1
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Goual L, Bounasri E, Vincenti M, Amédro P, Desprat R, Bernex F, Lemaitre JM, Pasquié JL, Lacampagne A, Thireau J, Meli AC. Generation of patient-specific induced pluripotent stem cell lines with Type 2 Long QT Syndrome and the KCNH2 c.379C > T pathogenic variant. Stem Cell Res 2023; 72:103192. [PMID: 37660555 DOI: 10.1016/j.scr.2023.103192] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023] Open
Abstract
Type 2 Long QT Syndrome (LQT2) is a rare genetic heart rhythm disorder causing life-threatening arrhythmias. We derived induced pluripotent stem cell (iPSC) lines from two patients with LQT2, aged 18 and 6, both carrying a heterozygous missense mutation on the 3rd and 11th exons of KCNH2. The iPSC lines exhibited normal genomes, expressed pluripotent markers, and differentiated into trilineage embryonic layers. These patient-specific iPSC lines provide a valuable model to study the molecular and functional impact of the hERG channel gene mutation in LQT2 and to develop personalized therapeutic approaches for this syndrome.
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Affiliation(s)
- Lamia Goual
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Elisa Bounasri
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France; MicroBrain Biotech S.A.S., Marly Le-Roi, France
| | - Marie Vincenti
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France; Pediatric and Congenital Cardiology Department, M3C Regional Reference CHD Centre, Clinical Investigation Centre, Montpellier University Hospital, Montpellier, France
| | - Pascal Amédro
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France; Pediatric and Congenital Cardiology Department, M3C Regional Reference CHD Centre, Clinical Investigation Centre, Montpellier University Hospital, Montpellier, France
| | | | - Florence Bernex
- RHEM, Réseau d'Histologie Expérimentale de Montpellier, Univ. Montpellier, BioCampus, CNRS, INSERM, Montpellier, France
| | | | - Jean-Luc Pasquié
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France; Department of Cardiology, CHU of Montpellier, Montpellier, France
| | - Alain Lacampagne
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Jérôme Thireau
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France.
| | - Albano C Meli
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France.
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2
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Alle Q, Le Borgne E, Bensadoun P, Lemey C, Béchir N, Gabanou M, Estermann F, Bertrand‐Gaday C, Pessemesse L, Toupet K, Desprat R, Vialaret J, Hirtz C, Noël D, Jorgensen C, Casas F, Milhavet O, Lemaitre J. A single short reprogramming early in life initiates and propagates an epigenetically related mechanism improving fitness and promoting an increased healthy lifespan. Aging Cell 2022; 21:e13714. [PMID: 36251933 PMCID: PMC9649606 DOI: 10.1111/acel.13714] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [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: 03/23/2022] [Revised: 08/11/2022] [Accepted: 08/31/2022] [Indexed: 01/25/2023] Open
Abstract
Recent advances in cell reprogramming showed that OSKM induction is able to improve cell physiology in vitro and in vivo. Here, we show that a single short reprogramming induction is sufficient to prevent musculoskeletal functions deterioration of mice, when applied in early life. In addition, in old age, treated mice have improved tissue structures in kidney, spleen, skin, and lung, with an increased lifespan of 15% associated with organ-specific differential age-related DNA methylation signatures rejuvenated by the treatment. Altogether, our results indicate that a single short reprogramming early in life might initiate and propagate an epigenetically related mechanism to promote a healthy lifespan.
