. To this purpose, we analysed DNAm profiles of cervical cancer and neuroblastoma cell lines (HeLa, BE(2)C and SH-SY5Y) exposed to 900 MHz GSM-modulated RF-EMF through an Illumina-based targeted deep bisulfite sequencing approach. Our findings showed that radiofrequency exposure did not affect the DNAm of Alu elements in any of the cell lines analysed. Conversely, it influenced DNAm of LINE-1 and ribosomal repeats in terms of both average profiles and organisation of methylated and unmethylated CpG sites, in different ways in each of the three cell lines studied.
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Affiliation(s)
- Francesco Ravaioli
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Maria Giulia Bacalini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, 40126 Bologna, Italy;
| | - Camilla Pellegrini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Chiara D’Silva
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Sara De Fanti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Chiara Pirazzini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy;
| | - Gianfranco Giorgi
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy;
| | - Brunella Del Re
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy;
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Baldelli L, Pirazzini C, Sambati L, Ravaioli F, Gentilini D, Calandra-Buonaura G, Guaraldi P, Franceschi C, Cortelli P, Garagnani P, Bacalini MG, Provini F. Epigenetic clocks suggest accelerated aging in patients with isolated REM Sleep Behavior Disorder. NPJ Parkinsons Dis 2023; 9:48. [PMID: 36997543 PMCID: PMC10063653 DOI: 10.1038/s41531-023-00492-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/08/2023] [Indexed: 04/03/2023] Open
Abstract
Isolated REM Sleep Behavior Disorder (iRBD) is the strongest prodromal marker for α-synucleinopathies. Overt α-synucleinopathies and aging share several mechanisms, but this relationship has been poorly investigated in prodromal phases. Using DNA methylation-based epigenetic clocks, we measured biological aging in videopolysomnography confirmed iRBD patients, videopolysomnography-negative and population-based controls. We found that iRBDs tended to be epigenetically older than controls, suggesting that accelerated aging characterizes prodromal neurodegeneration.
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Affiliation(s)
- Luca Baldelli
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Luisa Sambati
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Francesco Ravaioli
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Giovanna Calandra-Buonaura
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Pietro Guaraldi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Claudio Franceschi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, Russia
| | - Pietro Cortelli
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | | | - Federica Provini
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy.
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.
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3
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Dec E, Clement J, Cheng K, Church GM, Fossel MB, Rehkopf DH, Rosero-Bixby L, Kobor MS, Lin DT, Lu AT, Fei Z, Guo W, Chew YC, Yang X, Putra SED, Reiner AP, Correa A, Vilalta A, Pirazzini C, Passarino G, Monti D, Arosio B, Garagnani P, Franceschi C, Horvath S. Centenarian clocks: epigenetic clocks for validating claims of exceptional longevity. GeroScience 2023:10.1007/s11357-023-00731-7. [PMID: 36964402 PMCID: PMC10400760 DOI: 10.1007/s11357-023-00731-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/09/2023] [Indexed: 03/26/2023] Open
Abstract
Claims surrounding exceptional longevity are sometimes disputed or dismissed for lack of credible evidence. Here, we present three DNA methylation-based age estimators (epigenetic clocks) for verifying age claims of centenarians. The three centenarian clocks were developed based on n = 7039 blood and saliva samples from individuals older than 40, including n = 184 samples from centenarians, 122 samples from semi-supercentenarians (aged 105 +), and 25 samples from supercentenarians (aged 110 +). The oldest individual was 115 years old. Our most accurate centenarian clock resulted from applying a neural network model to a training set composed of individuals older than 40. An epigenome-wide association study of age in different age groups revealed that age effects in young individuals (age < 40) are correlated (r = 0.55) with age effects in old individuals (age > 90). We present a chromatin state analysis of age effects in centenarians. The centenarian clocks are expected to be useful for validating claims surrounding exceptional old age.
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Affiliation(s)
- Eric Dec
- Department of Pediatrics, Division of Genetics and Genomic Medicine, University of California, Irvine, USA.
| | - James Clement
- Betterhumans Inc., Gainesville, FL, USA
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Kaiyang Cheng
- Medical Informatics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | | | - David H Rehkopf
- Epidemiology & Population Health and Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Luis Rosero-Bixby
- Centro Centroamericano de Población, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Michael S Kobor
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - David Ts Lin
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Ake T Lu
- Dept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Zhe Fei
- Dept. of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Wei Guo
- Zymo Research Corp, Irvine, CA, USA
| | | | | | - Sulistyo E Dwi Putra
- Department of Biology, Faculty of Biotechnology, University of Surabaya, Surabaya, 60293, Indonesia
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Adolfo Correa
- Medicine and Population Health Science, University of Mississippi Medical Center, Jackson, USA
| | | | - Chiara Pirazzini
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bologna, Italy
| | - Giuseppe Passarino
- Department of Biology Ecology and Earth Science, University of Calabria, Rende, Italy
| | - Daniela Monti
- Department of Experimental and Clinical, Biomedical Sciences "Mario Serio" University of Florence, Florence, Italy
| | - Beatrice Arosio
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Paolo Garagnani
- Department of Medical and Surgical Sciences, University of Bologna, 40126, Bologna, Italy
- Alma Mater Research Institute On Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Department of Medical and Surgical Sciences, University of Bologna, 40126, Bologna, Italy
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, Russia
| | - Steve Horvath
- Dept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego, CA, USA.
- Dept. of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA.
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Kwiatkowska KM, Mavrogonatou E, Papadopoulou A, Sala C, Calzari L, Gentilini D, Bacalini MG, Dall’Olio D, Castellani G, Ravaioli F, Franceschi C, Garagnani P, Pirazzini C, Kletsas D. Heterogeneity of Cellular Senescence: Cell Type-Specific and Senescence Stimulus-Dependent Epigenetic Alterations. Cells 2023; 12:cells12060927. [PMID: 36980268 PMCID: PMC10047656 DOI: 10.3390/cells12060927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 03/22/2023] Open
Abstract
The aim of the present study was to provide a comprehensive characterization of whole genome DNA methylation patterns in replicative and ionizing irradiation- or doxorubicin-induced premature senescence, exhaustively exploring epigenetic modifications in three different human cell types: in somatic diploid skin fibroblasts and in bone marrow- and adipose-derived mesenchymal stem cells. With CpG-wise differential analysis, three epigenetic signatures were identified: (a) cell type- and treatment-specific signature; (b) cell type-specific senescence-related signature; and (c) cell type-transversal replicative senescence-related signature. Cluster analysis revealed that only replicative senescent cells created a distinct group reflecting notable alterations in the DNA methylation patterns accompanying this cellular state. Replicative senescence-associated epigenetic changes seemed to be of such an extent that they surpassed interpersonal dissimilarities. Enrichment in pathways linked to the nervous system and involved in the neurological functions was shown after pathway analysis of genes involved in the cell type-transversal replicative senescence-related signature. Although DNA methylation clock analysis provided no statistically significant evidence on epigenetic age acceleration related to senescence, a persistent trend of increased biological age in replicative senescent cultures of all three cell types was observed. Overall, this work indicates the heterogeneity of senescent cells depending on the tissue of origin and the type of senescence inducer that could be putatively translated to a distinct impact on tissue homeostasis.
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Affiliation(s)
| | - Eleni Mavrogonatou
- Laboratory of Cell Proliferation and Ageing, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, 15341 Athens, Greece
| | - Adamantia Papadopoulou
- Laboratory of Cell Proliferation and Ageing, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, 15341 Athens, Greece
| | - Claudia Sala
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Luciano Calzari
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, 20095 Milan, Italy
| | - Davide Gentilini
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, 20095 Milan, Italy
- Department of Brain and Behavioral Sciences, Università di Pavia, 27100 Pavia, Italy
| | | | - Daniele Dall’Olio
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy
| | - Gastone Castellani
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Francesco Ravaioli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy
| | - Claudio Franceschi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
- Laboratory of Systems Medicine of Healthy Aging, Institute of Biology and Biomedicine and Institute of Information Technology, Mathematics and Mechanics, Department of Applied Mathematics, N. I. Lobachevsky State University, 603022 Nizhny Novgorod, Russia
| | - Paolo Garagnani
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
- Correspondence: (P.G.); (C.P.); (D.K.)
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy
- Correspondence: (P.G.); (C.P.); (D.K.)
| | - Dimitris Kletsas
- Laboratory of Cell Proliferation and Ageing, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, 15341 Athens, Greece
- Correspondence: (P.G.); (C.P.); (D.K.)
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5
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Capri M, Conte M, Ciurca E, Pirazzini C, Garagnani P, Santoro A, Longo F, Salvioli S, Lau P, Moeller R, Jordan J, Illig T, Villanueva MM, Gruber M, Bürkle A, Franceschi C, Rittweger J. Long-term human spaceflight and inflammaging: Does it promote aging? Ageing Res Rev 2023; 87:101909. [PMID: 36918115 DOI: 10.1016/j.arr.2023.101909] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Spaceflight and its associated stressors, such as microgravity, radiation exposure, confinement, circadian derailment and disruptive workloads represent an unprecedented type of exposome that is entirely novel from an evolutionary stand point. Within this perspective, we aimed to review the effects of prolonged spaceflight on immune-neuroendocrine systems, brain and brain-gut axis, cardiovascular system and musculoskeletal apparatus, highlighting in particular the similarities with an accelerated aging process. In particular, spaceflight-induced muscle atrophy/sarcopenia and bone loss, vascular and metabolic changes, hyper and hypo reaction of innate and adaptive immune system appear to be modifications shared with the aging process. Most of these modifications are mediated by molecular events that include oxidative and mitochondrial stress, autophagy, DNA damage repair and telomere length alteration, among others, which directly or indirectly converge on the activation of an inflammatory response. According to the inflammaging theory of aging, such an inflammatory response could be a driver of an acceleration of the normal, physiological rate of aging and it is likely that all the systemic modifications in turn lead to an increase of inflammaging in a sort of vicious cycle. The most updated countermeasures to fight these modifications will be also discussed in the light of their possible application not only for astronauts' benefit, but also for older adults on the ground.
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Affiliation(s)
- Miriam Capri
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy; Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy
| | - Maria Conte
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy; Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy.
| | - Erika Ciurca
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy; Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy; Clinical Chemistry Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden; CNR Institute of Molecular Genetics, Unit of Bologna, Bologna, Italy; Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Aurelia Santoro
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy; Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy
| | - Federica Longo
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Stefano Salvioli
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy; IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Patrick Lau
- Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Ralf Moeller
- Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Jens Jordan
- Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany; Medical Faculty, University of Cologne, Cologne, Germany
| | - Thomas Illig
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Maria-Moreno Villanueva
- Human Performance Research Centre, Department of Sport Science, University of Konstanz, Konstanz, Germany
| | - Markus Gruber
- Human Performance Research Centre, Department of Sport Science, University of Konstanz, Konstanz, Germany
| | - Alexander Bürkle
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Claudio Franceschi
- Department of Applied Mathematics of the Institute of ITMM, National Research Lobachevsky State University of Nizhny Novgorod, the Russian Federation
| | - Jörn Rittweger
- Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany; Department of Pediatrics and Adolescent Medicine, University of Cologne, Cologne, Germany
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6
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Gensous N, Sala C, Pirazzini C, Ravaioli F, Milazzo M, Kwiatkowska KM, Marasco E, De Fanti S, Giuliani C, Pellegrini C, Santoro A, Capri M, Salvioli S, Monti D, Castellani G, Franceschi C, Bacalini MG, Garagnani P. A Targeted Epigenetic Clock for the Prediction of Biological Age. Cells 2022; 11:cells11244044. [PMID: 36552808 PMCID: PMC9777448 DOI: 10.3390/cells11244044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Epigenetic clocks were initially developed to track chronological age, but accumulating evidence indicates that they can also predict biological age. They are usually based on the analysis of DNA methylation by genome-wide methods, but targeted approaches, based on the assessment of a small number of CpG sites, are advisable in several settings. In this study, we developed a targeted epigenetic clock purposely optimized for the measurement of biological age. The clock includes six genomic regions mapping in ELOVL2, NHLRC1, AIM2, EDARADD, SIRT7 and TFAP2E genes, selected from a re-analysis of existing microarray data, whose DNA methylation is measured by EpiTYPER assay. In healthy subjects (n = 278), epigenetic age calculated using the targeted clock was highly correlated with chronological age (Spearman correlation = 0.89). Most importantly, and in agreement with previous results from genome-wide clocks, epigenetic age was significantly higher and lower than expected in models of increased (persons with Down syndrome, n = 62) and decreased (centenarians, n = 106; centenarians' offspring, n = 143; nutritional intervention in elderly, n = 233) biological age, respectively. These results support the potential of our targeted epigenetic clock as a new marker of biological age and open its evaluation in large cohorts to further promote the assessment of biological age in healthcare practice.
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Affiliation(s)
- Noémie Gensous
- Department of Internal Medicine and Clinical Immunology, CHU Bordeaux (Groupe Hospitalier Saint-André), 33077 Bordeaux, France
- UMR/CNRS 5164, ImmunoConcEpT, CNRS, University of Bordeaux, 33076 Bordeaux, France
| | - Claudia Sala
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Chiara Pirazzini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Via Altura 3, 40139 Bologna, Italy
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Maddalena Milazzo
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | | | - Elena Marasco
- Personal Genomics S.R.L., Via Roveggia, 43/B, 37134 Verona, Italy
| | - Sara De Fanti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Via Altura 3, 40139 Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology, Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Camilla Pellegrini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Via Altura 3, 40139 Bologna, Italy
| | - Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center, “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, 40126 Bologna, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center, “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, 40126 Bologna, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center, “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, 40126 Bologna, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50139 Florence, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging, Department of Applied Mathematics, Lobachevsky University, 603105 Nizhny Novgorod, Russia
| | - Maria Giulia Bacalini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Via Altura 3, 40139 Bologna, Italy
- Correspondence: ; Tel.: +39-051-6225977
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center, “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, 40126 Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, 14152 Huddinge, Sweden
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7
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Bolognesi G, Bacalini MG, Pirazzini C, Garagnani P, Giuliani C. Evolutionary Implications of Environmental Toxicant Exposure. Biomedicines 2022; 10:biomedicines10123090. [PMID: 36551846 PMCID: PMC9775150 DOI: 10.3390/biomedicines10123090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/03/2022] Open
Abstract
Homo sapiens have been exposed to various toxins and harmful compounds that change according to various phases of human evolution. Population genetics studies showed that such exposures lead to adaptive genetic changes; while observing present exposures to different toxicants, the first molecular mechanism that confers plasticity is epigenetic remodeling and, in particular, DNA methylation variation, a molecular mechanism proposed for medium-term adaptation. A large amount of scientific literature from clinical and medical studies revealed the high impact of such exposure on human biology; thus, in this review, we examine and infer the impact that different environmental toxicants may have in shaping human evolution. We first describe how environmental toxicants shape natural human variation in terms of genetic and epigenetic diversity, and then we describe how DNA methylation may influence mutation rate and, thus, genetic variability. We describe the impact of these substances on biological fitness in terms of reproduction and survival, and in conclusion, we focus on their effect on brain evolution and physiology.
