1
|
Despréaux P, Jeanton C, Desaulle D, Al Zallouha M, Verdin A, Momas I, Achard S. Innovative graph analysis method to assess gene expression modulation after fine particles exposures of 3D human airway epithelia. ENVIRONMENTAL RESEARCH 2023; 221:115296. [PMID: 36642119 DOI: 10.1016/j.envres.2023.115296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/27/2022] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Environmental particles have dramatic consequences for health, especially for the most vulnerable people, such as asthmatics. To better understand the impact on gene expression modulation of fine particles (PM2.5-0.3) from different emission sources, a 3D-airway model, a human bronchial epithelium (MucilAir-HF™) reconstructed from primary cells from healthy (EpiH) or asthmatic (EpiA) donors, was used. Repeated air-liquid exposures were performed, and epithelia were sacrificed to extract RNAs and assess gene expression. Data were analyzed according to the emission sources, physiological status, and exposure doses using a recent model consisting in a graph analysis on pairwise expression ratio. The results were compared with those from the classical ΔΔCt method. The graph analysis method proved to have better statistical properties than the classical ΔΔCt method and demonstrated that repeated PM2.5-0.3 exposures induced a dose-dependent up-regulation of the metabolic gene (CYP1B1) and a down-regulation of the inflammation gene (CXCL10). These modulations were greater for "industrial" than for "urban traffic" fine particles, and the effects were found to be greater after exposure of EpiA than EpiH, thus emphasizing the importance of the epithelium's physiological status in sensitivity to particles. Our study is original in terms of the experimental conditions and the graphical statistical analysis model established. The results highlight the importance of particle chemistry on the modulation of cellular and molecular responses, which may vary according to the individual's vulnerability.
Collapse
Affiliation(s)
- Philomène Despréaux
- Université Paris Cité, Faculté de Pharmacie, CRESS INSERM UMR 1153, équipe HERA (Health Environmental Risk Assessment), Paris, France
| | - Capucine Jeanton
- Université Paris Cité, Faculté de Pharmacie, CRESS INSERM UMR 1153, équipe HERA (Health Environmental Risk Assessment), Paris, France
| | - Dorota Desaulle
- Université Paris Cité, Faculté de Pharmacie, UR 7537 - BioSTM (Biostatistique, Traitement et Modélisation des données biologiques), Paris, France
| | - Margueritta Al Zallouha
- Université Paris Cité, Faculté de Pharmacie, CRESS INSERM UMR 1153, équipe HERA (Health Environmental Risk Assessment), Paris, France
| | - Anthony Verdin
- Université du Littoral Côte d'Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV) UR4492, SFR Condorcet CNRS 3417, Dunkerque, France
| | - Isabelle Momas
- Université Paris Cité, Faculté de Pharmacie, CRESS INSERM UMR 1153, équipe HERA (Health Environmental Risk Assessment), Paris, France
| | - Sophie Achard
- Université Paris Cité, Faculté de Pharmacie, CRESS INSERM UMR 1153, équipe HERA (Health Environmental Risk Assessment), Paris, France.
| |
Collapse
|
2
|
Atehortua Martinez LA, Curis E, Mekdad N, Larrieu C, Courtin C, Jourdren L, Blugeon C, Laplanche JL, Megarbane B, Marie-Claire C, Benturquia N. Individual differences in cocaine-induced conditioned place preference in male rats: Behavioral and transcriptomic evidence. J Psychopharmacol 2022; 36:1161-1175. [PMID: 36121009 PMCID: PMC9548661 DOI: 10.1177/02698811221123047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Substance use disorder emerges in a small proportion of drug users and has the characteristics of a chronic relapsing pathology. AIMS Our study aimed to demonstrate and characterize the variability in the expression of the rewarding effects of cocaine in the conditioned place preference (CPP) paradigm. METHODS A cocaine-CPP paradigm in male Sprague-Dawley rats with an extinction period of 12 days and reinstatement was conducted. A statistical model was developed to distinguish rats expressing or not a cocaine-induced place preference. RESULTS Two groups of rats were identified: rats that did express rewarding effects (CPP expression (CPPE), score >102 s) and rats that did not (no CPP expression (nCPPE), score between -85 and 59 s). These two groups did not show significant differences in a battery of behavioral tests. To identify differentially expressed genes in the CPPE and nCPPE groups, a whole-transcriptome ribonucleic acid-sequencing analysis was performed in the nucleus accumbens (NAc) 24 h after the CPP test. Four immediate early genes (Fos, Egr2, Nr4a1, and Zbtb37) were differentially expressed in the NAc of CPPE rats after expression of CPP. Variability in cocaine-induced place preference persisted in the CPPE and nCPPE groups after the extinction and reinstatement phases. Transcriptomic differences observed after reinstatement were distinct from those observed immediately after expression of CPP. CONCLUSION These new findings provide insights into the identification of mechanisms underlying interindividual variability in the response to cocaine's rewarding effects.