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Affiliation(s)
| | | | | | | | | | | | | | - Christelle Bertrand‐Gaday
- DMEM, Univ Montpellier, INRAEMontpellierFrance,RAM‐METAMUS, Univ Montpellier, INRAEMontpellierFrance
| | | | - Karine Toupet
- IRMB, Univ Montpellier, INSERMMontpellierFrance,ECELLFrance Montpellier Facility, Univ MontpellierMontpellierFrance
| | | | - Jérôme Vialaret
- IRMB, Univ Montpellier, INSERMMontpellierFrance,PPC Facility, CHU MontpellierMontpellierFrance
| | - Christophe Hirtz
- IRMB, Univ Montpellier, INSERMMontpellierFrance,PPC Facility, CHU MontpellierMontpellierFrance
| | - Danièle Noël
- IRMB, Univ Montpellier, INSERMMontpellierFrance,ECELLFrance Montpellier Facility, Univ MontpellierMontpellierFrance
| | - Christian Jorgensen
- IRMB, Univ Montpellier, INSERMMontpellierFrance,ECELLFrance Montpellier Facility, Univ MontpellierMontpellierFrance
| | - François Casas
- DMEM, Univ Montpellier, INRAEMontpellierFrance,RAM‐METAMUS, Univ Montpellier, INRAEMontpellierFrance
| | - Ollivier Milhavet
- SAFE‐iPSC Facility, CHU MontpellierMontpellierFrance,IRMB, Univ Montpellier, INSERM, CNRSMontpellierFrance
| | - Jean‐Marc Lemaitre
- IRMB, Univ Montpellier, INSERMMontpellierFrance,SAFE‐iPSC Facility, CHU MontpellierMontpellierFrance
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3
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Colombani S, Bernardin AA, Vincenti M, Amédro P, Desprat R, Bernex F, Lemaitre JM, Pasquié JL, Lacampagne A, Meli AC. Generation of catecholaminergic polymorphic ventricular tachycardia patient-specific induced pluripotent stem cell line. Stem Cell Res 2022; 60:102727. [PMID: 35245853 DOI: 10.1016/j.scr.2022.102727] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/24/2022] [Accepted: 02/23/2022] [Indexed: 11/24/2022] Open
Abstract
Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT) is a genetic disorder characterized by ventricular tachycardia, that can cause the heart to stop beating leading to death. The prevalence is 1/10.000 and in approximately 60% of cases, the syndrome can be due to a mutation of the cardiac ryanodine receptor gene (RyR2). We derived an induced pluripotent stem cell (iPSC) line from an 11-year-old patient blood-cells, carrying a heterozygous missense mutation on the 8th exon of the RyR2 N-terminal part. This reprogramed CPVT line displayed normal karyotype, expressed pluripotent markers and had a capacity to differentiate in trilineage embryonic layers.
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Affiliation(s)
- Sarah Colombani
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Albin A Bernardin
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Marie Vincenti
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France; Pediatric and Adult Congenital Cardiology Department, M3C Regional Reference CHD Center, CHU Montpellier, France
| | - Pascal Amédro
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France; Pediatric and Adult Congenital Cardiology Department, M3C Regional Reference CHD Center, CHU Montpellier, France
| | - Romain Desprat
- SAFE-iPSC Facility INGESTEM, CHU de Montpellier, Montpellier, France
| | - Florence Bernex
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Univ. Montpellier, INSERM, ICM, Montpellier, France; RHEM, Réseau d'Histologie Expérimentale de Montpellier, Univ. Montpellier, BioCampus, CNRS, INSERM, Montpellier, France
| | - Jean-Marc Lemaitre
- SAFE-iPSC Facility INGESTEM, CHU de Montpellier, Montpellier, France; Laboratory of Genome and Stem Cell Plasticity in Development and Aging, INSERM, Montpellier, France
| | - Jean-Luc Pasquié
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France; Department of Cardiology, CHU of Montpellier, Montpellier, France
| | - Alain Lacampagne
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Albano C Meli
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France.
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4
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Pichard L, Brondello JM, Becker F, Desprat R, De Ceuninck F, Pastoureau P, Noel D, Jorgensen C, Lemaitre JM. Establishment of a collection of human pluripotent stem cell lines (iPSC) from mesenchymal stem cells (MSC) from three healthy elderly donors. Stem Cell Res 2021; 53:102297. [PMID: 33780731 DOI: 10.1016/j.scr.2021.102297] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 02/17/2021] [Accepted: 03/14/2021] [Indexed: 11/27/2022] Open
Abstract
The study of molecular mechanism driving osteoarticular diseases like osteoarthritis or osteoporosis is impaired by the low accessibility to mesenchymal stem cells (MSC) from healthy donors (HD) for differential multi-omics analysis. Advances in cell reprogramming have, however, provided both a new source of human cells for laboratory research and a strategy to erase epigenetic marks involved in cell identity and the development of diseases. To unravel the pathological signatures on the MSC at the origin of cellular drifts during the formation of bone and cartilage, we previously developed iPSC from MSC of osteoarthritis donors. Here we present the derivation of three iPSCs from healthy age matched donors to model the disease and further identify (epi)genomic signatures of the pathology.