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Affiliation(s)
- Giorgia Bolognesi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via San Giacomo 12, 40126 Bologna, Italy
- Laboratory of Molecular Anthropology, Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Francesco Selmi 3, 40126 Bologna, Italy
| | - Maria Giulia Bacalini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, via Altura 3, 40139 Bologna, Italy
| | - Chiara Pirazzini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, via Altura 3, 40139 Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via San Giacomo 12, 40126 Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology, Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Francesco Selmi 3, 40126 Bologna, Italy
- Correspondence:
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8
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Baldelli L, Bacalini M, Pirazzini C, Sambati L, Mignani F, Guaraldi P, Gentilini D, Calandra-Buonaura G, Garagnani P, Cortelli P, Franceschi C, Provini F. Epigenetic clocks suggest accelerated ageing in isolated REM Sleep Behavior Disorder patients. Sleep Med 2022. [DOI: 10.1016/j.sleep.2022.05.610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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9
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Ravaioli F, Zampieri M, Morandi L, Pirazzini C, Pellegrini C, De Fanti S, Gensous N, Pirazzoli GL, Sambati L, Ghezzo A, Ciccarone F, Reale A, Monti D, Salvioli S, Caiafa P, Capri M, Bürkle A, Moreno-Villanueva M, Garagnani P, Franceschi C, Bacalini MG. DNA Methylation Analysis of Ribosomal DNA in Adults With Down Syndrome. Front Genet 2022; 13:792165. [PMID: 35571061 PMCID: PMC9094685 DOI: 10.3389/fgene.2022.792165] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 03/18/2022] [Indexed: 01/08/2023] Open
Abstract
Control of ribosome biogenesis is a critical aspect of the regulation of cell metabolism. As ribosomal genes (rDNA) are organized in repeated clusters on chromosomes 13, 14, 15, 21, and 22, trisomy of chromosome 21 confers an excess of rDNA copies to persons with Down syndrome (DS). Previous studies showed an alteration of ribosome biogenesis in children with DS, but the epigenetic regulation of rDNA genes has not been investigated in adults with DS so far. In this study, we used a targeted deep-sequencing approach to measure DNA methylation (DNAm) of rDNA units in whole blood from 69 adults with DS and 95 euploid controls. We further evaluated the expression of the precursor of ribosomal RNAs (RNA45S) in peripheral blood mononuclear cells (PBMCs) from the same subjects. We found that the rDNA promoter tends to be hypermethylated in DS concerning the control group. The analysis of epihaplotypes (the combination of methylated and unmethylated CpG sites along the same DNA molecule) showed a significantly lower intra-individual diversity in the DS group, which at the same time was characterized by a higher interindividual variability. Finally, we showed that RNA45S expression is lower in adults with DS. Collectively, our results suggest a rearrangement of the epigenetic profile of rDNA in DS, possibly to compensate for the extranumerary rDNA copies. Future studies should assess whether the regulation of ribosome biogenesis can contribute to the pathogenesis of DS and explain the clinical heterogeneity characteristic of the syndrome.
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Affiliation(s)
- Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Michele Zampieri
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Luca Morandi
- Functional and Molecular Neuroimaging Unit, IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Chiara Pirazzini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
| | | | - Sara De Fanti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | - Noémie Gensous
- Department of Internal Medicine and Clinical Immunology, CHU Bordeaux (Groupe Hospitalier Saint-André), Bordeaux, France
- UMR/CNRS 5164, ImmunoConcEpT, CNRS, University of Bordeaux, Bordeaux, France
| | | | - Luisa Sambati
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, U.O.C. Clinica Neurologica Rete Neurologica Metropolitana (NEUROMET), Bologna, Italy
| | | | - Fabio Ciccarone
- IRCCS San Raffaele Roma, Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy
| | - Anna Reale
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Rome, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Maria Moreno-Villanueva
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”—Unit of Bologna, Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging, Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Maria Giulia Bacalini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
- *Correspondence: Maria Giulia Bacalini,
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10
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Meoni G, Tenori L, Schade S, Licari C, Pirazzini C, Bacalini MG, Garagnani P, Turano P, Trenkwalder C, Franceschi C, Mollenhauer B, Luchinat C. Metabolite and lipoprotein profiles reveal sex-related oxidative stress imbalance in de novo drug-naive Parkinson's disease patients. NPJ Parkinsons Dis 2022; 8:14. [PMID: 35136088 PMCID: PMC8826921 DOI: 10.1038/s41531-021-00274-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 12/16/2021] [Indexed: 12/14/2022] Open
Abstract
Parkinson’s disease (PD) is the neurological disorder showing the greatest rise in prevalence from 1990 to 2016. Despite clinical definition criteria and a tremendous effort to develop objective biomarkers, precise diagnosis of PD is still unavailable at early stage. In recent years, an increasing number of studies have used omic methods to unveil the molecular basis of PD, providing a detailed characterization of potentially pathological alterations in various biological specimens. Metabolomics could provide useful insights to deepen our knowledge of PD aetiopathogenesis, to identify signatures that distinguish groups of patients and uncover responsive biomarkers of PD that may be significant in early detection and in tracking the disease progression and drug treatment efficacy. The present work is the first large metabolomic study based on nuclear magnetic resonance (NMR) with an independent validation cohort aiming at the serum characterization of de novo drug-naive PD patients. Here, NMR is applied to sera from large training and independent validation cohorts of German subjects. Multivariate and univariate approaches are used to infer metabolic differences that characterize the metabolite and the lipoprotein profiles of newly diagnosed de novo drug-naive PD patients also in relation to the biological sex of the subjects in the study, evidencing a more pronounced fingerprint of the pathology in male patients. The presence of a validation cohort allowed us to confirm altered levels of acetone and cholesterol in male PD patients. By comparing the metabolites and lipoproteins levels among de novo drug-naive PD patients, age- and sex-matched healthy controls, and a group of advanced PD patients, we detected several descriptors of stronger oxidative stress.
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Affiliation(s)
- Gaia Meoni
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Sesto Fiorentino, Florence, Italy
| | - Sebastian Schade
- Department of Clinical Neurophysiology, University Medical Center Goettingen, Goettingen, Germany
| | - Cristina Licari
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Sesto Fiorentino, Florence, Italy
| | | | - Claudia Trenkwalder
- University Medical Center Goettingen, Department of Neurology and Paracelsus-Elena-Klinik, Kassel, Germany
| | - Claudio Franceschi
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy. .,Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia.
| | - Brit Mollenhauer
- University Medical Center Goettingen, Department of Neurology and Paracelsus-Elena-Klinik, Kassel, Germany.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy. .,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Sesto Fiorentino, Florence, Italy.
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11
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Zago E, Dal Molin A, Dimitri GM, Xumerle L, Pirazzini C, Bacalini MG, Maturo MG, Azevedo T, Spasov S, Gómez-Garre P, Periñán MT, Jesús S, Baldelli L, Sambati L, Calandra-Buonaura G, Garagnani P, Provini F, Cortelli P, Mir P, Trenkwalder C, Mollenhauer B, Franceschi C, Liò P, Nardini C. Early downregulation of hsa-miR-144-3p in serum from drug-naïve Parkinson's disease patients. Sci Rep 2022; 12:1330. [PMID: 35079043 PMCID: PMC8789812 DOI: 10.1038/s41598-022-05227-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/28/2021] [Indexed: 12/18/2022] Open
Abstract
Advanced age represents one of the major risk factors for Parkinson's Disease. Recent biomedical studies posit a role for microRNAs, also known to be remodelled during ageing. However, the relationship between microRNA remodelling and ageing in Parkinson's Disease, has not been fully elucidated. Therefore, the aim of the present study is to unravel the relevance of microRNAs as biomarkers of Parkinson's Disease within the ageing framework. We employed Next Generation Sequencing to profile serum microRNAs from samples informative for Parkinson's Disease (recently diagnosed, drug-naïve) and healthy ageing (centenarians) plus healthy controls, age-matched with Parkinson's Disease patients. Potential microRNA candidates markers, emerging from the combination of differential expression and network analyses, were further validated in an independent cohort including both drug-naïve and advanced Parkinson's Disease patients, and healthy siblings of Parkinson's Disease patients at higher genetic risk for developing the disease. While we did not find evidences of microRNAs co-regulated in Parkinson's Disease and ageing, we report that hsa-miR-144-3p is consistently down-regulated in early Parkinson's Disease patients. Moreover, interestingly, functional analysis revealed that hsa-miR-144-3p is involved in the regulation of coagulation, a process known to be altered in Parkinson's Disease. Our results consistently show the down-regulation of hsa-mir144-3p in early Parkinson's Disease, robustly confirmed across a variety of analytical and experimental analyses. These promising results ask for further research to unveil the functional details of the involvement of hsa-mir144-3p in Parkinson's Disease.
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Affiliation(s)
| | | | - Giovanna Maria Dimitri
- Computer Laboratory, Department of Computer Science and Technology, University of Cambridge, Cambridge, UK
| | | | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | | | - Maria Giovanna Maturo
- Personal Genomics S.R.L., Verona, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Tiago Azevedo
- Computer Laboratory, Department of Computer Science and Technology, University of Cambridge, Cambridge, UK
| | - Simeon Spasov
- Computer Laboratory, Department of Computer Science and Technology, University of Cambridge, Cambridge, UK
| | - Pilar Gómez-Garre
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - María Teresa Periñán
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Silvia Jesús
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Luca Baldelli
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
| | - Luisa Sambati
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Giovanna Calandra-Buonaura
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 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
- Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy
| | - Federica Provini
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Pietro Cortelli
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Pablo Mir
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
| | - Claudia Trenkwalder
- Paracelsus-Elena-Klinik, Kliniktstrasse 16, 34128, Kassel, Germany
- Department of Neurosurgery, University Medical Center Göttingen, Göttingen, Germany
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, Kliniktstrasse 16, 34128, Kassel, Germany
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia.
| | - Pietro Liò
- Computer Laboratory, Department of Computer Science and Technology, University of Cambridge, Cambridge, UK
| | - Christine Nardini
- Personal Genomics S.R.L., Verona, Italy.
- Consiglio Nazionale delle Ricerche, Istituto per le Applicazioni del Calcolo "Mauro Picone", 00185, Rome, Italy.
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12
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Baldelli L, Schade S, Jesús S, Schreglmann SR, Sambati L, Gómez-Garre P, Halsband C, Calandra-Buonaura G, Adarmes-Gómez AD, Sixel-Döring F, Zenesini C, Pirazzini C, Garagnani P, Bacalini MG, Bhatia KP, Cortelli P, Mollenhauer B, Franceschi C, Mir P, Trenkwalder C, Provini F. Heterogeneity of prodromal Parkinson symptoms in siblings of Parkinson disease patients. NPJ Parkinsons Dis 2021; 7:78. [PMID: 34493736 PMCID: PMC8423761 DOI: 10.1038/s41531-021-00219-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/09/2021] [Indexed: 11/09/2022]
Abstract
A prodromal phase of Parkinson's disease (PD) may precede motor manifestations by decades. PD patients' siblings are at higher risk for PD, but the prevalence and distribution of prodromal symptoms are unknown. The study objectives were (1) to assess motor and non-motor features estimating prodromal PD probability in PD siblings recruited within the European PROPAG-AGEING project; (2) to compare motor and non-motor symptoms to the well-established DeNoPa cohort. 340 PD siblings from three sites (Bologna, Seville, Kassel/Goettingen) underwent clinical and neurological evaluations of PD markers. The German part of the cohort was compared with German de novo PD patients (dnPDs) and healthy controls (CTRs) from DeNoPa. Fifteen (4.4%) siblings presented with subtle signs of motor impairment, with MDS-UPDRS-III scores not clinically different from CTRs. Symptoms of orthostatic hypotension were present in 47 siblings (13.8%), no different to CTRs (p = 0.072). No differences were found for olfaction and overall cognition; German-siblings performed worse than CTRs in visuospatial-executive and language tasks. 3/147 siblings had video-polysomnography-confirmed REM sleep behavior disorder (RBD), none was positive on the RBD Screening Questionnaire. 173/300 siblings had <1% probability of having prodromal PD; 100 between 1 and 10%, 26 siblings between 10 and 80%, one fulfilled the criteria for prodromal PD. According to the current analysis, we cannot confirm the increased risk of PD siblings for prodromal PD. Siblings showed a heterogeneous distribution of prodromal PD markers and probability. Additional parameters, including strong disease markers, should be investigated to verify if these results depend on validity and sensitivity of prodromal PD criteria, or if siblings' risk is not elevated.
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Affiliation(s)
- Luca Baldelli
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
| | - Sebastian Schade
- Department of Clinical Neurophysiology, University Medical Center Göttingen, Göttingen, Germany.,Department of Neurosurgery, University Medical Center Göttingen, Göttingen, Germany
| | - Silvia Jesús
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Seville, Spain
| | | | - Luisa Sambati
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Pilar Gómez-Garre
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Seville, Spain
| | - Claire Halsband
- Department of Clinical Neurophysiology, University Medical Center Göttingen, Göttingen, Germany.,Department of Neurosurgery, University Medical Center Göttingen, Göttingen, Germany
| | - Giovanna Calandra-Buonaura
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Astrid Daniela Adarmes-Gómez
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Seville, Spain
| | - Friederike Sixel-Döring
- Paracelsus-Elena-Klinik Kassel, Kassel, Germany.,Neurologische Klinik, Philipps-University, Marburg, Germany
| | - Corrado Zenesini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | | | - Kailash P Bhatia
- University College London (UCL), Institute of Neurology, London, United Kingdom
| | - Pietro Cortelli
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik Kassel, Kassel, Germany.,Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | | | | | - Pablo Mir
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Seville, Spain
| | - Claudia Trenkwalder
- Department of Neurosurgery, University Medical Center Göttingen, Göttingen, Germany.,Paracelsus-Elena-Klinik Kassel, Kassel, Germany
| | - Federica Provini
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy. .,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.
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13
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Ahmed O, Mukarram A, Pirazzini C, Marasco EE, Pedrelli M, Minniti M, Gustafsson U, Pramfalk C, Binder C, Petrillo E, Garagnani PP, Daub C, Eriksson M, Parini P. Hepatic transcriptional effects of simvastatin and the possible impact on COVID-19. Atherosclerosis 2021. [PMCID: PMC8415860 DOI: 10.1016/j.atherosclerosis.2021.06.428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Bacalini MG, Gentilini D, Monti D, Garagnani P, Mari D, Cesari M, Ogliari G, Passarino G, Franceschi C, Pirazzini C, Arosio B. No association between frailty index and epigenetic clocks in Italian semi-supercentenarians. Mech Ageing Dev 2021; 197:111514. [PMID: 34098514 DOI: 10.1016/j.mad.2021.111514] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
Centenarians experience successful ageing, although they still present high heterogeneity in their health status. The frailty index is a biomarker of biological age, able to capture such heterogeneity, even at extreme old age. At the same time, other biomarkers (e.g., epigenetic clocks) may be informative the biological age of the individual and potentially describe the ageing status in centenarians. In this article, we explore the relationship between epigenetic clocks and frailty index in a cohort of Italian centenarians. No association was reported, suggesting that these two approaches may describe different aspects of the same ageing process.
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Affiliation(s)
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy; Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy; Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy
| | - Daniela Mari
- Laboratorio Sperimentale di Ricerche di Neuroendocrinologia Geriatrica ed Oncologica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Matteo Cesari
- Geriatric Unit, IRCCS Istituti Clinici Scientifici Maugeri, University of Milan, Milan, Italy
| | - Giulia Ogliari
- Department of Health Care for Older People (HCOP), Queen's Medical Centre, Nottingham University Hospitals NHS Trust, Derby Road, Nottingham, Nottinghamshire, NG7 2UH, UK
| | - Giuseppe Passarino
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Rende, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.
| | - Beatrice Arosio
- Geriatric Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
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15
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Garagnani P, Marquis J, Delledonne M, Pirazzini C, Marasco E, Kwiatkowska KM, Iannuzzi V, Bacalini MG, Valsesia A, Carayol J, Raymond F, Ferrarini A, Xumerle L, Collino S, Mari D, Arosio B, Casati M, Ferri E, Monti D, Nacmias B, Sorbi S, Luiselli D, Pettener D, Castellani G, Sala C, Passarino G, De Rango F, D'Aquila P, Bertamini L, Martinelli N, Girelli D, Olivieri O, Giuliani C, Descombes P, Franceschi C. Whole-genome sequencing analysis of semi-supercentenarians. eLife 2021; 10:57849. [PMID: 33941312 PMCID: PMC8096429 DOI: 10.7554/elife.57849] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
Extreme longevity is the paradigm of healthy aging as individuals who reached the extreme decades of human life avoided or largely postponed all major age-related diseases. In this study, we sequenced at high coverage (90X) the whole genome of 81 semi-supercentenarians and supercentenarians [105+/110+] (mean age: 106.6 ± 1.6) and of 36 healthy unrelated geographically matched controls (mean age 68.0 ± 5.9) recruited in Italy. The results showed that 105+/110+ are characterized by a peculiar genetic background associated with efficient DNA repair mechanisms, as evidenced by both germline data (common and rare variants) and somatic mutations patterns (lower mutation load if compared to younger healthy controls). Results were replicated in a second independent cohort of 333 Italian centenarians and 358 geographically matched controls. The genetics of 105+/110+ identified DNA repair and clonal haematopoiesis as crucial players for healthy aging and for the protection from cardiovascular events.