Collapse
Affiliation(s)
- Luisa Alessandra Atehortua Martinez
- Institut National de la Santé et de la Recherche Médicale UMR-S 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, Paris, France
| | - Emmanuel Curis
- UR 7537 BioSTM, Université Paris Cité, Paris, France,Laboratoire d’Hématologie, Hôpital Lariboisière, APHP, Paris, France
| | - Nawel Mekdad
- Institut National de la Santé et de la Recherche Médicale UMR-S 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, Paris, France
| | - Claire Larrieu
- Institut National de la Santé et de la Recherche Médicale UMR-S 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, Paris, France
| | - Cindie Courtin
- Institut National de la Santé et de la Recherche Médicale UMR-S 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, Paris, France
| | - Laurent Jourdren
- Genomic Facility, Institut de Biologie de l’École Normale Supérieure, École Normale Supérieure, Centre National pour la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, PSL Research University, Paris, France
| | - Corinne Blugeon
- Genomic Facility, Institut de Biologie de l’École Normale Supérieure, École Normale Supérieure, Centre National pour la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, PSL Research University, Paris, France
| | - Jean-Louis Laplanche
- Institut National de la Santé et de la Recherche Médicale UMR-S 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, Paris, France
| | - Bruno Megarbane
- Institut National de la Santé et de la Recherche Médicale UMR-S 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, Paris, France
| | - Cynthia Marie-Claire
- Institut National de la Santé et de la Recherche Médicale UMR-S 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, Paris, France
| | - Nadia Benturquia
- Institut National de la Santé et de la Recherche Médicale UMR-S 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, Paris, France,Nadia Benturquia, Institut National de la Santé et de la Recherche Médicale UMR-S 1144, Optimisation Thérapeutique en Neurospsychopharmacologie, Université de Paris Cité, Paris 75006, France.
| |
Collapse
|
3
|
Li Y, Jiang Y, Li Z, Yu Y, Chen J, Jia W, Kaow Ng Y, Ye F, Cheng Li S, Shen B. Both simulation and sequencing data reveal coinfections with multiple SARS-CoV-2 variants in the COVID-19 pandemic. Comput Struct Biotechnol J 2022; 20:1389-1401. [PMID: 35342534 PMCID: PMC8930779 DOI: 10.1016/j.csbj.2022.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/13/2022] [Accepted: 03/13/2022] [Indexed: 01/16/2023] Open
Abstract
SARS-CoV-2 is a single-stranded RNA betacoronavirus with a high mutation rate. The rapidly emerging SARS-CoV-2 variants could increase transmissibility and diminish vaccine protection. However, whether coinfection with multiple SARS-CoV-2 variants exists remains controversial. This study collected 12,986 and 4,113 SARS-CoV-2 genomes from the GISAID database on May 11, 2020 (GISAID20May11), and Apr 1, 2021 (GISAID21Apr1), respectively. With single-nucleotide variant (SNV) and network clique analyses, we constructed single-nucleotide polymorphism (SNP) coexistence networks and discovered maximal SNP cliques of sizes 16 and 34 in the GISAID20May11 and GISAID21Apr1 datasets, respectively. Simulating the transmission routes and SNV accumulations, we discovered a linear relationship between the size of the maximal clique and the number of coinfected variants. We deduced that the COVID-19 cases in GISAID20May11 and GISAID21Apr1 were coinfections with 3.20 and 3.42 variants on average, respectively. Additionally, we performed Nanopore sequencing on 42 COVID-19 patients and discovered recurrent heterozygous SNPs in twenty of the patients, including loci 8,782 and 28,144, which were crucial for SARS-CoV-2 lineage divergence. In conclusion, our findings reported SARS-CoV-2 variants coinfection in COVID-19 patients and demonstrated the increasing number of coinfected variants.