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Affiliation(s)
- Lydiane Pichard
- SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France; Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France
| | - Jean-Marc Brondello
- Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France
| | - Fabienne Becker
- SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Romain Desprat
- SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Frédéric De Ceuninck
- Institut de Recherches Servier, Center for Therapeutic Innovation, Immuno-inflammatory Disease, Croissy sur Seine, France
| | - Philippe Pastoureau
- Institut de Recherches Servier, Center for Therapeutic Innovation, Immuno-inflammatory Disease, Croissy sur Seine, France
| | - Daniele Noel
- Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France
| | - Christian Jorgensen
- Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France
| | - Jean-Marc Lemaitre
- SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France; Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France.
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5
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Barbeau S, Desprat R, Eymard B, Martinat C, Lemaitre JM, Legay C. Generation of a human induced pluripotent stem cell line (iPSC) from peripheral blood mononuclear cells of a patient with a myasthenic syndrome due to mutation in COLQ. Stem Cell Res 2020; 49:102106. [PMID: 33370874 DOI: 10.1016/j.scr.2020.102106] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/17/2020] [Accepted: 11/27/2020] [Indexed: 11/30/2022] Open
Abstract
Congenital myasthenic syndromes (CMS) are a class of inherited disorders affecting the neuromuscular junction, a synapse whose activity is essential for movement. CMS with acetylcholinesterase (AChE) deficiency are caused by mutations in COLQ, a collagen that anchors AChE in the synapse. To study the pathophysiological mechanisms of the disease in human cells, we have generated iPSC from a patient's Peripheral Blood Mononuclear cells (PBMC) by reprogramming these cells using a non-integrative method using Sendai viruses bearing the four Yamanaka factors Oct3/4, Sox2, Klf4, and L-Myc.
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Affiliation(s)
- Susie Barbeau
- Paris University, SPPIN CNRS 8003 Laboratory, Paris, France
| | - Romain Desprat
- SAFE-iPSC Facility INGESTEM, Univ. Montpellier, CHU de Montpellier, France
| | - Bruno Eymard
- Paris-Est Neuromuscular Center, Institut de Myologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Cécile Martinat
- INSERM UEVE UMR 861, Paris Saclay Univ. I-STEM, 91100 Corbeil-Essonnes, France
| | - Jean-Marc Lemaitre
- SAFE-iPSC Facility INGESTEM, Univ. Montpellier, CHU de Montpellier, France; Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France
| | - Claire Legay
- Paris University, SPPIN CNRS 8003 Laboratory, Paris, France.
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6
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Souidi M, Amédro P, Meyer P, Desprat R, Lemaître JM, Rivier F, Lacampagne A, Meli AC. Generation of three Duchenne Muscular Dystrophy patient-specific induced pluripotent stem cell lines DMD_YoTaz_PhyMedEXp, DMD_RaPer_PhyMedEXp, DMD_OuMen_PhyMedEXp (INSRMi008-A, INSRMi009-A and INSRMi010-A). Stem Cell Res 2020; 49:102094. [PMID: 33246213 DOI: 10.1016/j.scr.2020.102094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/03/2020] [Accepted: 11/15/2020] [Indexed: 10/23/2022] Open
Abstract
Duchenne Muscular Dystrophy (DMD) is a X-linked degenerative pathology with a prevalence of 1/3600-6000 boys due to the absence of functional dystrophin in muscles. This muscular disease leads to skeletal muscle damages, respiratory failure and in the later stages dilated cardiomyopathy (DCM) leading to heart failure. We generated iPSC lines from three different DMD patients carrying respectively deletions of exons 1, 52 and 55 in the dystrophin gene. The reprogrammed iPSC lines showed expression of pluripotent markers, capacity to differentiate in trilineage embryonic layers and a normal karyotype.
