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Davidson BA, Miranda AX, Reed SC, Bergman RE, Kemp JDJ, Reddy AP, Pantone MV, Fox EK, Dorand RD, Hurley PJ, Croessmann S, Park BH. An in vitro CRISPR screen of cell-free DNA identifies apoptosis as the primary mediator of cell-free DNA release. Commun Biol 2024; 7:441. [PMID: 38600351 PMCID: PMC11006667 DOI: 10.1038/s42003-024-06129-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
ABTRACT Clinical circulating cell-free DNA (cfDNA) testing is now routine, however test accuracy remains limited. By understanding the life-cycle of cfDNA, we might identify opportunities to increase test performance. Here, we profile cfDNA release across a 24-cell line panel and utilize a cell-free CRISPR screen (cfCRISPR) to identify mediators of cfDNA release. Our panel outlines two distinct groups of cell lines: one which releases cfDNA fragmented similarly to clinical samples and purported as characteristic of apoptosis, and another which releases larger fragments associated with vesicular or necrotic DNA. Our cfCRISPR screens reveal that genes mediating cfDNA release are primarily involved with apoptosis, but also identify other subsets of genes such as RNA binding proteins as potential regulators of cfDNA release. We observe that both groups of cells lines identified primarily produce cfDNA through apoptosis. These results establish the utility of cfCRISPR, genetically validate apoptosis as a major mediator of DNA release in vitro, and implicate ways to improve cfDNA assays.
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Affiliation(s)
- Brad A Davidson
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Adam X Miranda
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Sarah C Reed
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Riley E Bergman
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Justin D J Kemp
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Anvith P Reddy
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Morgan V Pantone
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Ethan K Fox
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - R Dixon Dorand
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Paula J Hurley
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Sarah Croessmann
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Ben Ho Park
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA.
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Andrade-Brito DE, Núñez-Ríos DL, Martínez-Magaña JJ, Nagamatsu ST, Rompala G, Zillich L, Witt SH, Clark SL, Lattig MC, Montalvo-Ortiz JL. Neuronal-specific methylome and hydroxymethylome analysis reveal significant loci associated with alcohol use disorder. Front Genet 2024; 15:1345410. [PMID: 38633406 PMCID: PMC11021708 DOI: 10.3389/fgene.2024.1345410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
Background: Alcohol use disorder (AUD) is a complex condition associated with adverse health consequences that affect millions of individuals worldwide. Epigenetic modifications, including DNA methylation (5 mC), have been associated with AUD and other alcohol-related traits. Epigenome-wide association studies (EWAS) have identified differentially methylated genes associated with AUD in human peripheral and brain tissue. More recently, epigenetic studies of AUD have also evaluated DNA hydroxymethylation (5 hmC) in the human brain. However, most of the epigenetic work in postmortem brain tissue has examined bulk tissue. In this study, we investigated neuronal-specific 5 mC and 5 hmC alterations at CpG sites associated with AUD in the human orbitofrontal cortex (OFC). Methods: Neuronal nuclei from the OFC were evaluated in 34 human postmortem brain samples (10 AUD, 24 non-AUD). Reduced representation oxidative bisulfite sequencing was used to assess 5 mC and 5 hmC at the genome-wide level. Differential 5 mC and 5 hmC were evaluated using the methylKit R package and significance was set at false discovery rate < 0.05 and differential methylation > 2. Functional enrichment analyses were performed, and gene-level convergence was evaluated in an independent dataset that assessed 5 mC and 5 hmC of AUD in bulk cortical tissue. Results: We identified 417 5 mC and 363 5hmC significant differential CpG sites associated with AUD, with 59% in gene promoters. Some of the identified genes have been previously implicated in alcohol consumption, including SYK, DNMT3A for 5 mC, GAD1, DLX1, DLX2, for 5 hmC and GATA4 in both. Convergence with a previous AUD 5 mC and 5 hmC study was observed for 28 genes. We also identified 5 and 35 differential regions for 5 mC and 5 hmC, respectively. Lastly, GWAS enrichment analysis showed an association with AUD for differential 5 mC genes. Discussion: This study reveals neuronal-specific methylome and hydroxymethylome dysregulation associated with AUD, identifying both previously reported and potentially novel gene associations with AUD. Our findings provide new insights into the epigenomic dysregulation of AUD in the human brain.