Collapse
Affiliation(s)
- Yinhu Li
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610212, China
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Yiqi Jiang
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Zhengtu Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Yonghan Yu
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Jiaxing Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
- Department of Computer Science, Hong Kong Baptist University, Hong Kong 999077, China
| | - Wenlong Jia
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Yen Kaow Ng
- Kotai Biotechnologies, Inc., Osaka 565-0871, Japan
| | - Feng Ye
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610212, China
| |
Collapse
|
4
|
Grillault Laroche D, Curis E, Bellivier F, Nepost C, Gross G, Etain B, Marie-Claire C. Network of co-expressed circadian genes, childhood maltreatment and sleep quality in bipolar disorders. Chronobiol Int 2021; 38:986-993. [PMID: 33781139 DOI: 10.1080/07420528.2021.1903028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bipolar disorder (BD) is a chronic and burdensome psychiatric disease, characterized by variations in mood and energy. The literature has consistently demonstrated an association between BD and childhood maltreatment (CM), and genetic variants of circadian genes have been associated with an increased vulnerability to develop BD. In this context, environmental factors such as CM may also contribute to the susceptibility to BD through alterations in the functioning of the biological clock linked to modifications of expression of circadian genes. In this study, we explored the associations between childhood maltreatment, sleep quality, and the level of expression of a comprehensive set of circadian genes in lymphoblastoid cell lines from patients with BD. The sample consisted of 52 Caucasian euthymic patients with a diagnosis of BD type 1 or type 2. The exposure to CM was assessed with the Childhood Trauma Questionnaire (CTQ), and the sleep quality was assessed using the Pittsburgh Sleep Quality Index. We measured the expression of 18 circadian genes using quantitative RT-PCR: ARNTL2, BHLHE40, BHLHE41, CLOCK, CRY1, CRY2, CSNK1D, CSNK1E, DBP, GSK3B, NPAS2, NR1D1, PER1, PER2, PER3, PPARGC1A, RORA, and RORB. Gene expression networks were analyzed with the disjoint graphs method. Compared to the other investigated transcripts, PPARGC1A was the only one whose expression level was differentially affected in patients who have experienced CM and, more specifically, physical abuse. We observed no significant effects of the other CTQ subscores (emotional and sexual abuses, physical and emotional neglects), nor of the sleep quality on the network of circadian genes expression. Although requiring replication in larger cohorts, the result obtained here is consistent with the hypothesis of an influence of CM exposure on circadian systems and highlights the importance of PPARGC1A in these processes.
Collapse
Affiliation(s)
- D Grillault Laroche
- Université de Paris, INSERM UMR-S 1144, Paris, France
- Département de Psychiatrie et de Médecine Addictologique, Hôpitaux Lariboisière-Fernand Widal, GHU APHP.Nord - Université de Paris, Paris, France
| | - E Curis
- Laboratoire de Biomathématiques, Université de Paris, Paris, France
- Service de Biostatistique et Information Médicale, Paris, France
| | - F Bellivier
- Université de Paris, INSERM UMR-S 1144, Paris, France
- Département de Psychiatrie et de Médecine Addictologique, Hôpitaux Lariboisière-Fernand Widal, GHU APHP.Nord - Université de Paris, Paris, France
| | - C Nepost
- Université de Paris, INSERM UMR-S 1144, Paris, France
| | - G Gross
- Université de Paris, INSERM UMR-S 1144, Paris, France
- Pôle Hospitalo-Universitaire de Psychiatrie d'Adultes et d'Addictologie du Grand Nancy, Centre Psychothérapique de Nancy, Laxou, France
- Faculté de Médecine, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - B Etain
- Université de Paris, INSERM UMR-S 1144, Paris, France
- Département de Psychiatrie et de Médecine Addictologique, Hôpitaux Lariboisière-Fernand Widal, GHU APHP.Nord - Université de Paris, Paris, France
| | | |
Collapse
|
5
|
Taccola C, Barneoud P, Cartot-Cotton S, Valente D, Schussler N, Saubaméa B, Chasseigneaux S, Cochois V, Mignon V, Curis E, Lochus M, Nicolic S, Dodacki A, Cisternino S, Declèves X, Bourasset F. Modifications of physical and functional integrity of the blood-brain barrier in an inducible mouse model of neurodegeneration. Neuropharmacology 2021; 191:108588. [PMID: 33940010 DOI: 10.1016/j.neuropharm.2021.108588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 04/10/2021] [Accepted: 04/20/2021] [Indexed: 12/28/2022]