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Affiliation(s)
- Monia Souidi
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Pascal Amédro
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France; Pediatric and Congenital Cardiology Department, M3C Regional Reference CHD Centre, Clinical Investigation Centre, Montpellier University Hospital, Montpellier, France
| | - Pierre Meyer
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France; Pediatric Neurology Department, Reference Center for Neuromuscular Diseases AOC, Clinical Investigation Centre, Montpellier University Hospital, Montpellier, France
| | - Romain Desprat
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; SAFE-iPSC Facility INGESTEM, CHU de Montpellier, Montpellier, France
| | - Jean-Marc Lemaître
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; SAFE-iPSC Facility INGESTEM, CHU de Montpellier, Montpellier, France; Laboratory of Genome and Stem Cell Plasticity in Development and Aging, INSERM, Montpellier, France
| | - François Rivier
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France; Pediatric Neurology Department, Reference Center for Neuromuscular Diseases AOC, Clinical Investigation Centre, Montpellier University Hospital, Montpellier, France
| | - Alain Lacampagne
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Albano C Meli
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France.
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7
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Gatinois V, Desprat R, Pichard L, Becker F, Goldenberg A, Balguerie X, Pellestor F, Lemaitre JM. iPSC reprogramming of fibroblasts from a patient with a Rothmund-Thomson syndrome RTS. Stem Cell Res 2020; 45:101807. [PMID: 32416578 DOI: 10.1016/j.scr.2020.101807] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/21/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023] Open
Abstract
Rothmund-Thomson Syndrome (RTS) is a rare autosomal recessive disease that manifests several clinical features of accelerated aging. These findings include atrophic skin and pigment changes, alopecia, osteopenia, cataracts, and an increased incidence of cancer for patients. Mutations in RECQL4 gene are responsible for cases of RTS. RECQL4 belongs to the RECQ DNA helicase family which has been shown to participate in many aspects of DNA metabolism. To be able to study the cellular defects related to the pathology, we derived an induced pluripotent cell line from RTS patient fibroblasts, with the ability to re-differentiate into the three embryonic germ layers.
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Affiliation(s)
- Vincent Gatinois
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; Laboratory of Genome and Stem Cell Plasticity in Development and Aging, INSERM UMR1183, Montpellier, France; Laboratory of Cytogenetics, ChromoStem Facility, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Romain Desprat
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; SAFE-iPSC Facility INGESTEM, CHU de Montpellier, Montpellier, France
| | - Lydiane Pichard
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; Laboratory of Genome and Stem Cell Plasticity in Development and Aging, INSERM UMR1183, Montpellier, France; SAFE-iPSC Facility INGESTEM, CHU de Montpellier, Montpellier, France
| | - Fabienne Becker
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; SAFE-iPSC Facility INGESTEM, CHU de Montpellier, Montpellier, France
| | - Alice Goldenberg
- Department of Medical genetics, CHU de Rouen, Univ Rouen, Inserm, Rouen U1079, France
| | | | - Franck Pellestor
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; Laboratory of Genome and Stem Cell Plasticity in Development and Aging, INSERM UMR1183, Montpellier, France; Laboratory of Cytogenetics, ChromoStem Facility, Univ Montpellier, CHU de Montpellier, Montpellier, France.
| | - Jean-Marc Lemaitre
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; SAFE-iPSC Facility INGESTEM, CHU de Montpellier, Montpellier, France.
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8
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Gatinois V, Desprat R, Becker F, Pichard L, Bernex F, Corsini C, Pellestor F, Lemaitre JM. Reprogramming of Human Peripheral Blood Mononuclear Cell (PBMC) from a patient suffering of a Werner syndrome resulting in iPSC line (REGUi003-A) maintaining a short telomere length. Stem Cell Res 2019; 39:101515. [PMID: 31404747 DOI: 10.1016/j.scr.2019.101515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 10/26/2022] Open
Abstract
Werner syndrome (WS) is a rare human autosomal recessive disorder characterized by early onset of aging-associated diseases, chromosomal instability, and cancer predisposition, without therapeutic treatment solution. Major clinical symptoms of WS include common age-associated diseases, such as insulin-resistant diabetes mellitus, and atherosclerosis. WRN, the gene responsible for the disease, encodes a RECQL-type DNA helicase with a role in telomere metabolism. We derived a stable iPSC line from 53 years old patient's PBMC, with a normal karyotype, but exhibiting a short telomere length, as a major aspect of the cellular phenotype involved in the pathology.