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Affiliation(s)
- Diego E. Andrade-Brito
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
- National Center of Post-Traumatic Stress Disorder, VA CT Healthcare, West Haven, CT, United States
| | - Diana L. Núñez-Ríos
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
- National Center of Post-Traumatic Stress Disorder, VA CT Healthcare, West Haven, CT, United States
| | - José Jaime Martínez-Magaña
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
- National Center of Post-Traumatic Stress Disorder, VA CT Healthcare, West Haven, CT, United States
| | - Sheila T. Nagamatsu
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
- National Center of Post-Traumatic Stress Disorder, VA CT Healthcare, West Haven, CT, United States
| | - Gregory Rompala
- Icahn School of Medicine at Mount Sinai, New York City, NY, United States
| | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Stephanie H. Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Shaunna L. Clark
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, College Station, TX, United States
| | - Maria C. Lattig
- Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia
| | - Janitza L. Montalvo-Ortiz
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
- National Center of Post-Traumatic Stress Disorder, VA CT Healthcare, West Haven, CT, United States
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53
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Kamathewatta KI, Kulappu Arachchige SN, Young ND, Condello AK, Wawegama NK, Browning GF. Transcriptomic analysis of the effects of tylosin on the protective immunity provided by the Mycoplasma gallisepticum vaccine Vaxsafe MG ts-304. Vet Microbiol 2024; 291:110029. [PMID: 38364466 DOI: 10.1016/j.vetmic.2024.110029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
The antimicrobial tylosin is commonly used to control mycoplasma infections, sometimes in combination with vaccination. However, the efficacy of a live mycoplasma vaccine, when combined with subsequent antimicrobial treatment, against the effects of subsequent infection with a virulent strain is unknown. This study employed differential gene expression analysis to evaluate the effects of tylosin on the protection provided by the live attenuated Vaxsafe MG ts-304 vaccine, which has been shown to be safe and to provide long-term protective immunity against infection with Mycoplasma gallisepticum. The transcriptional profiles of the tracheal mucosa revealed significantly enhanced inflammation, immune cell proliferation and adaptive immune responses in unvaccinated, untreated birds and in unvaccinated birds treated with tylosin 2 weeks after infection with virulent M. gallisepticum. These responses, indicative of the typical immune dysregulation caused by infection with M. gallisepticum, were less severe in the unvaccinated, tylosin-treated birds than in the unvaccinated, untreated birds. This was attributable to the effect of residual levels of tylosin in the tracheal mucosa on replication of virulent M. gallisepticum. These responses were not detected in vaccinated, tylosin-treated birds or in vaccinated, untreated birds after infection. The tracheal mucosal transcriptional profiles of these birds resembled those of unvaccinated, untreated, uninfected birds, suggesting a rapid and protective secondary immune response and effective vaccination. Overall, these results show that, although tylosin treatment reduced the duration of immunity, the initial protective immunity induced by Vaxsafe MG ts-304 lasted for at least 22 weeks after vaccination, even after the administration of tylosin for 16 weeks following vaccination.
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Affiliation(s)
- Kanishka I Kamathewatta
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Sathya N Kulappu Arachchige
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Anna Kanci Condello
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Nadeeka K Wawegama
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia.