Abstract
The inducible p25 overexpression mouse model recapitulate many hallmark features of Alzheimer's disase including progressive neuronal loss, elevated Aβ, tau pathology, cognitive dysfunction, and impaired synaptic plasticity. We chose p25 mice to evaluate the physical and functional integrity of the blood-brain barrier (BBB) in a context of Tau pathology (pTau) and severe neurodegeneration, at an early (3 weeks ON) and a late (6 weeks ON) stage of the pathology. Using in situ brain perfusion and confocal imaging, we found that the brain vascular surface area and the physical integrity of the BBB were unaltered in p25 mice. However, there was a significant 14% decrease in cerebrovascular volume in 6 weeks ON mice, possibly explained by a significant 27% increase of collagen IV in the basement membrane of brain capillaries. The function of the BBB transporters GLUT1 and LAT1 was evaluated by measuring brain uptake of d-glucose and phenylalanine, respectively. In 6 weeks ON p25 mice, d-glucose brain uptake was significantly reduced by about 17% compared with WT, without any change in the levels of GLUT1 protein or mRNA in brain capillaries. The brain uptake of phenylalanine was not significantly reduced in p25 mice compared with WT. Lack of BBB integrity, impaired BBB d-glucose transport have been observed in several mouse models of AD. In contrast, reduced cerebrovascular volume and an increased basement membrane thickness may be more specifically associated with pTau in mouse models of neurodegeneration.
Collapse
Affiliation(s)
- Camille Taccola
- Pharmacokinetics, Dynamics and Metabolism, Translational Medicine & Early Development, Sanofi, 3 Digue d'Alfortville, 94140, Alfortville, France; INSERM UMR-S 1144, UFR de Pharmacie, Faculté de Santé, Université de Paris, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Pascal Barneoud
- Rare and Neurologic Diseases Research Therapeutic Area, Sanofi, 1 Avenue Pierre Brossolette, 91380, Chilly-Mazarin, France
| | - Sylvaine Cartot-Cotton
- Pharmacokinetics, Dynamics and Metabolism, Translational Medicine & Early Development, Sanofi, 3 Digue d'Alfortville, 94140, Alfortville, France
| | - Delphine Valente
- Drug Metabolism & Pharmacokinetics, Research platform, Sanofi, 3 Digue d'Alfortville, 94140, Alfortville, France
| | - Nathalie Schussler
- Rare and Neurologic Diseases Research Therapeutic Area, Sanofi, 1 Avenue Pierre Brossolette, 91380, Chilly-Mazarin, France
| | - Bruno Saubaméa
- INSERM UMR-S 1144, UFR de Pharmacie, Faculté de Santé, Université de Paris, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Stéphanie Chasseigneaux
- INSERM UMR-S 1144, UFR de Pharmacie, Faculté de Santé, Université de Paris, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Véronique Cochois
- INSERM UMR-S 1144, UFR de Pharmacie, Faculté de Santé, Université de Paris, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Virginie Mignon
- INSERM UMR-S 1144, UFR de Pharmacie, Faculté de Santé, Université de Paris, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Emmanuel Curis
- Laboratoire de biomathématiques, plateau iB(2), EA 7537 « BioSTM », UFR de Pharmacie, Faculté de Santé, Université de Paris, 4 avenue de l'Observatoire, 75006, Paris, France; Service de bioinformatique et statistique médicale, hôpital Saint-Louis, APHP, 1, avenue Claude Vellefaux, 75010, Paris, France
| | - Murielle Lochus
- INSERM UMR-S 1144, UFR de Pharmacie, Faculté de Santé, Université de Paris, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Sophie Nicolic
- INSERM UMR-S 1144, UFR de Pharmacie, Faculté de Santé, Université de Paris, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Agnès Dodacki
- INSERM UMR-S 1144, UFR de Pharmacie, Faculté de Santé, Université de Paris, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Salvatore Cisternino
- INSERM UMR-S 1144, UFR de Pharmacie, Faculté de Santé, Université de Paris, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Xavier Declèves
- INSERM UMR-S 1144, UFR de Pharmacie, Faculté de Santé, Université de Paris, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Fanchon Bourasset
- Laboratoire de Recherches Intégratives en Neurosciences et Psychologie Cognitive, Université Bourgogne Franche-Comté, 19 rue Ambroise Paré, 25000, Besançon, France.