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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.,Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy
| | - Julien Marquis
- Nestlé Research, Société des Produits Nestlé SA, Lausanne, Switzerland
| | - Massimo Delledonne
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.,Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy
| | | | - Vincenzo Iannuzzi
- Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy
| | | | - Armand Valsesia
- Nestlé Research, Société des Produits Nestlé SA, Lausanne, Switzerland
| | - Jerome Carayol
- Nestlé Research, Société des Produits Nestlé SA, Lausanne, Switzerland
| | - Frederic Raymond
- Nestlé Research, Société des Produits Nestlé SA, Lausanne, Switzerland
| | - Alberto Ferrarini
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Luciano Xumerle
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Daniela Mari
- Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Beatrice Arosio
- Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy.,Geriatric Unit, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Martina Casati
- Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Evelyn Ferri
- Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy.,IRCCS Fondazione Don Carlo Gnocchi, Firenze, Italy
| | - Sandro Sorbi
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy.,IRCCS Fondazione Don Carlo Gnocchi, Firenze, Italy
| | - Donata Luiselli
- Department for the Cultural Heritage (DBC), University of Bologna, Ravenna, Italy
| | - Davide Pettener
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Francesco De Rango
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Patrizia D'Aquila
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Luca Bertamini
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.,Department of Medicine, Unit of Internal Medicine, University of Verona, Verona, Italy
| | - Nicola Martinelli
- Department of Medicine, Unit of Internal Medicine, University of Verona, Verona, Italy
| | - Domenico Girelli
- Department of Medicine, Unit of Internal Medicine, University of Verona, Verona, Italy
| | - Oliviero Olivieri
- Department of Medicine, Unit of Internal Medicine, University of Verona, Verona, Italy
| | - Cristina Giuliani
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy.,School of Anthropology and Museum Ethnography, University of Oxford, Oxford, United Kingdom
| | - Patrick Descombes
- Nestlé Research, Société des Produits Nestlé SA, Lausanne, Switzerland
| | - Claudio Franceschi
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Applied Mathematics and Laboratory of Systems Biology of Aging, Lobachevsky University, Nizhny Novgorod, Russian Federation
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16
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Pellegrini C, Pirazzini C, Sala C, Sambati L, Yusipov I, Kalyakulina A, Ravaioli F, Kwiatkowska KM, Durso DF, Ivanchenko M, Monti D, Lodi R, Franceschi C, Cortelli P, Garagnani P, Bacalini MG. A Meta-Analysis of Brain DNA Methylation Across Sex, Age, and Alzheimer's Disease Points for Accelerated Epigenetic Aging in Neurodegeneration. Front Aging Neurosci 2021; 13:639428. [PMID: 33790779 PMCID: PMC8006465 DOI: 10.3389/fnagi.2021.639428] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/05/2021] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by specific alterations of brain DNA methylation (DNAm) patterns. Age and sex, two major risk factors for AD, are also known to largely affect the epigenetic profiles in brain, but their contribution to AD-associated DNAm changes has been poorly investigated. In this study we considered publicly available DNAm datasets of four brain regions (temporal, frontal, entorhinal cortex, and cerebellum) from healthy adult subjects and AD patients, and performed a meta-analysis to identify sex-, age-, and AD-associated epigenetic profiles. In one of these datasets it was also possible to distinguish 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) profiles. We showed that DNAm differences between males and females tend to be shared between the four brain regions, while aging differently affects cortical regions compared to cerebellum. We found that the proportion of sex-dependent probes whose methylation is modified also during aging is higher than expected, but that differences between males and females tend to be maintained, with only a few probes showing age-by-sex interaction. We did not find significant overlaps between AD- and sex-associated probes, nor disease-by-sex interaction effects. On the contrary, we found that AD-related epigenetic modifications are significantly enriched in probes whose DNAm varies with age and that there is a high concordance between the direction of changes (hyper or hypo-methylation) in aging and AD, supporting accelerated epigenetic aging in the disease. In summary, our results suggest that age-associated DNAm patterns concur to the epigenetic deregulation observed in AD, providing new insights on how advanced age enables neurodegeneration.
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Affiliation(s)
- Camilla Pellegrini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Luisa Sambati
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Katarzyna M. Kwiatkowska
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Danielle F. Durso
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Raffaele Lodi
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Pietro Cortelli
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Applied Biomedical Research Center, Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy
- National Research Council of Italy Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza,” Unit of Bologna, Bologna, Italy
| | - Maria Giulia Bacalini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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17
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Pirazzini C, Azevedo T, Baldelli L, Bartoletti-Stella A, Calandra-Buonaura G, Dal Molin A, Dimitri GM, Doykov I, Gómez-Garre P, Hägg S, Hällqvist J, Halsband C, Heywood W, Jesús S, Jylhävä J, Kwiatkowska KM, Labrador-Espinosa MA, Licari C, Maturo MG, Mengozzi G, Meoni G, Milazzo M, Periñán-Tocino MT, Ravaioli F, Sala C, Sambati L, Schade S, Schreglmann S, Spasov S, Tenori L, Williams D, Xumerle L, Zago E, Bhatia KP, Capellari S, Cortelli P, Garagnani P, Houlden H, Liò P, Luchinat C, Delledonne M, Mills K, Mir P, Mollenhauer B, Nardini C, Pedersen NL, Provini F, Strom S, Trenkwalder C, Turano P, Bacalini MG, Franceschi C. A geroscience approach for Parkinson's disease: Conceptual framework and design of PROPAG-AGEING project. Mech Ageing Dev 2021; 194:111426. [PMID: 33385396 DOI: 10.1016/j.mad.2020.111426] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/07/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022]
Abstract
Advanced age is the major risk factor for idiopathic Parkinson's disease (PD), but to date the biological relationship between PD and ageing remains elusive. Here we describe the rationale and the design of the H2020 funded project "PROPAG-AGEING", whose aim is to characterize the contribution of the ageing process to PD development. We summarize current evidences that support the existence of a continuum between ageing and PD and justify the use of a Geroscience approach to study PD. We focus in particular on the role of inflammaging, the chronic, low-grade inflammation characteristic of elderly physiology, which can propagate and transmit both locally and systemically. We then describe PROPAG-AGEING design, which is based on the multi-omic characterization of peripheral samples from clinically characterized drug-naïve and advanced PD, PD discordant twins, healthy controls and "super-controls", i.e. centenarians, who never showed clinical signs of motor disability, and their offspring. Omic results are then validated in a large number of samples, including in vitro models of dopaminergic neurons and healthy siblings of PD patients, who are at higher risk of developing PD, with the final aim of identifying the molecular perturbations that can deviate the trajectories of healthy ageing towards PD development.
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Affiliation(s)
- Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Tiago Azevedo
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Luca Baldelli
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Italy
| | | | - Giovanna Calandra-Buonaura
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Italy
| | | | - Giovanna Maria Dimitri
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Ivan Doykov
- Centre for Inborn Errors of Metabolism, UCL Institute of Child Health, London, United Kingdom
| | - Pilar Gómez-Garre
- Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Unidad de Trastornos del Movimiento, Servicio de Neurología y NeurofisiologíaClínica, Instituto de Biomedicina de Sevilla, Seville, Spain; Centro de Investigación Biomédicaen Red sobreEnfermedades Neurodegenerativas (CIBERNED), Spain
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Hällqvist
- Centre for Inborn Errors of Metabolism, UCL Institute of Child Health, London, United Kingdom
| | - Claire Halsband
- Department of Clinical Neurophysiology, University Medical Center Göttingen, Göttingen, Germany; Department of Gerontopsychiatry, Rhein-Mosel-Fachklinik, Andernach, Germany
| | - Wendy Heywood
- Centre for Inborn Errors of Metabolism, UCL Institute of Child Health, London, United Kingdom; NIHR Great Ormond Street Biomedical Research Centre, Great Ormond Street Hospital and UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Silvia Jesús
- Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Unidad de Trastornos del Movimiento, Servicio de Neurología y NeurofisiologíaClínica, Instituto de Biomedicina de Sevilla, Seville, Spain; Centro de Investigación Biomédicaen Red sobreEnfermedades Neurodegenerativas (CIBERNED), Spain
| | - Juulia Jylhävä
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Miguel A Labrador-Espinosa
- Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Unidad de Trastornos del Movimiento, Servicio de Neurología y NeurofisiologíaClínica, Instituto de Biomedicina de Sevilla, Seville, Spain; Centro de Investigación Biomédicaen Red sobreEnfermedades Neurodegenerativas (CIBERNED), Spain
| | - Cristina Licari
- CERM, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Maria Giovanna Maturo
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giacomo Mengozzi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | | | - Maddalena Milazzo
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Teresa Periñán-Tocino
- Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Unidad de Trastornos del Movimiento, Servicio de Neurología y NeurofisiologíaClínica, Instituto de Biomedicina de Sevilla, Seville, Spain; Centro de Investigación Biomédicaen Red sobreEnfermedades Neurodegenerativas (CIBERNED), Spain
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Luisa Sambati
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Italy
| | - Sebastian Schade
- Department of Clinical Neurophysiology, University Medical Center Göttingen, Göttingen, Germany
| | - Sebastian Schreglmann
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Simeon Spasov
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Leonardo Tenori
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, Italy
| | - Dylan Williams
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Sabina Capellari
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Italy
| | - Pietro Cortelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, United Kingdom
| | - Pietro Liò
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Claudio Luchinat
- CERM, University of Florence, Sesto Fiorentino, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Italy
| | | | - Kevin Mills
- Centre for Inborn Errors of Metabolism, UCL Institute of Child Health, London, United Kingdom; NIHR Great Ormond Street Biomedical Research Centre, Great Ormond Street Hospital and UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Pablo Mir
- Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Unidad de Trastornos del Movimiento, Servicio de Neurología y NeurofisiologíaClínica, Instituto de Biomedicina de Sevilla, Seville, Spain; Centro de Investigación Biomédicaen Red sobreEnfermedades Neurodegenerativas (CIBERNED), Spain
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, Kassel, Germany; Department of Neurology, University Medical Centre Goettingen, Goettingen, Germany
| | - Christine Nardini
- Istituto per le Applicazioni del Calcolo Mauro Picone, CNR, Roma, Italy
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Federica Provini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Italy
| | - Stephen Strom
- Department of Laboratory Medicine, Karolinska Institute and Karolinska Universitetssjukhuset, 171 76, Stockholm, Sweden
| | - Claudia Trenkwalder
- Paracelsus-Elena-Klinik, Kassel, Germany; Department of Neurosurgery, University Medical Center Göttingen, Germany
| | - Paola Turano
- CERM, University of Florence, Sesto Fiorentino, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Italy
| | | | - Claudio Franceschi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
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18
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Yusipov I, Bacalini MG, Kalyakulina A, Krivonosov M, Pirazzini C, Gensous N, Ravaioli F, Milazzo M, Giuliani C, Vedunova M, Fiorito G, Gagliardi A, Polidoro S, Garagnani P, Ivanchenko M, Franceschi C. Age-related DNA methylation changes are sex-specific: a comprehensive assessment. Aging (Albany NY) 2020; 12:24057-24080. [PMID: 33276343 PMCID: PMC7762479 DOI: 10.18632/aging.202251] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/19/2020] [Indexed: 12/18/2022]
Abstract
The existence of a sex gap in human health and longevity has been widely documented. Autosomal DNA methylation differences between males and females have been reported, but so far few studies have investigated if DNA methylation is differently affected by aging in males and females. We performed a meta-analysis of 4 large whole blood datasets, comparing 4 aspects of epigenetic age-dependent remodeling between the two sexes: differential methylation, variability, epimutations and entropy. We reported that a large fraction (43%) of sex-associated probes undergoes age-associated DNA methylation changes, and that a limited number of probes show age-by-sex interaction. We experimentally validated 2 regions mapping in FIGN and PRR4 genes and showed sex-specific deviations of their methylation patterns in models of decelerated (centenarians) and accelerated (Down syndrome) aging. While we did not find sex differences in the age-associated increase in epimutations and entropy, we showed that the number of probes having an age-related increase in methylation variability is 15 times higher in males compared to females. Our results can offer new epigenetic tools to study the interaction between aging and sex and can pave the way to the identification of molecular triggers of sex differences in longevity and age-related diseases prevalence.
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Affiliation(s)
- Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia.,Mathematics of Future Technologies Center, Lobachevsky University, Nizhniy Novgorod, Russia
| | | | - Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Mikhail Krivonosov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Noémie Gensous
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum – University of Bologna, Bologna, Italy
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum – University of Bologna, Bologna, Italy
| | - Maddalena Milazzo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum – University of Bologna, Bologna, Italy
| | - Cristina Giuliani
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy.,School of Anthropology and Museum Ethnography, University of Oxford, Oxford, UK
| | - Maria Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhni Novgorod, Nizhni Novgorod, Russia
| | - Giovanni Fiorito
- Department of Biomedical Sciences, University of Sassari, Italy.,Department of Epidemiology and Public Health, MRC/HPA Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - Amedeo Gagliardi
- Italian Institute for Genomic Medicine (IIGM), Candiolo 10060, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo 10060, Italy
| | - Silvia Polidoro
- Department of Epidemiology and Public Health, MRC/HPA Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK.,Italian Institute for Genomic Medicine (IIGM), Candiolo 10060, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo 10060, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum – University of Bologna, Bologna, Italy.,Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Applied Biomedical Research Center (CRBA), Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy.,CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia.,Mathematics of Future Technologies Center, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia
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19
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Cugliari G, Catalano C, Guarrera S, Allione A, Casalone E, Russo A, Grosso F, Ferrante D, Viberti C, Aspesi A, Sculco M, Pirazzini C, Libener R, Mirabelli D, Magnani C, Dianzani I, Matullo G. DNA Methylation of FKBP5 as Predictor of Overall Survival in Malignant Pleural Mesothelioma. Cancers (Basel) 2020; 12:cancers12113470. [PMID: 33233407 PMCID: PMC7700347 DOI: 10.3390/cancers12113470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/22/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive tumor with median survival of 12 months and limited effective treatments. The scope of this study was to study the relationship between blood DNA methylation (DNAm) and overall survival (OS) aiming at a noninvasive prognostic test. We investigated a cohort of 159 incident asbestos exposed MPM cases enrolled in an Italian area with high incidence of mesothelioma. Considering 12 months as a cut-off for OS, epigenome-wide association study (EWAS) revealed statistically significant (p value = 7.7 × 10-9) OS-related differential methylation of a single-CpG (cg03546163), located in the 5'UTR region of the FKBP5 gene. This is an independent marker of prognosis in MPM patients with a better performance than traditional inflammation-based scores such as lymphocyte-to-monocyte ratio (LMR). Cases with DNAm < 0.45 at the cg03546163 had significantly poor survival compared with those showing DNAm ≥ 0.45 (mean: 243 versus 534 days; p value< 0.001). Epigenetic changes at the FKBP5 gene were robustly associated with OS in MPM cases. Our results showed that blood DNA methylation levels could be promising and dynamic prognostic biomarkers in MPM.
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Affiliation(s)
- Giovanni Cugliari
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
- Correspondence: (G.C.); (G.M.)
| | - Chiara Catalano
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
| | - Simonetta Guarrera
- Italian Institute for Genomic Medicine, IIGM, 10060 Candiolo, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Alessandra Allione
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
| | - Elisabetta Casalone
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
| | - Alessia Russo
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
| | - Federica Grosso
- Division of Medical Oncology, SS. Antonio e Biagio General Hospital, 15121 Alessandria, Italy;
| | - Daniela Ferrante
- Unit of Medical Statistics, Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (D.F.); (C.M.)
- Cancer Epidemiology Unit, CPO-Piemonte, 28100 Novara, Italy
| | - Clara Viberti
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
| | - Anna Aspesi
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy; (A.A.); (M.S.); (I.D.)
| | - Marika Sculco
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy; (A.A.); (M.S.); (I.D.)
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy;
| | - Roberta Libener
- Pathology Unit, SS. Antonio e Biagio General Hospital, 15122 Alessandria, Italy;
| | - Dario Mirabelli
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, 10126 Turin, Italy;
- Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates “G. Scansetti”, University of Turin, 10126 Turin, Italy
| | - Corrado Magnani
- Unit of Medical Statistics, Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (D.F.); (C.M.)
- Cancer Epidemiology Unit, CPO-Piemonte, 28100 Novara, Italy
- Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates “G. Scansetti”, University of Turin, 10126 Turin, Italy
| | - Irma Dianzani
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy; (A.A.); (M.S.); (I.D.)
- Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates “G. Scansetti”, University of Turin, 10126 Turin, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
- Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates “G. Scansetti”, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, AOU Città della Salute e della Scienza, 10126 Turin, Italy
- Correspondence: (G.C.); (G.M.)