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54
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Karjalainen MK, Karthikeyan S, Oliver-Williams C, Sliz E, Allara E, Fung WT, Surendran P, Zhang W, Jousilahti P, Kristiansson K, Salomaa V, Goodwin M, Hughes DA, Boehnke M, Fernandes Silva L, Yin X, Mahajan A, Neville MJ, van Zuydam NR, de Mutsert R, Li-Gao R, Mook-Kanamori DO, Demirkan A, Liu J, Noordam R, Trompet S, Chen Z, Kartsonaki C, Li L, Lin K, Hagenbeek FA, Hottenga JJ, Pool R, Ikram MA, van Meurs J, Haller T, Milaneschi Y, Kähönen M, Mishra PP, Joshi PK, Macdonald-Dunlop E, Mangino M, Zierer J, Acar IE, Hoyng CB, Lechanteur YTE, Franke L, Kurilshikov A, Zhernakova A, Beekman M, van den Akker EB, Kolcic I, Polasek O, Rudan I, Gieger C, Waldenberger M, Asselbergs FW, Hayward C, Fu J, den Hollander AI, Menni C, Spector TD, Wilson JF, Lehtimäki T, Raitakari OT, Penninx BWJH, Esko T, Walters RG, Jukema JW, Sattar N, Ghanbari M, Willems van Dijk K, Karpe F, McCarthy MI, Laakso M, Järvelin MR, Timpson NJ, Perola M, Kooner JS, Chambers JC, van Duijn C, Slagboom PE, Boomsma DI, Danesh J, Ala-Korpela M, Butterworth AS, Kettunen J. Genome-wide characterization of circulating metabolic biomarkers. Nature 2024; 628:130-138. [PMID: 38448586 PMCID: PMC10990933 DOI: 10.1038/s41586-024-07148-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/01/2024] [Indexed: 03/08/2024]
Abstract
Genome-wide association analyses using high-throughput metabolomics platforms have led to novel insights into the biology of human metabolism1-7. This detailed knowledge of the genetic determinants of systemic metabolism has been pivotal for uncovering how genetic pathways influence biological mechanisms and complex diseases8-11. Here we present a genome-wide association study for 233 circulating metabolic traits quantified by nuclear magnetic resonance spectroscopy in up to 136,016 participants from 33 cohorts. We identify more than 400 independent loci and assign probable causal genes at two-thirds of these using manual curation of plausible biological candidates. We highlight the importance of sample and participant characteristics that can have significant effects on genetic associations. We use detailed metabolic profiling of lipoprotein- and lipid-associated variants to better characterize how known lipid loci and novel loci affect lipoprotein metabolism at a granular level. We demonstrate the translational utility of comprehensively phenotyped molecular data, characterizing the metabolic associations of intrahepatic cholestasis of pregnancy. Finally, we observe substantial genetic pleiotropy for multiple metabolic pathways and illustrate the importance of careful instrument selection in Mendelian randomization analysis, revealing a putative causal relationship between acetone and hypertension. Our publicly available results provide a foundational resource for the community to examine the role of metabolism across diverse diseases.
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Affiliation(s)
- Minna K Karjalainen
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland.
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland.
- Northern Finland Birth Cohorts, Arctic Biobank, Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland.
| | - Savita Karthikeyan
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Clare Oliver-Williams
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Public Health Specialty Training Programme, Cambridge, UK
| | - Eeva Sliz
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elias Allara
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Wing Tung Fung
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kati Kristiansson
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Matt Goodwin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Lilian Fernandes Silva
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Xianyong Yin
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Jiangsu, China
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Matt J Neville
- NIHR Oxford Biomedical Research Centre, OUHFT Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Natalie R van Zuydam
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Ayse Demirkan
- Surrey Institute for People-Centred AI, University of Surrey, Guildford, UK
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK
| | - Jun Liu
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Christiana Kartsonaki
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Toomas Haller
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Pashupati P Mishra
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Peter K Joshi
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Erin Macdonald-Dunlop
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Jonas Zierer
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yara T E Lechanteur
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marian Beekman
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik B van den Akker
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
- Center for Computational Biology, Leiden University Medical Center, Leiden, The Netherlands
- The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Ivana Kolcic
- Department of Public Health, School of Medicine, University of Split, Split, Croatia
| | - Ozren Polasek
- Department of Public Health, School of Medicine, University of Split, Split, Croatia
| | - Igor Rudan
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Folkert W Asselbergs