| |
Collapse
|
6
|
Li Y, Toothaker JM, Ben-Simon S, Ozeri L, Schweitzer R, McCourt BT, McCourt CC, Werner L, Snapper SB, Shouval DS, Khatib S, Koren O, Agnihorti S, Tseng G, Konnikova L. In utero human intestine harbors unique metabolome, including bacterial metabolites. JCI Insight 2020; 5:138751. [PMID: 33001863 PMCID: PMC7710283 DOI: 10.1172/jci.insight.138751] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Symbiotic microbial colonization through the establishment of the intestinal microbiome is critical to many intestinal functions, including nutrient metabolism, intestinal barrier integrity, and immune regulation. Recent studies suggest that education of intestinal immunity may be ongoing in utero. However, the drivers of this process are unknown. The microbiome and its byproducts are one potential source. Whether a fetal intestinal microbiome exists is controversial, and whether microbially derived metabolites are present in utero is unknown. Here, we aimed to determine whether bacterial DNA and microbially derived metabolites can be detected in second trimester human intestinal samples. Although we were unable to amplify bacterial DNA from fetal intestines, we report a fetal metabolomic intestinal profile with an abundance of bacterially derived and host-derived metabolites commonly produced in response to microbiota. Though we did not directly assess their source and function, we hypothesize that these microbial-associated metabolites either come from the maternal microbiome and are vertically transmitted to the fetus to prime the fetal immune system and prepare the gastrointestinal tract for postnatal microbial encounters or are produced locally by bacteria that were below our detection threshold. A unique human fetal metabolomic intestinal profile is reported with an abundance of bacterially derived metabolites.
Collapse
Affiliation(s)
| | - Jessica M Toothaker
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Shira Ben-Simon
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Lital Ozeri
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Ron Schweitzer
- Analytical Chemistry Laboratory, Tel-Hai College, Upper Galilee, Israel
| | - Blake T McCourt
- Department of Pediatrics, Yale University, New Haven, Connecticut, USA
| | - Collin C McCourt
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lael Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Dror S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Soliman Khatib
- Analytical Chemistry Laboratory, Tel-Hai College, Upper Galilee, Israel.,Department of Natural Compounds and Analytical Chemistry, Migal Galilee Research Institute, Kiryat Shmona, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | | | | | - Liza Konnikova
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pediatrics, Yale University, New Haven, Connecticut, USA.,Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Reproductive Sciences and.,Program in Human and Translational Immunology, Yale University, New Haven, Connecticut, USA
| |
Collapse
|
7
|
Grillault Laroche D, Curis E, Bellivier F, Nepost C, Courtin C, Etain B, Marie-Claire C. Childhood maltreatment and HPA axis gene expression in bipolar disorders: A gene network analysis. Psychoneuroendocrinology 2020; 120:104753. [PMID: 32634746 DOI: 10.1016/j.psyneuen.2020.104753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/13/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Bipolar disorder (BD) is highly associated with childhood maltreatment (CM), the exposure to such early adversity being suggested to disrupt the expression of several biological pathways. This study aims at exploring associations between the mRNA levels of 9 HPA axis genes in lymphoblastoid cell lines from patients with BD according to their self-reported exposure to CM. METHODS The sample consisted of 33 Caucasian patients with a diagnosis of BD type 1, assessed for the exposure to CM with the Childhood Trauma Questionnaire (CTQ). Quantitative RT-PCR was performed on 9 transcripts of the HPA axis genes: DGKH, FKBP5, NR3C1, SGK1, SGK2, SGK3, SKA2, STAT5A and UCN. RT-qPCR data were analyzed using the method of disjoint gene networks with SARP.compo package for R. RESULTS We found no associations between CTQ total score and the amount of HPA axis transcripts neither in univariate analyses, nor with network analyses. Emotional abuse (EA) was associated with a significant decreased expression of two transcripts, DGKH (p = 0.009) and NR3C1 (p = 0.04). This was confirmed by the disjoint network analysis, which showed that NR3C1 and DGKH were expressed differently from the rest of the HPA axis network in presence of emotional abuse. DISCUSSION This study described the expression levels of a comprehensive set of HPA axis genes according to childhood maltreatment in a sample of patients with BD type 1 and suggested that emotional abuse decreased the expression of NR3C1 and DGKH. Our results require further replication in independent larger samples.