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20
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Minniti ME, Pedrelli M, Vedin L, Delbès A, Denis RG, Öörni K, Sala C, Pirazzini C, Thiagarajan D, Nurmi HJ, Grompe M, Mills K, Garagnani P, Ellis EC, Strom SC, Luquet SH, Wilson EM, Bial J, Steffensen KR, Parini P. Insights From Liver-Humanized Mice on Cholesterol Lipoprotein Metabolism and LXR-Agonist Pharmacodynamics in Humans. Hepatology 2020; 72:656-670. [PMID: 31785104 PMCID: PMC7496592 DOI: 10.1002/hep.31052] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIMS Genetically modified mice have been used extensively to study human disease. However, the data gained are not always translatable to humans because of major species differences. Liver-humanized mice (LHM) are considered a promising model to study human hepatic and systemic metabolism. Therefore, we aimed to further explore their lipoprotein metabolism and to characterize key hepatic species-related, physiological differences. APPROACH AND RESULTS Fah-/- , Rag2-/- , and Il2rg-/- knockout mice on the nonobese diabetic (FRGN) background were repopulated with primary human hepatocytes from different donors. Cholesterol lipoprotein profiles of LHM showed a human-like pattern, characterized by a high ratio of low-density lipoprotein to high-density lipoprotein, and dependency on the human donor. This pattern was determined by a higher level of apolipoprotein B100 in circulation, as a result of lower hepatic mRNA editing and low-density lipoprotein receptor expression, and higher levels of circulating proprotein convertase subtilisin/kexin type 9. As a consequence, LHM lipoproteins bind to human aortic proteoglycans in a pattern similar to human lipoproteins. Unexpectedly, cholesteryl ester transfer protein was not required to determine the human-like cholesterol lipoprotein profile. Moreover, LHM treated with GW3965 mimicked the negative lipid outcomes of the first human trial of liver X receptor stimulation (i.e., a dramatic increase of cholesterol and triglycerides in circulation). Innovatively, LHM allowed the characterization of these effects at a molecular level. CONCLUSIONS LHM represent an interesting translatable model of human hepatic and lipoprotein metabolism. Because several metabolic parameters displayed donor dependency, LHM may also be used in studies for personalized medicine.
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Affiliation(s)
- Mirko E. Minniti
- Department of Laboratory MedicineDivision of Clinical ChemistryKarolinska InstituteStockholmSweden
| | - Matteo Pedrelli
- Department of Laboratory MedicineDivision of Clinical ChemistryKarolinska InstituteStockholmSweden
| | - Lise‐Lotte Vedin
- Department of Laboratory MedicineDivision of Clinical ChemistryKarolinska InstituteStockholmSweden
| | - Anne‐Sophie Delbès
- Unit of Functional and Adaptive BiologyParis Diderot UniversitySorbonne Paris CitéParisFrance
| | - Raphaël G.P. Denis
- Unit of Functional and Adaptive BiologyParis Diderot UniversitySorbonne Paris CitéParisFrance
| | - Katariina Öörni
- Atherosclerosis Research LaboratoryWihuri Research InstituteHelsinkiFinland
| | - Claudia Sala
- Department of Physics and AstronomyUniversity of BolognaBolognaItaly
| | | | - Divya Thiagarajan
- Department of Laboratory MedicineClinical Research CenterKarolinska InstituteStockholmSweden
| | - Harri J. Nurmi
- Atherosclerosis Research LaboratoryWihuri Research InstituteHelsinkiFinland,Center of Excellence in Translational Cancer BiologyUniversity of HelsinkiBiomedicum HelsinkiHelsinkiFinland
| | - Markus Grompe
- Department of PediatricsOregon Stem Cell CenterOregon Health and Science UniversityPortlandOR,Yecuris CorporationTualatinOR
| | - Kevin Mills
- Center for Inborn Errors of MetabolismUniversity College LondonLondonUK
| | - Paolo Garagnani
- Department of Laboratory MedicineDivision of Clinical ChemistryKarolinska InstituteStockholmSweden,Department of Experimental, Diagnostic, and Specialty Medicine, and “L. Galvani” Interdepartmental Research CenterUniversity of BolognaBolognaItaly
| | - Ewa C.S. Ellis
- Department of Clinical ScienceIntervention and TechnologyDivision of SurgeryKarolinska Institute at Karolinska University Hospital HuddingeStockholmSweden
| | - Stephen C. Strom
- Department of Laboratory MedicineDivision of PathologyKarolinska InstituteStockholmSweden
| | - Serge H. Luquet
- Unit of Functional and Adaptive BiologyParis Diderot UniversitySorbonne Paris CitéParisFrance
| | | | | | - Knut R. Steffensen
- Department of Laboratory MedicineDivision of Clinical ChemistryKarolinska InstituteStockholmSweden
| | - Paolo Parini
- Department of Laboratory MedicineDivision of Clinical ChemistryKarolinska InstituteStockholmSweden,Department of MedicineMetabolism UnitKarolinska Institute at Karolinska University Hospital HuddingeStockholmSweden,Patient Area Nephrology and Endocrinology, Inflammation and Infection ThemeKarolinska University HospitalStockholmSweden
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21
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Kwiatkowska KM, Bacalini MG, Sala C, Kaziyama H, de Andrade DC, Terlizzi R, Giannini G, Cevoli S, Pierangeli G, Cortelli P, Garagnani P, Pirazzini C. Analysis of Epigenetic Age Predictors in Pain-Related Conditions. Front Public Health 2020; 8:172. [PMID: 32582603 PMCID: PMC7296181 DOI: 10.3389/fpubh.2020.00172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/20/2020] [Indexed: 01/31/2023] Open
Abstract
Chronic pain prevalence is high worldwide and increases at older ages. Signs of premature aging have been associated with chronic pain, but few studies have investigated aging biomarkers in pain-related conditions. A set of DNA methylation (DNAm)-based estimates of age, called “epigenetic clocks,” has been proposed as biological measures of age-related adverse processes, morbidity, and mortality. The aim of this study is to assess if different pain-related phenotypes show alterations in DNAm age. In our analysis, we considered three cohorts for which whole-blood DNAm data were available: heat pain sensitivity (HPS), including 20 monozygotic twin pairs discordant for heat pain temperature threshold; fibromyalgia (FM), including 24 cases and 20 controls; and headache, including 22 chronic migraine and medication overuse headache patients (MOH), 18 episodic migraineurs (EM), and 13 healthy subjects. We used the Horvath's epigenetic age calculator to obtain DNAm-based estimates of epigenetic age, telomere length, levels of 7 proteins in plasma, number of smoked packs of cigarettes per year, and blood cell counts. We did not find differences in epigenetic age acceleration, calculated using five different epigenetic clocks, between subjects discordant for pain-related phenotypes. Twins with high HPS had increased CD8+ T cell counts (nominal p = 0.028). HPS thresholds were negatively associated with estimated levels of GDF15 (nominal p = 0.008). FM patients showed decreased naive CD4+ T cell counts compared with controls (nominal p = 0.015). The severity of FM manifestations expressed through various evaluation tests was associated with decreased levels of leptin, shorter length of telomeres, and reduced CD8+ T and natural killer cell counts (nominal p < 0.05), while the duration of painful symptoms was positively associated with telomere length (nominal p = 0.034). No differences in DNAm-based estimates were detected for MOH or EM compared with controls. In summary, our study suggests that HPS, FM, and MOH/EM do not show signs of epigenetic age acceleration in whole blood, while HPS and FM are associated with DNAm-based estimates of immunological parameters, plasma proteins, and telomere length. Future studies should extend these observations in larger cohorts.
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Affiliation(s)
| | | | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Helena Kaziyama
- Department of Neurology, Pain Center, LIM 62, University of São Paulo, São Paulo, Brazil
| | - Daniel Ciampi de Andrade
- Department of Neurology, Pain Center, LIM 62, University of São Paulo, São Paulo, Brazil.,Pain Center, Instituto do Câncer do Estado de São Paulo, São Paulo, Brazil
| | | | - Giulia Giannini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Sabina Cevoli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Giulia Pierangeli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Pietro Cortelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Applied Biomedical Research Center (CRBA), Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy.,Unit of Bologna, CNR Institute of Molecular Genetics Luigi Luca Cavalli-Sforza, Bologna, Italy
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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22
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Sazzini M, Abondio P, Sarno S, Gnecchi-Ruscone GA, Ragno M, Giuliani C, De Fanti S, Ojeda-Granados C, Boattini A, Marquis J, Valsesia A, Carayol J, Raymond F, Pirazzini C, Marasco E, Ferrarini A, Xumerle L, Collino S, Mari D, Arosio B, Monti D, Passarino G, D'Aquila P, Pettener D, Luiselli D, Castellani G, Delledonne M, Descombes P, Franceschi C, Garagnani P. Genomic history of the Italian population recapitulates key evolutionary dynamics of both Continental and Southern Europeans. BMC Biol 2020; 18:51. [PMID: 32438927 PMCID: PMC7243322 DOI: 10.1186/s12915-020-00778-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/01/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The cline of human genetic diversity observable across Europe is recapitulated at a micro-geographic scale by variation within the Italian population. Besides resulting from extensive gene flow, this might be ascribable also to local adaptations to diverse ecological contexts evolved by people who anciently spread along the Italian Peninsula. Dissecting the evolutionary history of the ancestors of present-day Italians may thus improve the understanding of demographic and biological processes that contributed to shape the gene pool of European populations. However, previous SNP array-based studies failed to investigate the full spectrum of Italian variation, generally neglecting low-frequency genetic variants and examining a limited set of small effect size alleles, which may represent important determinants of population structure and complex adaptive traits. To overcome these issues, we analyzed 38 high-coverage whole-genome sequences representative of population clusters at the opposite ends of the cline of Italian variation, along with a large panel of modern and ancient Euro-Mediterranean genomes. RESULTS We provided evidence for the early divergence of Italian groups dating back to the Late Glacial and for Neolithic and distinct Bronze Age migrations having further differentiated their gene pools. We inferred adaptive evolution at insulin-related loci in people from Italian regions with a temperate climate, while possible adaptations to pathogens and ultraviolet radiation were observed in Mediterranean Italians. Some of these adaptive events may also have secondarily modulated population disease or longevity predisposition. CONCLUSIONS We disentangled the contribution of multiple migratory and adaptive events in shaping the heterogeneous Italian genomic background, which exemplify population dynamics and gene-environment interactions that played significant roles also in the formation of the Continental and Southern European genomic landscapes.
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Affiliation(s)
- Marco Sazzini
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy.
| | - Paolo Abondio
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Stefania Sarno
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | | | - Matteo Ragno
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Sara De Fanti
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Claudia Ojeda-Granados
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara "Fray Antonio Alcalde" and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Alessio Boattini
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Julien Marquis
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
- Current Address: Lausanne Genomic Technologies Facility, University of Lausanne, Lausanne, Switzerland
| | - Armand Valsesia
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Jerome Carayol
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | | | - Chiara Pirazzini
- IRCCS Bologna Institute of Neurological Sciences, Bologna, Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna, Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Alberto Ferrarini
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
- Current Address: Menarini Silicon Biosystems SpA, Castel Maggiore, Bologna, Italy
| | - Luciano Xumerle
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Daniela Mari
- Geriatric Unit, Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Beatrice Arosio
- Geriatric Unit, Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Patrizia D'Aquila
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Davide Pettener
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Gastone Castellani
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Massimo Delledonne
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Claudio Franceschi
- Department of Applied Mathematics, Institute of Information Technology, Lobachevsky University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Paolo Garagnani
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy.
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna, Bologna, Italy.
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden.
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23
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Bacalini MG, Franceschi C, Gentilini D, Ravaioli F, Zhou X, Remondini D, Pirazzini C, Giuliani C, Marasco E, Gensous N, Di Blasio AM, Ellis E, Gramignoli R, Castellani G, Capri M, Strom S, Nardini C, Cescon M, Grazi GL, Garagnani P. Molecular Aging of Human Liver: An Epigenetic/Transcriptomic Signature. J Gerontol A Biol Sci Med Sci 2019; 74:1-8. [PMID: 29554203 DOI: 10.1093/gerona/gly048] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 12/12/2022] Open
Abstract
The feasibility of liver transplantation from old healthy donors suggests that this organ is able to preserve its functionality during aging. To explore the biological basis of this phenomenon, we characterized the epigenetic profile of liver biopsies collected from 45 healthy liver donors ranging from 13 to 90 years old using the Infinium HumanMethylation450 BeadChip. The analysis indicates that a large remodeling in DNA methylation patterns occurs, with 8,823 age-associated differentially methylated CpG probes. Notably, these age-associated changes tended to level off after the age of 60, as confirmed by Horvath's clock. Using stringent selection criteria, we further identified a DNA methylation signature of aging liver including 75 genomic regions. We demonstrated that this signature is specific for liver compared to other tissues and that it is able to detect biological age-acceleration effects associated with obesity. Finally, we combined DNA methylation measurements with available expression data. Although the intersection between the two omic characterizations was low, both approaches suggested a previously unappreciated role of epithelial-mesenchymal transition and Wnt-signaling pathways in the aging of human liver.
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Affiliation(s)
| | - Claudio Franceschi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Italy.,DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy.,CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Italy
| | - Francesco Ravaioli
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy
| | - Xiaoyuan Zhou
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, PR China.,University of Chinese Academy of Sciences, Beijing, PR China.,Department of Neurology, University of San Francisco, California
| | - Daniel Remondini
- Department of Physics and Astronomy (DIFA) and INFN Sez. Bologna, Alma Mater Studiorum, Italy
| | | | - Cristina Giuliani
- Department of Biological Geological and Environmental Sciences, Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Italy
| | - Elena Marasco
- CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy
| | - Noémie Gensous
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy
| | | | - Ewa Ellis
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Roberto Gramignoli
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Gastone Castellani
- CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy.,Department of Biological Geological and Environmental Sciences, Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Italy
| | - Miriam Capri
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy.,CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy
| | - Stephen Strom
- Department of Laboratory Medicine, Karolinska Institute and Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Christine Nardini
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,CNR IAC "Mauro Picone", Roma, Italy.,Personal Genomics S.r.l., Verona, Italy
| | - Matteo Cescon
- General Surgery and Transplant Unit, Department of Medical and Surgical Sciences, Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | | | - Paolo Garagnani
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy.,CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna, Italy.,Institute of Molecular Genetics (IGM)-CNR, Unit of Bologna, Italy.,Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopaedic Institute, Bologna, Italy
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24
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Giuliani C, Sazzini M, Pirazzini C, Bacalini MG, Marasco E, Ruscone GAG, Fang F, Sarno S, Gentilini D, Di Blasio AM, Crocco P, Passarino G, Mari D, Monti D, Nacmias B, Sorbi S, Salvarani C, Catanoso M, Pettener D, Luiselli D, Ukraintseva S, Yashin A, Franceschi C, Garagnani P. Impact of demography and population dynamics on the genetic architecture of human longevity. Aging (Albany NY) 2019; 10:1947-1963. [PMID: 30089705 PMCID: PMC6128422 DOI: 10.18632/aging.101515] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 07/26/2018] [Indexed: 02/07/2023]
Abstract
The study of the genetics of longevity has been mainly addressed by GWASs that considered subjects from different populations to reach higher statistical power. The "price to pay" is that population-specific evolutionary histories and trade-offs were neglected in the investigation of gene-environment interactions. We propose a new “diachronic” approach that considers processes occurred at both evolutionary and lifespan timescales. We focused on a well-characterized population in terms of evolutionary history (i.e. Italians) and we generated genome-wide data for 333 centenarians from the peninsula and 773 geographically-matched healthy individuals. Obtained results showed that: (i) centenarian genomes are enriched for an ancestral component likely shaped by pre-Neolithic migrations; (ii) centenarians born in Northern Italy unexpectedly clustered with controls from Central/Southern Italy suggesting that Neolithic and Bronze Age gene flow did not favor longevity in this population; (iii) local past adaptive events in response to pathogens and targeting arachidonic acid metabolism became favorable for longevity; (iv) lifelong changes in the frequency of several alleles revealed pleiotropy and trade-off mechanisms crucial for longevity. Therefore, we propose that demographic history and ancient/recent population dynamics need to be properly considered to identify genes involved in longevity, which can differ in different temporal/spatial settings.