- Amsterdam University Medical Centers, Department of Cardiology, University of Amsterdam, Amsterdam, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Genomics Research Center, Abbvie, Cambridge, MA, USA
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - James F Wilson
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- InFLAMES Research Flagship, University of Turku, Turku, Finland
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Tonu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Naveed Sattar
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Fredrik Karpe
- NIHR Oxford Biomedical Research Centre, OUHFT Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Marjo-Riitta Järvelin
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Markus Perola
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Diabetes and Obesity Research Program, University of Helsinki, Helsinki, Finland
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Cornelia van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - P Eline Slagboom
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Mika Ala-Korpela
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Johannes Kettunen
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
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Townsend EC, Cheong JZA, Radzietza M, Fritz B, Malone M, Bjarnsholt T, Ousey K, Swanson T, Schultz G, Gibson ALF, Kalan LR. What is slough? Defining the proteomic and microbial composition of slough and its implications for wound healing. Wound Repair Regen 2024:10.1111/wrr.13170. [PMID: 38558438 PMCID: PMC11442687 DOI: 10.1111/wrr.13170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/06/2024] [Accepted: 02/19/2024] [Indexed: 04/04/2024]
Abstract
Slough is a well-known feature of non-healing wounds. This pilot study aims to determine the proteomic and microbiologic components of slough as well as interrogate the associations between wound slough components and wound healing. Ten subjects with slow-to-heal wounds and visible slough were enrolled. Aetiologies included venous stasis ulcers, post-surgical site infections and pressure ulcers. Patient co-morbidities and wound healing outcome at 3-months post-sample collection was recorded. Debrided slough was analysed microscopically, through untargeted proteomics, and high-throughput bacterial 16S-ribosomal gene sequencing. Microscopic imaging revealed wound slough to be amorphous in structure and highly variable. 16S-profiling found slough microbial communities to associate with wound aetiology and location on the body. Across all subjects, slough largely consisted of proteins involved in skin structure and formation, blood-clot formation and immune processes. To predict variables associated with wound healing, protein, microbial and clinical datasets were integrated into a supervised discriminant analysis. This analysis revealed that healing wounds were enriched for proteins involved in skin barrier development and negative regulation of immune responses. While wounds that deteriorated over time started off with a higher baseline Bates-Jensen Wound Assessment Score and were enriched for anaerobic bacterial taxa and chronic inflammatory proteins. To our knowledge, this is the first study to integrate clinical, microbiome, and proteomic data to systematically characterise wound slough and integrate it into a single assessment to predict wound healing outcome. Collectively, our findings underscore how slough components can help identify wounds at risk of continued impaired healing and serves as an underutilised biomarker.
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Affiliation(s)
- Elizabeth C Townsend
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - J Z Alex Cheong
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael Radzietza
- Infectious Diseases and Microbiology, Western Sydney University, Sydney, Australia
| | - Blaine Fritz
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Matthew Malone
- Infectious Diseases and Microbiology, Western Sydney University, Sydney, Australia
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital, Copenhagen, Denmark
- International Wound Infection Institute, London, UK
| | - Karen Ousey
- International Wound Infection Institute, London, UK
- Institute of Skin Integrity and Infection Prevention, University of Huddersfield, West Yorkshire, UK
| | | | - Gregory Schultz
- International Wound Infection Institute, London, UK
- Department of Obstetrics and Gynecology, University of Florida, Gainesville, Florida, USA
| | - Angela L F Gibson
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Lindsay R Kalan
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- International Wound Infection Institute, London, UK
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
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56