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Affiliation(s)
- Vincent Gatinois
- Laboratory of Genome and Stem Cell Plasticity in Development and Aging, Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France; Laboratory of Cytogenetics, ChromoStem Facility, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Romain Desprat
- SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Fabienne Becker
- SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Lydiane Pichard
- Laboratory of Genome and Stem Cell Plasticity in Development and Aging, Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France; SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Florence Bernex
- Institut de Recherche en Cancérologie de Montpellier, Univ Montpellier, INSERM, U1194, Montpellier, France; Network of Experimental Histology, Univ Montpellier, BioCampus, CNRS, UMS3426, Montpellier, France
| | - Carole Corsini
- Medical Genetics Department, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Franck Pellestor
- Laboratory of Genome and Stem Cell Plasticity in Development and Aging, Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France; Laboratory of Cytogenetics, ChromoStem Facility, Univ Montpellier, CHU de Montpellier, Montpellier, France; SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France.
| | - Jean-Marc Lemaitre
- Laboratory of Genome and Stem Cell Plasticity in Development and Aging, Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France; SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France.
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9
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Rivera-Mulia JC, Schwerer H, Besnard E, Desprat R, Trevilla-Garcia C, Sima J, Bensadoun P, Zouaoui A, Gilbert DM, Lemaitre JM. Cellular senescence induces replication stress with almost no affect on DNA replication timing. Cell Cycle 2018; 17:1667-1681. [PMID: 29963964 DOI: 10.1080/15384101.2018.1491235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Organismal aging entails a gradual decline of normal physiological functions and a major contributor to this decline is withdrawal of the cell cycle, known as senescence. Senescence can result from telomere diminution leading to a finite number of population doublings, known as replicative senescence (RS), or from oncogene overexpression, as a protective mechanism against cancer. Senescence is associated with large-scale chromatin re-organization and changes in gene expression. Replication stress is a complex phenomenon, defined as the slowing or stalling of replication fork progression and/or DNA synthesis, which has serious implications for genome stability, and consequently in human diseases. Aberrant replication fork structures activate the replication stress response leading to the activation of dormant origins, which is thought to be a safeguard mechanism to complete DNA replication on time. However, the relationship between replicative stress and the changes in the spatiotemporal program of DNA replication in senescence progression remains unclear. Here, we studied the DNA replication program during senescence progression in proliferative and pre-senescent cells from donors of various ages by single DNA fiber combing of replicated DNA, origin mapping by sequencing short nascent strands and genome-wide profiling of replication timing (TRT). We demonstrate that, progression into RS leads to reduced replication fork rates and activation of dormant origins, which are the hallmarks of replication stress. However, with the exception of a delay in RT of the CREB5 gene in all pre-senescent cells, RT was globally unaffected by replication stress during entry into either oncogene-induced or RS. Consequently, we conclude that RT alterations associated with physiological and accelerated aging, do not result from senescence progression. Our results clarify the interplay between senescence, aging and replication programs and demonstrate that RT is largely resistant to replication stress.
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Affiliation(s)
| | - Hélène Schwerer
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France
| | - Emilie Besnard
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France
| | - Romain Desprat
- c Stem cell Core Facility SAFE-iPS INGESTEM , CHU Montpellier, Saint Eloi Hospital , Montpellier Cedex , France
| | | | - Jiao Sima
- a Department of Biological Science , Florida State University , Tallahassee , FL , USA
| | - Paul Bensadoun
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France
| | - Anissa Zouaoui
- c Stem cell Core Facility SAFE-iPS INGESTEM , CHU Montpellier, Saint Eloi Hospital , Montpellier Cedex , France
| | - David M Gilbert
- a Department of Biological Science , Florida State University , Tallahassee , FL , USA.,d Center for Genomics and Personalized Medicine , Florida State University , Tallahassee , FL , USA
| | - Jean-Marc Lemaitre
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France.,c Stem cell Core Facility SAFE-iPS INGESTEM , CHU Montpellier, Saint Eloi Hospital , Montpellier Cedex , France
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10
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Abstract
Recent advances in genome-sequencing technology have led to the complete mapping of DNA replication initiation sites in the human genome. This thorough origin mapping facilitates understanding of the relationship between replication initiation events, transcription, and chromatin modifications, and allows the characterization of consensus sequences of potential replication origins. This unit provides a detailed protocol for isolation and sequence analysis of nascent DNA strands. Two variations of the protocol based on non-overlapping assumptions are described below, addressing potential bias issues for whole-genome analyses.