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Affiliation(s)
- Cristina Giuliani
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy.,School of Anthropology and Museum Ethnography, University of Oxford, Oxford, UK.,Interdepartmental Center "L. Galvani," (CIG), University of Bologna, Bologna, Italy
| | - Marco Sazzini
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Chiara Pirazzini
- IRCCS, Institute of Neurological Sciences of Bologna, Bologna, Italy
| | | | - Elena Marasco
- Interdepartmental Center "L. Galvani," (CIG), University of Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.,Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Guido Alberto Gnecchi Ruscone
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Fang Fang
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Stefania Sarno
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Davide Gentilini
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | | | - Paolina Crocco
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Daniela Mari
- Geriatric Unit, Department of Medical Sciences and Community Health, Milan, Italy.,Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
| | - Sandro Sorbi
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy.,IRCCS Don Gnocchi, Florence, Italy
| | - Carlo Salvarani
- Azienda Ospedaliera-IRCCS, Reggio Emilia, Italy.,Department of Surgical, Medical, Dental and Morphological Sciences with Interest Transplant, Oncological and Regenerative Medicine, , Italy
| | | | - Davide Pettener
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Department for the Cultural Heritage (DBC), University of Bologna, Ravenna, Italy
| | - Svetlana Ukraintseva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Anatoliy Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Claudio Franceschi
- IRCCS, Institute of Neurological Sciences of Bologna, Bologna, Italy.,Co-senior authors
| | - 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, S-141 86 Stockholm, Sweden.,CNR Institute of Molecular Genetics, Unit of Bologna, Bologna, Italy.,Rizzoli Orthopaedic Institute, Laboratory of Cell Biology, Bologna, Italy.,Co-senior authors
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25
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Ulbar F, Montemurro T, Jofra T, Capri M, Comai G, Bertuzzo V, Lavazza C, Mandelli A, Viganò M, Budelli S, Bacalini MG, Pirazzini C, Garagnani P, Giudice V, Sollazzo D, Curti A, Arpinati M, La Manna G, Cescon M, Pinna AD, Franceschi C, Battaglia M, Giordano R, Catani L, Lemoli RM. Regulatory T cells from patients with end-stage organ disease can be isolated, expanded and cryopreserved according good manufacturing practice improving their function. J Transl Med 2019; 17:250. [PMID: 31383037 PMCID: PMC6683529 DOI: 10.1186/s12967-019-2004-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/27/2019] [Indexed: 12/16/2022] Open
Abstract
Background Here, we isolated, expanded and functionally characterized regulatory T cells (Tregs) from patients with end stage kidney and liver disease, waiting for kidney/liver transplantation (KT/LT), with the aim to establish a suitable method to obtain large numbers of immunomodulatory cells for adoptive immunotherapy post-transplantation. Methods We first established a preclinical protocol for expansion/isolation of Tregs from peripheral blood of LT/KT patients. We then scaled up and optimized such protocol according to good manufacturing practice (GMP) to obtain high numbers of purified Tregs which were phenotypically and functionally characterized in vitro and in vivo in a xenogeneic acute graft-versus-host disease (aGVHD) mouse model. Specifically, immunodepressed mice (NOD-SCID-gamma KO mice) received human effector T cells with or without GMP-produced Tregs to prevent the onset of xenogeneic GVHD. Results Our small scale Treg isolation/expansion protocol generated functional Tregs. Interestingly, cryopreservation/thawing did not impair phenotype/function and DNA methylation pattern of FOXP3 gene of the expanded Tregs. Fully functional Tregs were also isolated/expanded from KT and LT patients according to GMP. In the mouse model, GMP Tregs from LT or KT patient proved to be safe and show a trend toward reduced lethality of acute GVHD. Conclusions These data demonstrate that expanded/thawed GMP-Tregs from patients with end-stage organ disease are fully functional in vitro. Moreover, their infusion is safe and results in a trend toward reduced lethality of acute GVHD in vivo, further supporting Tregs-based adoptive immunotherapy in solid organ transplantation. Electronic supplementary material The online version of this article (10.1186/s12967-019-2004-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Ulbar
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Tiziana Montemurro
- Cell Factory, Unit of Cellular Therapy and Cryobiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Tatiana Jofra
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Giorgia Comai
- Nephrology Dialysis and Renal Transplant Unit, Department of Experimental Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Valentina Bertuzzo
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Cristiana Lavazza
- Cell Factory, Unit of Cellular Therapy and Cryobiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandra Mandelli
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Mariele Viganò
- Cell Factory, Unit of Cellular Therapy and Cryobiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvia Budelli
- Cell Factory, Unit of Cellular Therapy and Cryobiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,EPIGET LAB, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | | | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, 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.,Unit of Bologna, CNR Institute of Molecular Genetics, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Valeria Giudice
- Azienda Ospedaliero-Universitaria di Bologna S. Orsola-Malpighi, Bologna, Italy
| | - Daria Sollazzo
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Antonio Curti
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Mario Arpinati
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Gaetano La Manna
- Nephrology Dialysis and Renal Transplant Unit, Department of Experimental Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Matteo Cescon
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | | | | | - Manuela Battaglia
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Rosaria Giordano
- Cell Factory, Unit of Cellular Therapy and Cryobiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lucia Catani
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy.
| | - Roberto Massimo Lemoli
- Azienda Ospedaliero-Universitaria di Bologna S. Orsola-Malpighi, Bologna, Italy.,Clinic of Hematology, Department of Internal Medicine (DiMI), University of Genoa, Genoa, Italy.,IRCCS Ospedale Policlinico S. Martino, Genoa, Italy
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26
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Montesanto A, Bonfigli AR, De Luca M, Crocco P, Garagnani P, Marasco E, Pirazzini C, Giuliani C, Romagnoli F, Franceschi C, Passarino G, Testa R, Olivieri F, Rose G. Erythropoietin (EPO) haplotype associated with all-cause mortality in a cohort of Italian patients with Type-2 Diabetes. Sci Rep 2019; 9:10395. [PMID: 31316151 PMCID: PMC6637129 DOI: 10.1038/s41598-019-46894-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 06/27/2019] [Indexed: 01/04/2023] Open
Abstract
Type-2 Diabetes (T2D), diabetic complications, and their clinical risk factors harbor a substantial genetic component but the genetic factors contributing to overall diabetes mortality remain unknown. Here, we examined the association between genetic variants at 21 T2D-susceptibility loci and all-cause mortality in an elderly cohort of 542 Italian diabetic patients who were followed for an average of 12.08 years. Univariate Cox regression analyses detected age, waist-to-hip ratio (WHR), glycosylated haemoglobin (HbA1c), diabetes duration, retinopathy, nephropathy, chronic kidney disease (CKD), and anaemia as predictors of all-cause mortality. When Cox proportional hazards multivariate models adjusted for these factors were run, three erythropoietin (EPO) genetic variants in linkage disequilibrium (LD) with each other (rs1617640-T/G, rs507392-T/C and rs551238-A/C) were significantly (False Discovery Rate < 0.1) associated with mortality. Haplotype multivariate analysis revealed that patients carrying the G-C-C haplotype have an increased probability of survival, while an opposite effect was observed among subjects carrying the T-T-A haplotype. Our findings provide evidence that the EPO gene is an independent predictor of mortality in patients with T2D. Thus, understanding the mechanisms by which the genetic variability of EPO affects the mortality of T2D patients may provide potential targets for therapeutic interventions to improve the survival of these patients.
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Affiliation(s)
- Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy
| | | | - Maria De Luca
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Paolina Crocco
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Cristina Giuliani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Fabio Romagnoli
- Diabetology Unit, IRCCS INRCA, National Institute, Ancona, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy
| | - Roberto Testa
- Clinical Laboratory and Molecular Diagnostics, IRCCS INRCA, Ancona, Italy
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy.,Center of Clinical Pathology and Innovative Therapy, National Institute IRCCS INRCA, Ancona, Italy
| | - Giuseppina Rose
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy.
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27
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De Francesco D, Wit FW, Bürkle A, Oehlke S, Kootstra NA, Winston A, Franceschi C, Garagnani P, Pirazzini C, Libert C, Grune T, Weber D, Jansen EH, Sabin CA, Reiss P. Do people living with HIV experience greater age advancement than their HIV-negative counterparts? AIDS 2019; 33:259-268. [PMID: 30325781 PMCID: PMC6319574 DOI: 10.1097/qad.0000000000002063] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/28/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVES Despite successful antiretroviral therapy, people living with HIV (PLWH) may show signs of premature/accentuated aging. We compared established biomarkers of aging in PLWH, appropriately chosen HIV-negative individuals, and blood donors, and explored factors associated with biological age advancement. DESIGN Cross-sectional analysis of 134 PLWH on suppressive antiretroviral therapy, 79 lifestyle-comparable HIV-negative controls aged 45 years or older from the Co-morBidity in Relation to AIDS (COBRA) cohort, and 35 age-matched blood donors. METHODS Biological age was estimated using a validated algorithm based on 10 biomarkers. Associations between 'age advancement' (biological minus chronological age) and HIV status/parameters, lifestyle, cytomegalovirus (CMV), hepatitis B (HBV) and hepatitis C virus (HCV) infections were investigated using linear regression. RESULTS The average (95% CI) age advancement was greater in both HIV-positive [13.2 (11.6-14.9) years] and HIV-negative [5.5 (3.8-7.2) years] COBRA participants compared with blood donors [-7.0 (-4.1 to -9.9) years, both P's < 0.001)], but also in HIV-positive compared with HIV-negative participants (P < 0.001). Chronic HBV, higher anti-CMV IgG titer and CD8 T-cell count were each associated with increased age advancement, independently of HIV-status/group. Among HIV-positive participants, age advancement was increased by 3.5 (0.1-6.8) years among those with nadir CD4+ T-cell count less than 200 cells/μl and by 0.1 (0.06-0.2) years for each additional month of exposure to saquinavir. CONCLUSION Both treated PLWH and lifestyle-comparable HIV-negative individuals show signs of age advancement compared with blood donors, to which persistent CMV, HBV co-infection and CD8+ T-cell activation may have contributed. Age advancement remained greatest in PLWH and was related to prior immunodeficiency and cumulative saquinavir exposure.
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Affiliation(s)
| | - Ferdinand W. Wit
- Department of Global Health, Academic Medical Center and Amsterdam Institute for Global Health and Development
- Stichting HIV Monitoring, Amsterdam, The Netherlands
| | - Alexander Bürkle
- Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - Sebastian Oehlke
- Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands
| | - Alan Winston
- Division of Infectious Diseases, Imperial College London, London, UK
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum Universitá di Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum Universitá di Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum Universitá di Bologna, Bologna, Italy
| | - Claude Libert
- Department of Biomedical Molecular Biology, Ghent University
- Center for Inflammation Research, Flanders Institute for Biotechnology, Ghent, Belgium
| | - Tilman Grune
- Department of Molecular Toxicology, German Institute of Human Nutrition, Nuthetal, Germany
| | - Daniela Weber
- Department of Molecular Toxicology, German Institute of Human Nutrition, Nuthetal, Germany
| | - Eugène H.J.M. Jansen
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Peter Reiss
- Department of Global Health, Academic Medical Center and Amsterdam Institute for Global Health and Development
- Stichting HIV Monitoring, Amsterdam, The Netherlands
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28
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Gensous N, Franceschi C, Blomberg BB, Pirazzini C, Ravaioli F, Gentilini D, Di Blasio AM, Garagnani P, Frasca D, Bacalini MG. Responders and non-responders to influenza vaccination: A DNA methylation approach on blood cells. Exp Gerontol 2018; 105:94-100. [PMID: 29360511 PMCID: PMC5989724 DOI: 10.1016/j.exger.2018.01.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/20/2017] [Accepted: 01/16/2018] [Indexed: 01/11/2023]
Abstract
Several evidences indicate that aging negatively affects the effectiveness of influenza vaccination. Although it is well established that immunosenescence has an important role in vaccination response, the molecular pathways underlying this process are largely unknown. Given the importance of epigenetic remodeling in aging, here we analyzed the relationship between responsiveness to influenza vaccination and DNA methylation profiles in healthy subjects of different ages. Peripheral blood mononuclear cells were collected from 44 subjects (age range: 19-90 years old) immediately before influenza vaccination. Subjects were subsequently classified as responders or non-responders according to hemagglutination inhibition assay 4-6 weeks after the vaccination. Baseline whole genome DNA methylation in peripheral blood mononuclear cells was analyzed using the Illumina® Infinium 450 k microarray. Differential methylation analysis between the two groups (responders and non-responders) was performed through an analysis of variance, correcting for age, sex and batch. We identified 83 CpG sites having a nominal p-value <.001 and absolute difference in DNA methylation of at least 0.05 between the two groups. For some CpG sites, we observed age-dependent decrease or increase in methylation, which in some cases was specific for the responders and non-responders groups. Finally, we divided the cohort in two subgroups including younger (age < 50) and older (age ≥ 50) subjects and compared DNA methylation between responders and non-responders, correcting for sex and batch in each subgroup. We identified 142 differentially methylated CpG sites in the young subgroup and 305 in the old subgroup, suggesting a larger epigenetic remodeling at older ages. Interestingly, some of the differentially methylated probes mapped in genes involved in immunosenescence (CD40) and in innate immunity responses (CXCL16, ULK1, BCL11B, BTC). In conclusion, the analysis of epigenetic landscape can shed light on the biological basis of vaccine responsiveness during aging, possibly providing new appropriate biomarkers of this process.
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Affiliation(s)
- Noémie Gensous
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy; Interdepartmental Center "L. Galvani", University of Bologna, Bologna, Italy; IRCCS Institute of Neurological Sciences, Bologna, Italy.
| | - Bonnie B Blomberg
- Institute of Molecular Genetics (IGM)-CNR, Unit of Bologna, Bologna, Italy.
| | | | - Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.
| | - Davide Gentilini
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy; Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy; Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, S-141 86 Stockholm, Sweden; Institute of Molecular Genetics (IGM)-CNR, Unit of Bologna, Bologna, Italy; Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopaedic Institute, Bologna, Italy.
| | - Daniela Frasca
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, USA.
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29
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Bellessort B, Bachelot A, Grouthier V, De Lombares C, Narboux-Neme N, Garagnani P, Pirazzini C, Astigiano S, Mastracci L, Fontaine A, Alfama G, Duvernois-Berthet E, Levi G. Comparative analysis of molecular signatures suggests the use of gabapentin for the management of endometriosis-associated pain. J Pain Res 2018; 11:715-725. [PMID: 29692624 PMCID: PMC5903492 DOI: 10.2147/jpr.s163611] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background It has been repetitively shown that the transcription factors DLX5 and DLX6 are drastically downregulated in endometriotic lesions when compared with eutopic endometrium. These findings suggest that regulatory cascades involving DLX5/6 might be at the origin of endometriosis symptoms such as chronic pelvic pain (CPP). We have shown that inactivation of Dlx5 and Dlx5/6 in the mouse uterus results in an endometrial phenotype reminiscent of endometriosis. Methods We focused on genes that present a similar deregulation in endometriosis and in Dlx5/6-null mice in search of new endometriosis targets. Results We confirmed a strong reduction of DLX5 expression in endometriosis implants. We identified a signature of 30 genes similarly deregulated in human endometriosis implants and in Dlx5/6-null mouse uteri, reinforcing the notion that the downregulation of Dlx5/6 is an early event in the progress of endometriosis. CACNA2D3, a component of the α2δ family of voltage-dependent calcium channel complex, was strongly overexpressed both in mutant mouse uteri and in endometriosis implants, were also CACNA2D1 and CACNA2D2, other members of the α2δ family involved in nociception, are upregulated. Conclusion Comparative analysis of gene expression signatures from endometriosis and mouse models showed that calcium channel subunits α2δ involved in nociception can be targets for the treatment of endometriosis-associated pain. CACNA2D3 has been associated with pain sensitization and heat nociception in animal models. In patients, CACNA2D3 variants were associated with reduced sensitivity to acute noxious stimuli. As α2δs were targets of gabapentinoid analgesics, the results suggested the use of these drugs for the treatment of endometriosis-associated pain. Indeed, recent small-scale clinical studies have shown that gabapentin could be effective in women with CPP. The findings of this study reinforce the need for a large definitive trial.