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Navrazhina K, Renert-Yuval Y, Khattri S, Hamade H, Meariman M, Andrews E, Kim M, NandyMazumdar M, Gour DS, Bose S, Williams SC, Garcet S, Correa da Rosa J, Gottlieb AB, Krueger JG, Guttman-Yassky E. Tape strips detect molecular alterations and cutaneous biomarkers in skin of patients with hidradenitis suppurativa. J Am Acad Dermatol 2024; 90:749-758. [PMID: 38049071 PMCID: PMC11238548 DOI: 10.1016/j.jaad.2023.11.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Hidradenitis suppurativa (HS) has a high unmet need for better treatments. Biopsies are considered the gold standard for studying molecular alterations in skin. A reproducible, minimally invasive approach is needed for longitudinal monitoring in trials and in pediatric populations. OBJECTIVE To determine whether skin tape strips can detect molecular alterations in HS and identify biomarkers of disease activity. METHODS We performed RNA sequencing on tape strips collected from lesional and healthy-appearing (nonlesional) HS skin (n = 22) and healthy controls (n = 21). We correlated the expression of skin biomarkers between tape strips and a previously published gene-signature of HS biopsies. RESULTS Tape strips detected upregulation of known HS biomarkers (eg, Interleukin[IL]-17A) in nonlesional and/or lesional skin and also identified novel clinically actionable targets, including OX40 and JAK3. The expression of Th17 and tumor necrosis factor-α pathways were highly correlated between tape strips and biopsies. HS clinical severity was significantly associated with expression of biomarkers (eg tumor necrosis factor-α , IL-17 A/F, OX40, JAK1-3, IL-4R) in HS lesional and/or nonlesional skin. LIMITATIONS Sample size. Tape stripping is limited in depth. CONCLUSION This study validates tape strips as a minimally-invasive approach to identify cutaneous biomarkers in HS. This provides a novel avenue for monitoring treatment efficacy and a potential step toward individualized therapy in HS.
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Affiliation(s)
- Kristina Navrazhina
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York; Laboratory for Investigative Dermatology, Rockefeller University, New York, New York
| | - Yael Renert-Yuval
- Laboratory for Investigative Dermatology, Rockefeller University, New York, New York; Pediatric Dermatology Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saakshi Khattri
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hassan Hamade
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marguerite Meariman
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elizabeth Andrews
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Madeline Kim
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Monali NandyMazumdar
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Digpal S Gour
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Swaroop Bose
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Samuel C Williams
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sandra Garcet
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Joel Correa da Rosa
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alice B Gottlieb
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - James G Krueger
- Laboratory for Investigative Dermatology, Rockefeller University, New York, New York
| | - Emma Guttman-Yassky
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York.
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57
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Koehn LM, Steele JR, Schittenhelm RB, Turner BJ, Nicolazzo JA. Sex-Dependent Changes to the Intestinal and Hepatic Abundance of Drug Transporters and Metabolizing Enzymes in the SOD1 G93A Mouse Model of Amyotrophic Lateral Sclerosis. Mol Pharm 2024; 21:1756-1767. [PMID: 38415587 DOI: 10.1021/acs.molpharmaceut.3c01089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by death and dysfunction of motor neurons that result in a rapidly progressing loss of motor function. While there are some data on alterations at the blood-brain barrier (BBB) in ALS and their potential impact on CNS trafficking of drugs, little is reported on the impact of this disease on the expression of drug-handling proteins in the small intestine and liver. This may impact the dosing of the many medicines that individuals with ALS are prescribed. In the present study, a proteomic evaluation was performed on small intestine and liver samples from postnatal day 120 SOD1G93A mice (a model of familial ALS that harbors a human mutant form of superoxide dismutase 1) and wild-type (WT) littermates (n = 7/genotype/sex). Untargeted, quantitative proteomics was undertaken using either label-based [tandem mass tag (TMT)] or label-free [data-independent acquisition (DIA)] acquisition strategies on high-resolution mass spectrometric instrumentation. Copper chaperone for superoxide dismutase (CCS) was significantly higher in SOD1G93A samples compared to the WT samples for both sexes and tissues, therefore representing a potential biomarker for ALS in this mouse model. Relative to WT mice, male SOD1G93A mice had significantly different proteins (Padj < 0.05, |fold-change|>1.2) in the small intestine (male 22, female 1) and liver (male 140, female 3). This included an up-regulation of intestinal transporters for dietary glucose [solute carrier (SLC) SLC5A1] and cholesterol (Niemann-Pick c1-like 1), as well as for several drugs (e.g., SLC15A1), in the male SOD1G93A mice. There was both an up-regulation (e.g., SLCO2A1) and down-regulation (ammonium transporter rh type b) of transporters in the male SOD1G93A liver. In addition, there was both an up-regulation (e.g., phosphoenolpyruvate carboxykinase) and down-regulation (e.g., carboxylesterase 1) of metabolizing enzymes in the male SOD1G93A liver. This proteomic data set identified male-specific changes to key small intestinal and hepatic transporters and metabolizing enzymes that may have important implications for the bioavailability of nutrients and drugs in individuals with ALS.