Collapse
Affiliation(s)
- D Grillault Laroche
- Unité INSERM UMR-S 1144 Optimisation thérapeutique en Neuropsychopharmacologie, Paris, France; AP-HP, GHU Saint-Louis - Lariboisière-F. Widal, Pôle de Psychiatrie et de Médecine Addictologique, Paris, France; Université de Paris, Paris, France.
| | - E Curis
- Laboratoire de Biomathématiques, EA 7537 BioSTM, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Service de Bioinformatique et Information Médicale, Hôpital Saint-Louis, AP-HP, Paris, France
| | - F Bellivier
- Unité INSERM UMR-S 1144 Optimisation thérapeutique en Neuropsychopharmacologie, Paris, France; AP-HP, GHU Saint-Louis - Lariboisière-F. Widal, Pôle de Psychiatrie et de Médecine Addictologique, Paris, France; Université de Paris, Paris, France
| | - C Nepost
- Unité INSERM UMR-S 1144 Optimisation thérapeutique en Neuropsychopharmacologie, Paris, France
| | - C Courtin
- Unité INSERM UMR-S 1144 Optimisation thérapeutique en Neuropsychopharmacologie, Paris, France
| | - B Etain
- Unité INSERM UMR-S 1144 Optimisation thérapeutique en Neuropsychopharmacologie, Paris, France; AP-HP, GHU Saint-Louis - Lariboisière-F. Widal, Pôle de Psychiatrie et de Médecine Addictologique, Paris, France; Université de Paris, Paris, France
| | - C Marie-Claire
- Unité INSERM UMR-S 1144 Optimisation thérapeutique en Neuropsychopharmacologie, Paris, France
| |
Collapse
|
8
|
Metabolomics analysis of human acute graft-versus-host disease reveals changes in host and microbiota-derived metabolites. Nat Commun 2019; 10:5695. [PMID: 31836702 PMCID: PMC6910937 DOI: 10.1038/s41467-019-13498-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 11/13/2019] [Indexed: 02/08/2023] Open
Abstract
Despite improvement in clinical management, allogeneic hematopoietic stem cell transplantation (HSCT) is still hampered by high morbidity and mortality rates, mainly due to graft versus host disease (GvHD). Recently, it has been demonstrated that the allogeneic immune response might be influenced by external factors such as tissues microenvironment or host microbiota. Here we used high throughput metabolomics to analyze two cohorts of genotypically HLA-identical related recipient and donor pairs. Metabolomic profiles markedly differ between recipients and donors. At the onset of acute GvHD, in addition to host-derived metabolites, we identify significant variation in microbiota-derived metabolites, especially in aryl hydrocarbon receptor (AhR) ligands, bile acids and plasmalogens. Altogether, our findings support that the allogeneic immune response during acute GvHD might be influenced by bile acids and by the decreased production of AhR ligands by microbiota that could limit indoleamine 2,3-dioxygenase induction and influence allogeneic T cell reactivity. Graft versus host disease (GvHD) still hinders allogeneic hematopoietic stem cell transplantation. Here, the authors use metabolomics to analyze two cohorts of paired transplant recipients and donors, identifying significant differences in both host- and microbiota-derived metabolites.
Collapse
|
9
|
Selecting reference genes in RT-qPCR based on equivalence tests: a network based approach. Sci Rep 2019; 9:16231. [PMID: 31700128 PMCID: PMC6838083 DOI: 10.1038/s41598-019-52217-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 10/14/2019] [Indexed: 01/18/2023] Open
Abstract
Because quantitative reverse transcription PCR (RT-qPCR) gene expression data are compositional, amounts of quantified RNAs must be normalized using reference genes. However, the two most used methods to select reference genes (NormFinder and geNorm) ignore the compositional nature of RT-qPCR data, and often lead to different results making reliable reference genes selection difficult. We propose a method, based on all pairwise equivalence tests on ratio of gene expressions, to select genes that are stable enough to be used as reference genes among a set a candidate genes. This statistical procedure controls the error of selecting an inappropriate gene. Application to 30 candidate reference genes commonly used in human studies, assessed by RT-qPCR in RNA samples from lymphoblastoid cell lines of 14 control subjects and 26 patients with bipolar disorder, allowed to select 7 reference genes. This selection was consistent with geNorm's ranking, less with NormFinder's ranking. Our results provide an important fundamental basis for reference genes identification using sound statistics taking into account the compositional nature of RT-qPCR data. The method, implemented in the SARP.compo package for R (available on the CRAN), can be used more generally to prove that a set of genes shares a common expression pattern.
Collapse
|