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Affiliation(s)
- Brice Bellessort
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
| | - Anne Bachelot
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France.,AP-HP, Department of Endocrinology and Reproductive Medicine, Reference Center for Rare Endocrine Diseases, Pitié-Salpêtrière Hospital, UPMC, Paris, France
| | - Virginie Grouthier
- AP-HP, Department of Endocrinology and Reproductive Medicine, Reference Center for Rare Endocrine Diseases, Pitié-Salpêtrière Hospital, UPMC, Paris, France
| | - Camille De Lombares
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
| | - Nicolas Narboux-Neme
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna, Italy
| | - Simonetta Astigiano
- Department of Integrated Oncological Therapies, San Martino Hospital, Genova, Italy
| | - Luca Mastracci
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genoa, Genova, Italy.,Division of Anatomic Pathology, Department of Surgical Science and Integrated Diagnostics, University of Genoa, Genova, Italy
| | - Anastasia Fontaine
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
| | - Gladys Alfama
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
| | - Evelyne Duvernois-Berthet
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
| | - Giovanni Levi
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
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30
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Durso DF, Bacalini MG, Sala C, Pirazzini C, Marasco E, Bonafé M, do Valle ÍF, Gentilini D, Castellani G, Faria AMC, Franceschi C, Garagnani P, Nardini C. Acceleration of leukocytes' epigenetic age as an early tumor and sex-specific marker of breast and colorectal cancer. Oncotarget 2017; 8:23237-23245. [PMID: 28423572 PMCID: PMC5410300 DOI: 10.18632/oncotarget.15573] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/12/2017] [Indexed: 01/12/2023] Open
Abstract
Changes in blood epigenetic age have been associated with several pathological conditions and have recently been described to anticipate cancer development. In this work, we analyze a publicly available leukocytes methylation dataset to evaluate the relation between DNA methylation age and the prospective development of specific types of cancer. We calculated DNA methylation age acceleration using five state-of-the-art estimators (three multi-site: Horvath, Hannum, Weidner; and two CpG specific: ELOV2 and FHL2) in a cohort including 845 subjects from the EPIC-Italy project and we compared 424 samples that remained cancer-free over the approximately ten years of follow-up with 235 and 166 subjects who developed breast and colorectal cancer, respectively. We show that the epigenetic age estimated from blood DNA methylation data is statistically significantly associated to future breast and male colorectal cancer development. These results are corroborated by survival analysis that shows significant association between age acceleration and cancer incidence suggesting that the chance of developing age-related diseases may be predicted by circulating epigenetic markers, with a dependence upon tumor type, sex and age estimator. These are encouraging results towards the non-invasive and perspective usage of epigenetic biomarkers.
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Affiliation(s)
- Danielle Fernandes Durso
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy.,National Counsel of Technological and Scientific Development (CNPq), Ministry of Science Technology and Innovation (MCTI), Brasilia, Brazil
| | | | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, S-141 86 Stockholm, Sweden
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Massimiliano Bonafé
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | | | - Davide Gentilini
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, S-141 86 Stockholm, Sweden
| | - Ana Maria Caetano Faria
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy.,Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, S-141 86 Stockholm, Sweden
| | - Christine Nardini
- Personal Genomics S.r.l., Verona, Italy.,CNR IAC "Mauro Picone", Italy
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Bacalini MG, Deelen J, Pirazzini C, De Cecco M, Giuliani C, Lanzarini C, Ravaioli F, Marasco E, van Heemst D, Suchiman HED, Slieker R, Giampieri E, Recchioni R, Marcheselli F, Salvioli S, Vitale G, Olivieri F, Spijkerman AMW, Dollé MET, Sedivy JM, Castellani G, Franceschi C, Slagboom PE, Garagnani P. Systemic Age-Associated DNA Hypermethylation of ELOVL2 Gene: In Vivo and In Vitro Evidences of a Cell Replication Process. J Gerontol A Biol Sci Med Sci 2017; 72:1015-1023. [PMID: 27672102 DOI: 10.1093/gerona/glw185] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 08/26/2016] [Indexed: 12/17/2022] Open
Abstract
Epigenetic remodeling is one of the major features of the aging process. We recently demonstrated that DNA methylation of ELOVL2 and FHL2 CpG islands is highly correlated with age in whole blood. Here we investigated several aspects of age-associated hypermethylation of ELOVL2 and FHL2. We showed that ELOVL2 methylation is significantly different in primary dermal fibroblast cultures from donors of different ages. Using epigenomic data from public resources, we demonstrated that most of the tissues show ELOVL2 and FHL2 hypermethylation with age. Interestingly, ELOVL2 hypermethylation was not found in tissues with very low replication rate. We demonstrated that ELOVL2 hypermethylation is associated with in vitro cell replication rather than with senescence. We confirmed intra-individual hypermethylation of ELOVL2 and FHL2 in longitudinally assessed participants from the Doetinchem Cohort Study. Finally we showed that, although the methylation of the two loci is not associated with longevity/mortality in the Leiden Longevity Study, ELOVL2 methylation is associated with cytomegalovirus status in nonagenarians, which could be informative of a higher number of replication events in a fraction of whole-blood cells. Collectively, these results indicate that ELOVL2 methylation is a marker of cell divisions occurring during human aging.
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Affiliation(s)
- Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy.,Personal Genomics S.r.l., Verona, Italy
| | - Joris Deelen
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands.,Max Planck Institute for Biology of Ageing, Köln, Germany
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
| | - Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics, Brown University, Providence, Rhode Island
| | | | - Catia Lanzarini
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
| | | | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine
| | - Diana van Heemst
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands
| | - H Eka D Suchiman
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands
| | - Roderick Slieker
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands
| | - Enrico Giampieri
- Department of Physics and Astronomy, University of Bologna, Italy
| | - Rina Recchioni
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy
| | - Fiorella Marcheselli
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
| | - Giovanni Vitale
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Italy
| | - Fabiola Olivieri
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy.,Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | | | - Martijn E T Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics, Brown University, Providence, Rhode Island
| | | | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine.,Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy.,IRCCS Institute of Neurological Sciences, Bologna, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
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32
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Giuliani C, Pirazzini C, Delledonne M, Xumerle L, Descombes P, Marquis J, Mengozzi G, Monti D, Bellizzi D, Passarino G, Luiselli D, Franceschi C, Garagnani P. Centenarians as extreme phenotypes: An ecological perspective to get insight into the relationship between the genetics of longevity and age-associated diseases. Mech Ageing Dev 2017; 165:195-201. [DOI: 10.1016/j.mad.2017.02.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/14/2017] [Accepted: 02/20/2017] [Indexed: 10/20/2022]
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Booiman T, Wit FW, Maurer I, De Francesco D, Sabin CA, Harskamp AM, Prins M, Garagnani P, Pirazzini C, Franceschi C, Fuchs D, Gisslén M, Winston A, Reiss P, Kootstra NA. High Cellular Monocyte Activation in People Living With Human Immunodeficiency Virus on Combination Antiretroviral Therapy and Lifestyle-Matched Controls Is Associated With Greater Inflammation in Cerebrospinal Fluid. Open Forum Infect Dis 2017; 4:ofx108. [PMID: 28680905 PMCID: PMC5494939 DOI: 10.1093/ofid/ofx108] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/23/2017] [Indexed: 12/03/2022] Open
Abstract
Background Increased monocyte activation and intestinal damage have been shown to be predictive for the increased morbidity and mortality observed in treated people living with human immunodeficiency virus (PLHIV). Methods A cross-sectional analysis of cellular and soluble markers of monocyte activation, coagulation, intestinal damage, and inflammation in plasma and cerebrospinal fluid (CSF) of PLHIV with suppressed plasma viremia on combination antiretroviral therapy and age and demographically comparable HIV-negative individuals participating in the Comorbidity in Relation to AIDS (COBRA) cohort and, where appropriate, age-matched blood bank donors (BBD). Results People living with HIV, HIV-negative individuals, and BBD had comparable percentages of classical, intermediate, and nonclassical monocytes. Expression of CD163, CD32, CD64, HLA-DR, CD38, CD40, CD86, CD91, CD11c, and CX3CR1 on monocytes did not differ between PLHIV and HIV-negative individuals, but it differed significantly from BBD. Principal component analysis revealed that 57.5% of PLHIV and 62.5% of HIV-negative individuals had a high monocyte activation profile compared with 2.9% of BBD. Cellular monocyte activation in the COBRA cohort was strongly associated with soluble markers of monocyte activation and inflammation in the CSF. Conclusions People living with HIV and HIV-negative COBRA participants had high levels of cellular monocyte activation compared with age-matched BBD. High monocyte activation was predictive for inflammation in the CSF.
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Affiliation(s)
- Thijs Booiman
- Department of Experimental Immunology and.,Amsterdam Institute for Global Health and Development, Netherlands
| | - Ferdinand W Wit
- Department of Global Health and Division of Infectious Disease, Academic Medical Center, University of Amsterdam, Netherlands.,Amsterdam Institute for Global Health and Development, Netherlands
| | | | - Davide De Francesco
- Department of Infection and Population Health, University College London, United Kingdom
| | - Caroline A Sabin
- Department of Infection and Population Health, University College London, United Kingdom
| | | | - Maria Prins
- Public Health Service, Amsterdam, Netherlands
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum Universita di Bologna, Italy
| | - Chiara Pirazzini
- Istituto di Ricovero e Cura a Carattere Scientifico, Institute of Neurological Sciences of Bologna, Bellaria Hospital, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum Universita di Bologna, Italy
| | - Dietmar Fuchs
- Division of Biological Chemistry, Biocenter Innsbruck Medical University Center for Chemistry and Biomedicine, Austria
| | - Magnus Gisslén
- Institute of Biomedicine, Department of Infectious Diseases, the Sahlgrenska Academy at the University of Gothenburg, Sweden
| | - Alan Winston
- Imperial College of Science, Technology and Medicine, London, United Kingdom
| | - Peter Reiss
- Department of Global Health and Division of Infectious Disease, Academic Medical Center, University of Amsterdam, Netherlands.,Amsterdam Institute for Global Health and Development, Netherlands.,HIV Monitoring Foundation, Amsterdam, Netherlands; and
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Giorgi G, Pirazzini C, Bacalini MG, Giuliani C, Garagnani P, Capri M, Bersani F, Del Re B. Assessing the combined effect of extremely low-frequency magnetic field exposure and oxidative stress on LINE-1 promoter methylation in human neural cells. Radiat Environ Biophys 2017; 56:193-200. [PMID: 28258386 DOI: 10.1007/s00411-017-0683-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/11/2017] [Indexed: 06/06/2023]
Abstract
Extremely low frequency magnetic fields (ELF-MF) have been classified as "possibly carcinogenic", but their genotoxic effects are still unclear. Recent findings indicate that epigenetic mechanisms contribute to the genome dysfunction and it is well known that they are affected by environmental factors. To our knowledge, to date the question of whether exposure to ELF-MF can influence epigenetic modifications has been poorly addressed. In this paper, we investigated whether exposure to ELF-MF alone and in combination with oxidative stress (OS) can affect DNA methylation, which is one of the most often studied epigenetic modification. To this end, we analyzed the DNA methylation levels of the 5'untranslated region (5'UTR) of long interspersed nuclear element-1s (LINE-1 or L1), which are commonly used to evaluate the global genome methylation level. Human neural cells (BE(2)C) were exposed for 24 and 48 h to extremely low frequency pulsed magnetic field (PMF; 50 Hz, 1 mT) in combination with OS. The methylation levels of CpGs located in L1 5'UTR region were measured by MassARRAY EpiTYPER. The results indicate that exposures to the single agents PMF and OS induced weak decreases and increases of DNA methylation levels at different CpGs. However, the combined exposure to PMF and OS lead to significant decrease of DNA methylation levels at different CpG sites. Most of the changes were transient, suggesting that cells can restore homeostatic DNA methylation patterns. The results are discussed and future research directions outlined.
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Affiliation(s)
- Gianfranco Giorgi
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via S. Giacomo 12, 40126, Bologna, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via S. Giacomo 12, 40126, Bologna, Italy
| | - Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences (BiGeA), Centre for Genome Biology, University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via S. Giacomo 12, 40126, Bologna, Italy
- CIG-Interdepartmental Centre "L. Galvani" for Bioinformatics, Biophysics and Biocomplexity, Piazza di Porta San Donato 1, 40126, Bologna, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via S. Giacomo 12, 40126, Bologna, Italy
- CIG-Interdepartmental Centre "L. Galvani" for Bioinformatics, Biophysics and Biocomplexity, Piazza di Porta San Donato 1, 40126, Bologna, Italy
| | - Ferdinando Bersani
- DIFA Department of Physics and Astronomy, University of Bologna, via Berti Pichat 6/2, 40127, Bologna, Italy
| | - Brunella Del Re
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, via Selmi 3, 40126, Bologna, Italy.
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35
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Durso DF, Bacalini MG, do Valle ÍF, Pirazzini C, Bonafé M, Castellani G, Faria AMC, Franceschi C, Garagnani P, Nardini C. Aberrant methylation patterns in colorectal cancer: a meta-analysis. Oncotarget 2017; 8:12820-12830. [PMID: 28086223 PMCID: PMC5355058 DOI: 10.18632/oncotarget.14590] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 12/27/2016] [Indexed: 12/30/2022] Open
Abstract
Colorectal cancer is among the leading causes of cancer death worldwide. Despite numerous molecular characterizations of the phenomenon, the exact dynamics of its onset and progression remain elusive. Colorectal cancer onset has been characterized by changes in DNA methylation profiles, that, owing to the stability of their patterns, are promising candidates to shed light on the molecular events laying at the base of this phenomenon.To exploit this stability and reinforce it, we conducted a meta-analysis on publicly available DNA methylation datasets generated on: normal colorectal, adenoma (ADE) and adenocarcinoma (CRC) samples using the Illumina 450k array, in the systems medicine frame, searching for tumor gene episignatures, to produce a carefully selected list of potential drivers, markers and targets of the disease. The analysis proceeds from a differential meta-analysis of the methylation profiles using an analytical pipeline recently developed by our group [1], through network reconstruction, topological and functional analyses, to finally highlight relevant epigenomic features. Our results show that genes already highlighted for their genetic or transcriptional alteration in colorectal cancer are also differentially methylated, reinforcing -regardless of the level of cellular control- their role in the complex of alterations involved in tumorigenesis.These findings were finally validated in an independent cohort from The Cancer Genome Atlas (TCGA).
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Affiliation(s)
- Danielle Fernandes Durso
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- National Counsel of Technological and Scientific Development (CNPq), ministry of science technology and innovation (MCTI), Brasilia, Brazil
| | | | - Ítalo Faria do Valle
- CAPES Foundation, Ministry of Education of Brazil–Brasília (DF), Brazil
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | | | - Massimiliano Bonafé
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Ana Maria Caetano Faria
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- IRCCS Institute of Neurological Sciences, Bologna, Italy
- Interdepartmental Center “L. Galvani”, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Interdepartmental Center “L. Galvani”, University of Bologna, Bologna, Italy
- Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna, Italy
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36
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Affiliation(s)
- Paolo Garagnani
- Dipartimento di Medicina Specialistica Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy.
| | - Rossana Terlizzi
- IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy.,Dipartimento di Scienze Neurologiche, Università di Bologna, Bologna, Italy
| | - Sabina Cevoli
- IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy.,Dipartimento di Scienze Neurologiche, Università di Bologna, Bologna, Italy
| | - Sabina Capellari
- IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy.,Dipartimento di Scienze Neurologiche, Università di Bologna, Bologna, Italy
| | - Giulia Pierangeli
- IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy.,Dipartimento di Scienze Neurologiche, Università di Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Dipartimento di Medicina Specialistica Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy
| | - Maria Giulia Bacalini
- Dipartimento di Medicina Specialistica Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy
| | - Claudio Franceschi
- Dipartimento di Medicina Specialistica Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy
| | - Pietro Cortelli
- IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy.,Dipartimento di Scienze Neurologiche, Università di Bologna, Bologna, Italy
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37
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Giuliani C, Sazzini M, Bacalini MG, Pirazzini C, Marasco E, Fontanesi E, Franceschi C, Luiselli D, Garagnani P. Epigenetic Variability across Human Populations: A Focus on DNA Methylation Profiles of the KRTCAP3, MAD1L1 and BRSK2 Genes. Genome Biol Evol 2016; 8:2760-73. [PMID: 27503294 PMCID: PMC5630933 DOI: 10.1093/gbe/evw186] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Natural epigenetic diversity has been suggested as a key mechanism in microevolutionary processes due to its capability to create phenotypic variability within individuals and populations. It constitutes an important reservoir of variation potentially useful for rapid adaptation in response to environmental stimuli. The analysis of population epigenetic structure represents a possible tool to study human adaptation and to identify external factors that are able to naturally shape human DNA methylation variability. The aim of this study is to investigate the dynamics that create epigenetic diversity between and within different human groups. To this end, we first used publicly available epigenome-wide data to explore population-specific DNA methylation changes that occur at macro-geographic scales. Results from this analysis suggest that nutrients, UVA exposure and pathogens load might represent the main environmental factors able to shape DNA methylation profiles. Then, we evaluated DNA methylation of candidate genes (KRTCAP3, MAD1L1, and BRSK2), emerged from the previous analysis, in individuals belonging to different populations from Morocco, Nigeria, Philippines, China, and Italy, but living in the same Italian city. DNA methylation of the BRSK2 gene is significantly different between Moroccans and Nigerians (pairwise t-test: CpG 6 P-value = 5.2*10 (-) (3); CpG 9 P-value = 2.6*10 (-) (3); CpG 10 P-value = 3.1*10 (-) (3); CpG 11 P-value = 2.8*10 (-) (3)). Comprehensively, these results suggest that DNA methylation diversity is a source of variability in human groups at macro and microgeographical scales and that population demographic and adaptive histories, as well as the individual ancestry, actually influence DNA methylation profiles.