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Affiliation(s)
- Haiqing Fu
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
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11
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Besnard E, Desprat R, Ryan M, Kahli M, Aladjem MI, Lemaitre JM. Best practices for mapping replication origins in eukaryotic chromosomes. ACTA ACUST UNITED AC 2014; 64:22.18.1-13. [PMID: 25181303 DOI: 10.1002/0471143030.cb2218s64] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 11/08/2022]
Abstract
Understanding the regulatory principles ensuring complete DNA replication in each cell division is critical for deciphering the mechanisms that maintain genomic stability. Recent advances in genome sequencing technology facilitated complete mapping of DNA replication sites and helped move the field from observing replication patterns at a handful of single loci to analyzing replication patterns genome-wide. These advances address issues, such as the relationship between replication initiation events, transcription, and chromatin modifications, and identify potential replication origin consensus sequences. This unit summarizes the technological and fundamental aspects of replication profiling and briefly discusses novel insights emerging from mining large datasets, published in the last 3 years, and also describes DNA replication dynamics on a whole-genome scale.
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Affiliation(s)
- Emilie Besnard
- Laboratory of Genome Plasticity and Aging, Institute of Functional Genomics, CNRS UMR5203, INSERM U661, UMI, Montpellier, France
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12
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Bai Q, Desprat R, Klein B, Lemaitre JM, De Vos J. Embryonic Stem Cells or Induced Pluripotent Stem Cells? A DNA Integrity Perspective. Curr Gene Ther 2013; 13:93-8. [DOI: 10.2174/1566523211313020003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 12/31/2012] [Accepted: 01/02/2013] [Indexed: 12/13/2022]
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Cayrou C, Coulombe P, Vigneron A, Stanojcic S, Ganier O, Peiffer I, Rivals E, Puy A, Laurent-Chabalier S, Desprat R, Méchali M. Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res 2011; 21:1438-49. [PMID: 21750104 DOI: 10.1101/gr.121830.111] [Citation(s) in RCA: 247] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In metazoans, thousands of DNA replication origins (Oris) are activated at each cell cycle. Their genomic organization and their genetic nature remain elusive. Here, we characterized Oris by nascent strand (NS) purification and a genome-wide analysis in Drosophila and mouse cells. We show that in both species most CpG islands (CGI) contain Oris, although methylation is nearly absent in Drosophila, indicating that this epigenetic mark is not crucial for defining the activated origin. Initiation of DNA synthesis starts at the borders of CGI, resulting in a striking bimodal distribution of NS, suggestive of a dual initiation event. Oris contain a unique nucleotide skew around NS peaks, characterized by G/T and C/A overrepresentation at the 5' and 3' of Ori sites, respectively. Repeated GC-rich elements were detected, which are good predictors of Oris, suggesting that common sequence features are part of metazoan Oris. In the heterochromatic chromosome 4 of Drosophila, Oris correlated with HP1 binding sites. At the chromosome level, regions rich in Oris are early replicating, whereas Ori-poor regions are late replicating. The genome-wide analysis was coupled with a DNA combing analysis to unravel the organization of Oris. The results indicate that Oris are in a large excess, but their activation does not occur at random. They are organized in groups of site-specific but flexible origins that define replicons, where a single origin is activated in each replicon. This organization provides both site specificity and Ori firing flexibility in each replicon, allowing possible adaptation to environmental cues and cell fates.
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Desprat R, Thierry-Mieg D, Lailler N, Lajugie J, Schildkraut C, Thierry-Mieg J, Bouhassira EE. Predictable dynamic program of timing of DNA replication in human cells. Genome Res 2009; 19:2288-99. [PMID: 19767418 DOI: 10.1101/gr.094060.109] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The organization of mammalian DNA replication is poorly understood. We have produced high-resolution dynamic maps of the timing of replication in human erythroid, mesenchymal, and embryonic stem (ES) cells using TimEX, a method that relies on gaussian convolution of massive, highly redundant determinations of DNA copy-number variations during S phase to produce replication timing profiles. We first obtained timing maps of 3% of the genome using high-density oligonucleotide tiling arrays and then extended the TimEX method genome-wide using massively parallel sequencing. We show that in untransformed human cells, timing of replication is highly regulated and highly synchronous, and that many genomic segments are replicated in temporal transition regions devoid of initiation, where replication forks progress unidirectionally from origins that can be hundreds of kilobases away. Absence of initiation in one transition region is shown at the molecular level by single molecule analysis of replicated DNA (SMARD). Comparison of ES and erythroid cells replication patterns revealed that these cells replicate about 20% of their genome in different quarters of S phase. Importantly, we detected a strong inverse relationship between timing of replication and distance to the closest expressed gene. This relationship can be used to predict tissue-specific timing of replication profiles from expression data and genomic annotations. We also provide evidence that early origins of replication are preferentially located near highly expressed genes, that mid-firing origins are located near moderately expressed genes, and that late-firing origins are located far from genes.