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Affiliation(s)
- Cristina Giuliani
- Department of Biological Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Italy
| | - Marco Sazzini
- Department of Biological Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Italy
| | - Elisa Fontanesi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Italy IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Donata Luiselli
- Department of Biological Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Italy Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy
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38
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Castellani GC, Menichetti G, Garagnani P, Giulia Bacalini M, Pirazzini C, Franceschi C, Collino S, Sala C, Remondini D, Giampieri E, Mosca E, Bersanelli M, Vitali S, Valle IFD, Liò P, Milanesi L. Systems medicine of inflammaging. Brief Bioinform 2016; 17:527-40. [PMID: 26307062 PMCID: PMC4870395 DOI: 10.1093/bib/bbv062] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/29/2015] [Indexed: 12/30/2022] Open
Abstract
Systems Medicine (SM) can be defined as an extension of Systems Biology (SB) to Clinical-Epidemiological disciplines through a shifting paradigm, starting from a cellular, toward a patient centered framework. According to this vision, the three pillars of SM are Biomedical hypotheses, experimental data, mainly achieved by Omics technologies and tailored computational, statistical and modeling tools. The three SM pillars are highly interconnected, and their balancing is crucial. Despite the great technological progresses producing huge amount of data (Big Data) and impressive computational facilities, the Bio-Medical hypotheses are still of primary importance. A paradigmatic example of unifying Bio-Medical theory is the concept of Inflammaging. This complex phenotype is involved in a large number of pathologies and patho-physiological processes such as aging, age-related diseases and cancer, all sharing a common inflammatory pathogenesis. This Biomedical hypothesis can be mapped into an ecological perspective capable to describe by quantitative and predictive models some experimentally observed features, such as microenvironment, niche partitioning and phenotype propagation. In this article we show how this idea can be supported by computational methods useful to successfully integrate, analyze and model large data sets, combining cross-sectional and longitudinal information on clinical, environmental and omics data of healthy subjects and patients to provide new multidimensional biomarkers capable of distinguishing between different pathological conditions, e.g. healthy versus unhealthy state, physiological versus pathological aging.
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Bacalini MG, Boattini A, Gentilini D, Giampieri E, Pirazzini C, Giuliani C, Fontanesi E, Remondini D, Capri M, Del Rio A, Luiselli D, Vitale G, Mari D, Castellani G, Di Blasio AM, Salvioli S, Franceschi C, Garagnani P. Erratum: A meta-analysis on age-associated changes in blood DNA methylation: results from an original analysis pipeline for Infinium 450k data. Aging (Albany NY) 2016; 8:831. [PMID: 27182624 PMCID: PMC4925831 DOI: 10.18632/aging.100915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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40
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Bellessort B, Le Cardinal M, Bachelot A, Narboux-Nême N, Garagnani P, Pirazzini C, Barbieri O, Mastracci L, Jonchere V, Duvernois-Berthet E, Fontaine A, Alfama G, Levi G. Dlx5 and Dlx6 control uterine adenogenesis during post-natal maturation: possible consequences for endometriosis. Hum Mol Genet 2016; 25:97-108. [PMID: 26512061 DOI: 10.1093/hmg/ddv452] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 10/25/2015] [Indexed: 09/19/2023] Open
Abstract
Dlx5 and Dlx6 are two closely associated homeobox genes which code for transcription factors involved in the control of steroidogenesis and reproduction. Inactivation of Dlx5/6 in the mouse results in a Leydig cell defect in the male and in ovarian insufficiency in the female. DLX5/6 are also strongly expressed by the human endometrium but their function in the uterus is unknown. The involvement of DLX5/6 in human uterine pathology is suggested by their strong downregulation in endometriotic lesions and upregulation in endometrioïd adenocarcinomas. We first show that Dlx5/6 expression begins in Müllerian ducts epithelia and persists then in the uterine luminal and glandular epithelia throughout post-natal maturation and in the adult. We then use a new mouse model in which Dlx5 and Dlx6 can be simultaneously inactivated in the endometrium using a Pgr(cre/+) allele. Post-natal inactivation of Dlx5/6 in the uterus results in sterility without any obvious ovarian involvement. The uteri of Pgr(cre/+); Dlx5/6(flox/flox) mice present very few uterine glands and numerous abnormally large and branched invaginations of the uterine lumen. In Dlx5/6 mutant uteri, the expression of genes involved in gland formation (Foxa2) and in epithelial remodelling during implantation (Msx1) is significantly reduced. Furthermore, we show that DLX5 is highly expressed in human endometrial glandular epithelium and that its expression is affected in endometriosis. We conclude that Dlx5 and Dlx6 expression determines uterine architecture and adenogenesis and is needed for implantation. Given their importance for female reproduction, DLX5 and DLX6 must be regarded as interesting targets for future clinical research.
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Affiliation(s)
- Brice Bellessort
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France
| | - Marine Le Cardinal
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France
| | - Anne Bachelot
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France, AP-HP, Department of Endocrinology and Reproductive Medicine, Centre de Référence des Maladies Endocriniennes Rares de la Croissance, Pitié-Salpêtrière Hospital (Groupe Hospitalier Pitié-Salpêtrière), Université Pierre et Marie Curie, Site Pitié, 75013 Paris, France
| | - Nicolas Narboux-Nême
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy, Interdepartmental Center 'L. Galvani', University of Bologna, Bologna 40126, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy, Interdepartmental Center 'L. Galvani', University of Bologna, Bologna 40126, Italy
| | - Ottavia Barbieri
- Department of Experimental Medicine (DIMES) and, IRCCS AOU San Martino-IST, National Institute for Cancer Research, Genova, Italy and
| | - Luca Mastracci
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, Division of Anatomic Pathology, Department of Surgical Science and Integrated Diagnostics (DISC), University of Genoa, Genova, Italy
| | - Vincent Jonchere
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France
| | - Evelyne Duvernois-Berthet
- Department of Régulations, Développement et Diversité Moléculaire, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Anastasia Fontaine
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France
| | - Gladys Alfama
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France
| | - Giovanni Levi
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France,
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Fortney K, Dobriban E, Garagnani P, Pirazzini C, Monti D, Mari D, Atzmon G, Barzilai N, Franceschi C, Owen AB, Kim SK. Genome-Wide Scan Informed by Age-Related Disease Identifies Loci for Exceptional Human Longevity. PLoS Genet 2015; 11:e1005728. [PMID: 26677855 PMCID: PMC4683064 DOI: 10.1371/journal.pgen.1005728] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 11/16/2015] [Indexed: 11/20/2022] Open
Abstract
We developed a new statistical framework to find genetic variants associated with extreme longevity. The method, informed GWAS (iGWAS), takes advantage of knowledge from large studies of age-related disease in order to narrow the search for SNPs associated with longevity. To gain support for our approach, we first show there is an overlap between loci involved in disease and loci associated with extreme longevity. These results indicate that several disease variants may be depleted in centenarians versus the general population. Next, we used iGWAS to harness information from 14 meta-analyses of disease and trait GWAS to identify longevity loci in two studies of long-lived humans. In a standard GWAS analysis, only one locus in these studies is significant (APOE/TOMM40) when controlling the false discovery rate (FDR) at 10%. With iGWAS, we identify eight genetic loci to associate significantly with exceptional human longevity at FDR < 10%. We followed up the eight lead SNPs in independent cohorts, and found replication evidence of four loci and suggestive evidence for one more with exceptional longevity. The loci that replicated (FDR < 5%) included APOE/TOMM40 (associated with Alzheimer’s disease), CDKN2B/ANRIL (implicated in the regulation of cellular senescence), ABO (tags the O blood group), and SH2B3/ATXN2 (a signaling gene that extends lifespan in Drosophila and a gene involved in neurological disease). Our results implicate new loci in longevity and reveal a genetic overlap between longevity and age-related diseases and traits, including coronary artery disease and Alzheimer’s disease. iGWAS provides a new analytical strategy for uncovering SNPs that influence extreme longevity, and can be applied more broadly to boost power in other studies of complex phenotypes. Longevity is a complex phenotype, and few genetic variants that affect lifespan have been identified. However, aging and disease are closely related, and a great deal is known about the genetic basis of disease risk. Here, we show using genome-wide association studies (GWAS) of longevity and disease that there is an overlap between loci involved in longevity and loci involved in several diseases, such as Alzheimer’s disease and coronary artery disease. We then develop a new statistical framework to find genetic variants associated with extreme longevity. The method, informed GWAS (iGWAS), takes advantage of knowledge from 14 large studies of disease and disease-related traits in order to narrow the search for SNPs associated with longevity. Using iGWAS, we found eight SNPs that are significant in our discovery cohorts, and we were able to validate four of these in replication studies of long-lived subjects. Our results implicate new loci in longevity and reveal a genetic overlap between longevity and age-related diseases and traits. Beyond the study of human longevity, iGWAS can be applied to boost statistical power in any GWAS of a target phenotype by using larger GWAS of genetically-related conditions.
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Affiliation(s)
- Kristen Fortney
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Edgar Dobriban
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine Experimental Pathology, University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research, St. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine Experimental Pathology, University of Bologna, Bologna, Italy
- Interdepartmental Centre "L. Galvani" CIG, University of Bologna, Bologna, Italy
| | - Daniela Monti
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence, Florence, Italy
| | - Daniela Mari
- Department of Medical Sciences, University of Milan, Milan, Italy
- Geriatric Unit, IRCCS Ca' Grande Foundation, Maggiore Policlinico Hospital, Milan, Italy
| | - Gil Atzmon
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Nir Barzilai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine Experimental Pathology, University of Bologna, Bologna, Italy
- IRCCS, Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Art B. Owen
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Stuart K. Kim
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail:
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42
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Giuliani C, Cilli E, Bacalini MG, Pirazzini C, Sazzini M, Gruppioni G, Franceschi C, Garagnani P, Luiselli D. Inferring chronological age from DNA methylation patterns of human teeth. Am J Phys Anthropol 2015; 159:585-95. [PMID: 26667772 DOI: 10.1002/ajpa.22921] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Current methods to determine chronological age from modern and ancient remains rely on both morphological and molecular approaches. However, low accuracy and the lack of standardized protocols make the development of alternative methods for the estimation of individual's age even more urgent for several research fields, such as biological anthropology, biodemography, forensics, evolutionary genetics, and ancient DNA studies. Therefore, the aim of this study is to identify genomic regions whose DNA methylation level correlates with age in modern teeth. METHODS We used MALDI-TOF mass spectrometry to analyze DNA methylation levels of specific CpGs located in the ELOVL2, FHL2, and PENK genes. We considered methylation data from cementum, dentin and pulp of 21 modern teeth (from 17 to 77 years old) to construct a mathematical model able to exploit DNA methylation values to predict age of the individuals. RESULTS The median difference between the real age and that estimated using DNA methylation values is 1.20 years (SD = 1.9) if DNA is recovered from both cementum and pulp of the same modern teeth, 2.25 years (SD = 2.5) if DNA is recovered from dental pulp, 2.45 years (SD = 3.3) if DNA is extracted from cementum and 7.07 years (SD = 7.0) when DNA is recovered from dentin only. DISCUSSION We propose for the first time the evaluation of DNA methylation at ELOVL2, FHL2, and PENK genes as a powerful tool to predict age in modern teeth for anthropological applications. Future studies are needed to apply this method also to historical and relatively ancient human teeth.
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Affiliation(s)
- Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage (DBC), Laboratories of Physical Anthropology and Ancient DNA, University of Bologna, Ravenna, 48121, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy
| | - Marco Sazzini
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy
| | - Giorgio Gruppioni
- Department of Cultural Heritage (DBC), Laboratories of Physical Anthropology and Ancient DNA, University of Bologna, Ravenna, 48121, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy.,IRCCS Institute of Neurological Sciences, Bologna, 40139, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy.,Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy
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43
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Horvath S, Pirazzini C, Bacalini MG, Gentilini D, Di Blasio AM, Delledonne M, Mari D, Arosio B, Monti D, Passarino G, De Rango F, D'Aquila P, Giuliani C, Marasco E, Collino S, Descombes P, Garagnani P, Franceschi C. Decreased epigenetic age of PBMCs from Italian semi-supercentenarians and their offspring. Aging (Albany NY) 2015; 7:1159-70. [PMID: 26678252 PMCID: PMC4712339 DOI: 10.18632/aging.100861] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Given the dramatic increase in ageing populations, it is of great importance to understand the genetic and molecular determinants of healthy ageing and longevity. Semi-supercentenarians (subjects who reached an age of 105-109 years) arguably represent the gold standard of successful human ageing because they managed to avoid or postpone the onset of major age-related diseases. Relatively few studies have looked at epigenetic determinants of extreme longevity in humans. Here we test whether families with extreme longevity are epigenetically distinct from controls according to an epigenetic biomarker of ageing which is known as "epigenetic clock". We analyze the DNA methylation levels of peripheral blood mononuclear cells (PBMCs) from Italian families constituted of 82 semi-supercentenarians (mean age: 105.6 ± 1.6 years), 63 semi-supercentenarians' offspring (mean age: 71.8 ± 7.8 years), and 47 age-matched controls (mean age: 69.8 ± 7.2 years). We demonstrate that the offspring of semi-supercentenarians have a lower epigenetic age than age-matched controls (age difference=5.1 years, p=0.00043) and that centenarians are younger (8.6 years) than expected based on their chronological age. By contrast, no significant difference could be observed for estimated blood cell counts (such as naïve or exhausted cytotoxic T cells or helper T cells). Future studies will be needed to replicate these findings in different populations and to extend them to other tissues. Overall, our results suggest that epigenetic processes might play a role in extreme longevity and healthy human ageing.
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Affiliation(s)
- Steve Horvath
- Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Biostatistics, School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
- Interdepartmental Center "L. Galvani", University of Bologna, 40126 Bologna, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
- Interdepartmental Center "L. Galvani", University of Bologna, 40126 Bologna, Italy
- Personal Genomics S.r.l., 37134 Verona, Italy
| | - Davide Gentilini
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milan, Italy
| | | | - Massimo Delledonne
- Personal Genomics S.r.l., 37134 Verona, Italy
- Functional Genomics Center, Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Daniela Mari
- Geriatric Unit, Department of Medical Sciences and Community Health, University of Milan, 20122 Milan, Italy
- Geriatric Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Beatrice Arosio
- Geriatric Unit, Department of Medical Sciences and Community Health, University of Milan, 20122 Milan, Italy
- Geriatric Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50139 Florence, Italy
| | | | | | - Patrizia D'Aquila
- Department of Cell Biology, University of Calabria, 87036 Rende, Italy
| | - Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, 40126 Bologna, Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
- Interdepartmental Center "L. Galvani", University of Bologna, 40126 Bologna, Italy
| | - Sebastiano Collino
- Molecular Biomarkers, Nestlé Institute of Health Sciences SA, 1015 Lausanne, Switzerland
| | - Patrick Descombes
- Functional Genomics, Nestlé Institute of Health Sciences SA, 1015 Lausanne, Switzerland
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
- Interdepartmental Center "L. Galvani", University of Bologna, 40126 Bologna, Italy
- CRBA, Center for Applied Biomedical Research, St. Orsola-Malpighi University Hospital, 40138 Bologna, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
- Interdepartmental Center "L. Galvani", University of Bologna, 40126 Bologna, Italy
- CNR, Institute of Organic Synthesis and Photoreactivity (ISOF), 40129 Bologna, Italy
- IRCCS, Institute of Neurological Sciences of Bologna, 40139 Bologna, Italy
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Giampieri E, Remondini D, Bacalini MG, Garagnani P, Pirazzini C, Yani SL, Giuliani C, Menichetti G, Zironi I, Sala C, Capri M, Franceschi C, Bürkle A, Castellani G. Statistical strategies and stochastic predictive models for the MARK-AGE data. Mech Ageing Dev 2015. [PMID: 26209580 DOI: 10.1016/j.mad.2015.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
MARK-AGE aims at the identification of biomarkers of human aging capable of discriminating between the chronological age and the effective functional status of the organism. To achieve this, given the structure of the collected data, a proper statistical analysis has to be performed, as the structure of the data are non trivial and the number of features under study is near to the number of subjects used, requiring special care to avoid overfitting. Here we described some of the possible strategies suitable for this analysis. We also include a description of the main techniques used, to explain and justify the selected strategies. Among other possibilities, we suggest to model and analyze the data with a three step strategy.