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Affiliation(s)
- Romain Desprat
- Department of Medicine and Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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15
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Desprat R, Bouhassira EE. Gene specificity of suppression of transgene-mediated insertional transcriptional activation by the chicken HS4 insulator. PLoS One 2009; 4:e5956. [PMID: 19536296 PMCID: PMC2694267 DOI: 10.1371/journal.pone.0005956] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [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: 01/30/2009] [Accepted: 04/17/2009] [Indexed: 11/18/2022] Open
Abstract
Insertional mutagenesis has emerged as a major obstacle for gene therapy based on vectors that integrate randomly in the genome. Reducing the genotoxicity of genomic viral integration can, in first approximation, be equated with reducing the risk of oncogene activation, at least in the case of therapeutic payloads that have no known oncogenic potential, such as the globin genes. An attractive solution to the problem of oncogene activation is the inclusion of insulators/enhancer-blockers in the viral vectors. In this study we have used Recombinase-Mediated Cassette Exchange to characterize the effect of integration of globin therapeutic cassettes in the presence or absence of the chicken HS4 and three other putative insulators inserted near Stil, Tal1 and MAP17, three well-known cellular proto-oncogenes in the SCL/Tal1 locus. We show that insertion of a Locus Control Region-driven globin therapeutic globin transgene had a dramatic activating effect on Tal1 and Map17, the two closest genes, a minor effect on Stil, and no effect on Cyp4x1, a non-expressed gene. Of the four element tested, cHS4 was the only one that was able to suppress this transgene-mediated insertional transcriptional activation. cHS4 had a strong suppressive effect on the activation expression of Map17 but has little or no effect on expression of Tal1. The suppressive activity of cHS4 is therefore promoter specific. Importantly, the observed suppressive effect of cHS4 on Map17 activation did not depend on its intercalation between the LCR and the Map 17 promoter. Rather, presence of one or two copies of cHS4 anywhere within the transgene was sufficient to almost completely block the activation of Map17. Therefore, at this complex locus, suppression of transgene-mediated insertional transcriptional activation by cHS4 could not be adequately explained by models that predict that cHS4 can only suppress expression through an enhancer-blocking activity that requires intercalation between an enhancer and a promoter. This has important implications for our theoretical understanding of the possible effects of the insertion of cHS4 on gene therapy vectors. We also show that cHS4 decreased the level of expression of the globin transgene. Therefore, the benefits of partially preventing insertional gene activation are in part negated by the lower expression level of the transgene. A cost/benefit analysis of the utility of incorporation of insulators in gene therapy vectors will require further studies in which the effects of insulators on both the therapeutic gene and the flanking genes are determined at a large number of integration sites. Identification of insulators with minimal promoter specificity would also be of great value.
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Affiliation(s)
- Romain Desprat
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Eric E. Bouhassira
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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Kiprilov EN, Awan A, Desprat R, Velho M, Clement CA, Byskov AG, Andersen CY, Satir P, Bouhassira EE, Christensen ST, Hirsch RE. Human embryonic stem cells in culture possess primary cilia with hedgehog signaling machinery. ACTA ACUST UNITED AC 2008; 180:897-904. [PMID: 18332216 PMCID: PMC2265400 DOI: 10.1083/jcb.200706028] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [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: 12/12/2022]
Abstract
Human embryonic stem cells (hESCs) are potential therapeutic tools and models of human development. With a growing interest in primary cilia in signal transduction pathways that are crucial for embryological development and tissue differentiation and interest in mechanisms regulating human hESC differentiation, demonstrating the existence of primary cilia and the localization of signaling components in undifferentiated hESCs establishes a mechanistic basis for the regulation of hESC differentiation. Using electron microscopy (EM), immunofluorescence, and confocal microscopies, we show that primary cilia are present in three undifferentiated hESC lines. EM reveals the characteristic 9 + 0 axoneme. The number and length of cilia increase after serum starvation. Important components of the hedgehog (Hh) pathway, including smoothened, patched 1 (Ptc1), and Gli1 and 2, are present in the cilia. Stimulation of the pathway results in the concerted movement of Ptc1 out of, and smoothened into, the primary cilium as well as up-regulation of GLI1 and PTC1. These findings show that hESCs contain primary cilia associated with working Hh machinery.
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Affiliation(s)
- Enko N Kiprilov
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Desprat R, Bouhassira EE. β-Globin expression cassette 2.0: Optimizing gene therapy cassettes using RMCE. Blood Cells Mol Dis 2007. [DOI: 10.1016/j.bcmd.2006.10.040] [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] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Feng YQ, Desprat R, Fu H, Olivier E, Lin CM, Lobell A, Gowda SN, Aladjem MI, Bouhassira EE. DNA methylation supports intrinsic epigenetic memory in mammalian cells. PLoS Genet 2006; 2:e65. [PMID: 16683039 PMCID: PMC1449906 DOI: 10.1371/journal.pgen.0020065] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [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: 09/09/2005] [Accepted: 03/17/2006] [Indexed: 12/31/2022] Open
Abstract
We have investigated the role of DNA methylation in the initiation and maintenance of silenced chromatin in somatic mammalian cells. We found that a mutated transgene, in which all the CpG dinucleotides have been eliminated, underwent transcriptional silencing to the same extent as the unmodified transgene. These observations demonstrate that DNA methylation is not required for silencing. The silenced CpG-free transgene exhibited all the features of heterochromatin, including silencing of transcriptional activity, delayed DNA replication, lack of histone H3 and H4 acetylation, lack of H3-K4 methylation, and enrichment in tri-methyl-H3-K9. In contrast, when we tested for transgene reactivation using a Cre recombinase-mediated inversion assay, we observed a marked difference between a CpG-free and an unmodified transgene: the CpG-free transgene resumed transcription and did not exhibit markers of heterochromatin whereas the unmodified transgene remained silenced. These data indicate that methylation of CpG residues conferred epigenetic memory in this system. These results also suggest that replication delay, lack of histone H3 and H4 acetylation, H3-K4 methylation, and enrichment in tri-methyl-H3-K9 are not sufficient to confer epigenetic memory. We propose that DNA methylation within transgenes serves as an intrinsic epigenetic memory to permanently silence transgenes and prevent their reactivation.
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Affiliation(s)
- Yong-Qing Feng
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Romain Desprat
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Haiqing Fu
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Emmanuel Olivier
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Chii Mei Lin
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Amanda Lobell
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Shilpa N Gowda
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Mirit I Aladjem
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Eric E Bouhassira
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
- * To whom correspondence should be addressed. E-mail:
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Abstract
Immunoreactive dynorphin (ir-Dyn) was measured in maternal blood, umbilical vein and amniotic fluid after its extraction by passage through Sep Pak (C18 Waters). No significant change was observed in the plasma level of ir-Dyn in the first and second trimester of pregnancy as compared with plasma obtained from non-pregnant women. However, a 2.2 fold increase in ir-Dyn levels was observed during the third trimester as well as at delivery (1.07 and 1.09 pmoles per ml, respectively as compared with 0.48 pmoles per ml in control plasma). High levels of ir-Dyn were also found in the amniotic fluid (0.83 pmoles per ml) and the umbilical vein plasma (2.2 pmoles per ml). High pressure liquid chromatography analysis of maternal plasma ir-Dyn obtained at the end of the third trimester of pregnancy revealed the presence of multiple forms of ir-Dyn, the major peaks corresponding to the elution time of some previously identified placental ir-compounds namely Dyn-(1-11) and Dyn-(1-13). These data indicate that the levels of ir-Dyn in the maternal plasma at the third trimester of pregnancy and at delivery increase, a placental contribution to this phenomenon could be speculated.
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