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Affiliation(s)
- Enrico Giampieri
- Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy; Physics and Astronomy Department, Viale Berti Pichat 6/2, University of Bologna, Bologna, Italy.
| | - Daniel Remondini
- Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy; Physics and Astronomy Department, Viale Berti Pichat 6/2, University of Bologna, Bologna, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine, Via S. Giacomo, 12 University of Bologna, Bologna, Italy; Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Via S. Giacomo, 12 University of Bologna, Bologna, Italy; Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine, Via S. Giacomo, 12 University of Bologna, Bologna, Italy; Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy
| | - Stella Lukas Yani
- Department of Experimental, Diagnostic and Specialty Medicine, Via S. Giacomo, 12 University of Bologna, Bologna, Italy; Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy; Institute for Biomedical Aging Research, University of Innsbruck, Austria
| | - Cristina Giuliani
- Department of Experimental, Diagnostic and Specialty Medicine, Via S. Giacomo, 12 University of Bologna, Bologna, Italy; Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy
| | - Giulia Menichetti
- Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy; Physics and Astronomy Department, Viale Berti Pichat 6/2, University of Bologna, Bologna, Italy
| | - Isabella Zironi
- Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy; Physics and Astronomy Department, Viale Berti Pichat 6/2, University of Bologna, Bologna, Italy
| | - Claudia Sala
- Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy; Physics and Astronomy Department, Viale Berti Pichat 6/2, University of Bologna, Bologna, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, Via S. Giacomo, 12 University of Bologna, Bologna, Italy; Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Via S. Giacomo, 12 University of Bologna, Bologna, Italy; Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Gastone Castellani
- Interdepartmental Center Galvani "CIG", Via Selmi, 3 University of Bologna, Bologna, Italy; Physics and Astronomy Department, Viale Berti Pichat 6/2, University of Bologna, Bologna, Italy
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45
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Capri M, Santoro A, Garagnani P, Bacalini MG, Pirazzini C, Olivieri F, Procopio A, Salvioli S, Franceschi C. Genes of human longevity: an endless quest? Curr Vasc Pharmacol 2015; 12:707-17. [PMID: 24350927 DOI: 10.2174/1570161111666131219110301] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/21/2013] [Accepted: 10/31/2013] [Indexed: 11/22/2022]
Abstract
Human longevity is a complex trait in which genetics, epigenetics, environmental and stochasticity differently contribute. To disentangle the complexity, our studies on genetics of longevity were, at the beginning, mainly focused on the extreme phenotypes, i.e. centenarians who escaped the major age-related diseases compared with cross sectional cohorts. Recently, we implemented this model by studying centenarians' offspring and offspring of non-long lived parents. In association, during studies on many candidate genes SNPs, positively or negatively correlated with longevity have been identified. The results obtained on Insulin-like Growth Factor 1 Receptor (IGF1R) polymorphisms showed a correlation between specific genetic variants combinations and the low plasma level of IGF1 in centenarians, suggesting an impact of the IGF-I/insulin pathway on human longevity. This pathway together with mammalian target of rapamycin (mTOR) will be reviewed as being the most promising for longevity. Further, we will summarise the role of apolipoprotein E (APOE) variants in human longevity since the results of the large European project GEHA (Genetics of Healthy Aging) indicate APOE among the chromosomal loci associated with longevity. On the other hand, the identification of longevity-related genes does not explain the mechanisms of healthy aging and longevity rather pose questions on epigenetic contribution, gene regulation and the interactions with essential genomes, i.e. mitochondrial DNA and microbiota. To fully disentangle what appears to be an endless quest, all the components of the complexity of human longevity genetics are taken into account.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum- University of Bologna, Via S. Giacomo, 12, 40126 Bologna, Italy.
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46
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Bacalini MG, Gentilini D, Boattini A, Giampieri E, Pirazzini C, Giuliani C, Fontanesi E, Scurti M, Remondini D, Capri M, Cocchi G, Ghezzo A, Del Rio A, Luiselli D, Vitale G, Mari D, Castellani G, Fraga M, Di Blasio AM, Salvioli S, Franceschi C, Garagnani P. Identification of a DNA methylation signature in blood cells from persons with Down Syndrome. Aging (Albany NY) 2015; 7:82-96. [PMID: 25701644 PMCID: PMC4359691 DOI: 10.18632/aging.100715] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Down Syndrome (DS) is characterized by a wide spectrum of clinical signs, which include segmental premature aging of central nervous and immune systems. Although it is well established that the causative defect of DS is the trisomy of chromosome 21, the molecular bases of its phenotype are still largely unknown. We used the Infinium HumanMethylation450 BeadChip to investigate DNA methylation patterns in whole blood from 29 DS persons, using their relatives (mothers and unaffected siblings) as controls. This family-based model allowed us to monitor possible confounding effects on DNA methylation patterns deriving from genetic and environmental factors. Although differentially methylated regions (DMRs) displayed a genome-wide distribution, they were enriched on chromosome 21. DMRs mapped in genes involved in developmental functions, including embryonic development (HOXA family) and haematological (RUNX1 and EBF4) and neuronal (NCAM1) development. Moreover, genes involved in the regulation of chromatin structure (PRMD8, KDM2B, TET1) showed altered methylation. The data also showed that several pathways are affected in DS, including PI3K-Akt signaling. In conclusion, we identified an epigenetic signature of DS that sustains a link between developmental defects and disease phenotype, including segmental premature aging.
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Affiliation(s)
- Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy.,Personal Genomics S.r.l., Verona 37134, Italy
| | - Davide Gentilini
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan 20095, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40126, Italy
| | - Enrico Giampieri
- Department of Physics and Astronomy, University of Bologna, Bologna 40126, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40126, Italy
| | - Elisa Fontanesi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Maria Scurti
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, Bologna 40126, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Guido Cocchi
- Department of Medical and Surgical Sciences-Neonatology and Neonatal Intensive Care Unit, University of Bologna, Bologna 40126, Italy
| | - Alessandro Ghezzo
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy
| | - Alberto Del Rio
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Institute of Organic Synthesis and Photoreactivity (ISOF) National Research Council (CNR), Bologna 40126, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40126, Italy
| | - Giovanni Vitale
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan 20095, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Milan 20095, Italy
| | - Daniela Mari
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20095, Italy.,Geriatric Unit, IRCCS Ca' Granda Foundation Maggiore Policlinico Hospital, Milan 20095, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna 40126, Italy
| | - Mario Fraga
- Cancer Epigenetics Laboratory, Instituto Universitario de de Oncología del Principado de Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain.,Department of Immunology & Oncology, Centro Nacional de Biotecnología/CNB-CSIC, Cantoblanco, Madrid, Spain
| | - Anna Maria Di Blasio
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan 20095, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy.,IRCCS Institute of Neurological Sciences, Bologna 40126, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy.,Personal Genomics S.r.l., Verona 37134, Italy.,Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna 40138, Italy
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Bacalini MG, Boattini A, Gentilini D, Giampieri E, Pirazzini C, Giuliani C, Fontanesi E, Remondini D, Capri M, Del Rio A, Luiselli D, Vitale G, Mari D, Castellani G, Di Blasio AM, Salvioli S, Franceschi C, Garagnani P. A meta-analysis on age-associated changes in blood DNA methylation: results from an original analysis pipeline for Infinium 450k data. Aging (Albany NY) 2015; 7:97-109. [PMID: 25701668 PMCID: PMC4359692 DOI: 10.18632/aging.100718] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Aging is characterized by a profound remodeling of the epigenetic architecture in terms of DNA methylation patterns. To date the most effective tool to study genome wide DNA methylation changes is Infinium HumanMethylation450 BeadChip (Infinium 450k). Despite the wealth of tools for Infinium 450k analysis, the identification of the most biologically relevant DNA methylation changes is still challenging. Here we propose an analytical pipeline to select differentially methylated regions (DMRs), tailored on microarray architecture, which is highly effective in highlighting biologically relevant results. The pipeline groups microarray probes on the basis of their localization respect to CpG islands and genic sequences and, depending on probes density, identifies DMRs through a single-probe or a region-centric approach that considers the concomitant variation of multiple adjacent CpG probes. We successfully applied this analytical pipeline on 3 independent Infinium 450k datasets that investigated age-associated changes in blood DNA methylation. We provide a consensus list of genes that systematically vary in DNA methylation levels from 0 to 100 years and that have a potentially relevant role in the aging process.
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Affiliation(s)
- Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy.,Personal Genomics S.r.l., Verona 37134, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40126, Italy
| | - Davide Gentilini
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Milan 20095, Italy
| | - Enrico Giampieri
- Department of Physics and Astronomy, University of Bologna, Bologna 40126, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40126, Italy
| | - Elisa Fontanesi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, Bologna 40126, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Alberto Del Rio
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Institute of Organic Synthesis and Photoreactivity (ISOF) National Research Council (CNR), Bologna 40126, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40126, Italy
| | - Giovanni Vitale
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Milan 20095, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Daniela Mari
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.,Geriatric Unit, IRCCS Ca' Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna 40126, Italy
| | - Anna Maria Di Blasio
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Milan 20095, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy.,IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy.,Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna 40138, Italy
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48
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Horvath S, Garagnani P, Bacalini MG, Pirazzini C, Salvioli S, Gentilini D, Di Blasio AM, Giuliani C, Tung S, Vinters HV, Franceschi C. Accelerated epigenetic aging in Down syndrome. Aging Cell 2015; 14:491-5. [PMID: 25678027 PMCID: PMC4406678 DOI: 10.1111/acel.12325] [Citation(s) in RCA: 336] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2014] [Indexed: 12/24/2022] Open
Abstract
Down Syndrome (DS) entails an increased risk of many chronic diseases that are typically associated with older age. The clinical manifestations of accelerated aging suggest that trisomy 21 increases the biological age of tissues, but molecular evidence for this hypothesis has been sparse. Here, we utilize a quantitative molecular marker of aging (known as the epigenetic clock) to demonstrate that trisomy 21 significantly increases the age of blood and brain tissue (on average by 6.6 years, P = 7.0 × 10−14).
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Affiliation(s)
- Steve Horvath
- Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA
- Biostatistics Fielding School of Public Health University of California Los Angeles Los Angeles CA 90095 USA
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna 40126 Italy
- Interdepartmental Center ‘L. Galvani’ University of Bologna Bologna 40126 Italy
- CNR Applied Biomedical Research Center S. Orsola‐Malpighi Polyclinic Bologna 40138 Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna 40126 Italy
- Interdepartmental Center ‘L. Galvani’ University of Bologna Bologna 40126 Italy
- Personal Genomics S.r.l. Verona 37134 Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna 40126 Italy
- Interdepartmental Center ‘L. Galvani’ University of Bologna Bologna 40126 Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna 40126 Italy
- Interdepartmental Center ‘L. Galvani’ University of Bologna Bologna 40126 Italy
| | - Davide Gentilini
- Center of Research and Biomedical Technology Istituto Auxologico Italiano IRCCS Via Zucchi 18 Cusano Milanino 20095 Milan Italy
| | - Anna Maria Di Blasio
- Center of Research and Biomedical Technology Istituto Auxologico Italiano IRCCS Via Zucchi 18 Cusano Milanino 20095 Milan Italy
| | - Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences University of Bologna Bologna 40126 Italy
| | - Spencer Tung
- Department of Neurology and Department of Pathology and Laboratory Medicine David Geffen School of Medicine at UCLA Los Angeles CA 90095 USA
| | - Harry V. Vinters
- Department of Neurology and Department of Pathology and Laboratory Medicine David Geffen School of Medicine at UCLA Los Angeles CA 90095 USA
| | - Claudio Franceschi
- Interdepartmental Center ‘L. Galvani’ University of Bologna Bologna 40126 Italy
- IRCCS Institute of Neurological Sciences of Bologna 40139 Bologna Italy
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49
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Giuliani C, Bacalini MG, Sazzini M, Pirazzini C, Franceschi C, Garagnani P, Luiselli D. The epigenetic side of human adaptation: hypotheses, evidences and theories. Ann Hum Biol 2014; 42:1-9. [PMID: 25413580 DOI: 10.3109/03014460.2014.961960] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
CONTEXT Epigenetics represents a still unexplored research field in the understanding of micro- and macro-evolutionary mechanisms, as epigenetic changes create phenotypic diversity within both individuals and populations. OBJECTIVE The purpose of this review is to dissect the landscape of studies focused on DNA methylation, one of the most described epigenetic mechanisms, emphasizing the aspects that could be relevant in human adaptations. METHODS Theories and results here considered were collected from the most recent papers published. RESULTS The matter of DNA methylation inheritance is here described as well as the recent evolutionary theories regarding the role of DNA methylation-and epigenetics in a broader sense-in human evolution. The complex relation between (1) DNA methylation and genetic variability and (2) DNA methylation and the environmental stimuli crucial in shaping genetic and phenotypic variability through the human lineage-such as diet, climate and pathogens exposure-are described. Papers about population epigenetics are also illustrated due to their high relevance in this context. CONCLUSION Genetic, epigenetic and phenotypic variations of the species, together with cultural ones, are considerably shaped by a vast range of environmental stimuli, thus representing the foundation of all human bio-cultural adaptations.
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Affiliation(s)
- Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology and Centre for Genome Biology
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50
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Quercia S, Candela M, Giuliani C, Turroni S, Luiselli D, Rampelli S, Brigidi P, Franceschi C, Bacalini MG, Garagnani P, Pirazzini C. From lifetime to evolution: timescales of human gut microbiota adaptation. Front Microbiol 2014; 5:587. [PMID: 25408692 PMCID: PMC4219431 DOI: 10.3389/fmicb.2014.00587] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 10/17/2014] [Indexed: 12/21/2022] Open
Abstract
Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota (GM) is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The GM continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations in diet or specific host physiological and immunological needs at different ages. On the other hand, the microbiota plasticity was strategic to face changes in lifestyle and dietary habits along the course of the recent evolutionary history, that has driven the passage from Paleolithic hunter-gathering societies to Neolithic agricultural farmers to modern Westernized societies.
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Affiliation(s)
- Sara Quercia
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Cristina Giuliani
- BiGEA, Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Donata Luiselli
- BiGEA, Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna Bologna, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Claudio Franceschi
- DIMES, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna Bologna, Italy ; CIG, Interdepartmental Centre "L. Galvani" CIG, University of Bologna Bologna, Italy ; IRCSS, Institute of Neurological Sciences of Bologna Bologna, Italy ; IGM-CNR, Institute of Molecular Genetics, Unit of Bologna IOR Bologna, Italy ; CNR, Institute of Organic Synthesis and Photoreactivity (ISOF) Bologna, Italy
| | - Maria Giulia Bacalini
- DIMES, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna Bologna, Italy ; CIG, Interdepartmental Centre "L. Galvani" CIG, University of Bologna Bologna, Italy
| | - Paolo Garagnani
- DIMES, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna Bologna, Italy ; CIG, Interdepartmental Centre "L. Galvani" CIG, University of Bologna Bologna, Italy ; CRBA, Center for Applied Biomedical Research, St. Orsola-Malpighi University Hospital Bologna, Italy
| | - Chiara Pirazzini
- DIMES, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna Bologna, Italy ; CIG, Interdepartmental Centre "L. Galvani" CIG, University of Bologna Bologna, Italy
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