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Affiliation(s)
- Liam M Koehn
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Joel R Steele
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Bradley J Turner
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, Victoria, Australia
| | - Joseph A Nicolazzo
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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Bradamante G, Nguyen VH, Incarbone M, Meir Z, Bente H, Donà M, Lettner N, Scheid OM, Gutzat R. Two ARGONAUTE proteins loaded with transposon-derived small RNAs are associated with the reproductive cell lineage in Arabidopsis. THE PLANT CELL 2024; 36:863-880. [PMID: 38060984 PMCID: PMC10980394 DOI: 10.1093/plcell/koad295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 11/23/2023] [Indexed: 04/01/2024]
Abstract
In sexually propagating organisms, genetic, and epigenetic mutations are evolutionarily relevant only if they occur in the germline and are hence transmitted to the next generation. In contrast to most animals, plants are considered to lack an early segregating germline, implying that somatic cells can contribute genetic information to progeny. Here we demonstrate that 2 ARGONAUTE proteins, AGO5 and AGO9, mark cells associated with sexual reproduction in Arabidopsis (Arabidopsis thaliana) throughout development. Both AGOs are loaded with dynamically changing small RNA populations derived from highly methylated, pericentromeric, long transposons. Sequencing of single stem cell nuclei revealed that many of these transposons are co-expressed within an AGO5/9 expression domain in the shoot apical meristem (SAM). Co-occurrence of transposon expression and specific ARGONAUTE (AGO) expression in the SAM is reminiscent of germline features in animals and supports the existence of an early segregating germline in plants. Our results open the path to investigating transposon biology and epigenome dynamics at cellular resolution in the SAM stem cell niche.
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Affiliation(s)
- Gabriele Bradamante
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Vu Hoang Nguyen
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Marco Incarbone
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Zohar Meir
- Faculty of Mathematics and Computer Science & Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Heinrich Bente
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Mattia Donà
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Nicole Lettner
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Ruben Gutzat
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
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Sams MP, Iansavitchous J, Astridge M, Rysan H, Xu LS, Rodrigues de Oliveira B, DeKoter RP. N-Acetylcysteine Alters Disease Progression and Increases Janus Kinase Mutation Frequency in a Mouse Model of Precursor B-Cell Acute Lymphoblastic Leukemia. J Pharmacol Exp Ther 2024; 389:40-50. [PMID: 38336380 DOI: 10.1124/jpet.123.002000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
B-cell acute lymphoblastic leukemia (B-ALL) is the most prevalent type of cancer in young children and is associated with high levels of reactive oxygen species (ROS). The antioxidant N-acetylcysteine (NAC) was tested for its ability to alter disease progression in a mouse model of B-ALL. Mb1-CreΔPB mice have deletions in genes encoding PU.1 and Spi-B in B cells and develop B-ALL at 100% incidence. Treatment of Mb1-CreΔPB mice with NAC in drinking water significantly reduced the frequency of CD19+ pre-B-ALL cells infiltrating the thymus at 11 weeks of age. However, treatment with NAC did not reduce leukemia progression or increase survival by a median 16 weeks of age. NAC significantly altered gene expression in leukemias in treated mice. Mice treated with NAC had increased frequencies of activating mutations in genes encoding Janus kinases 1 and 3. In particular, frequencies of Jak3 R653H mutations were increased in mice treated with NAC compared with control drinking water. NAC opposed oxidization of PTEN protein ROS in cultured leukemia cells. These results show that NAC alters leukemia progression in this mouse model, ultimately selecting for leukemias with high Jak3 R653H mutation frequencies. SIGNIFICANCE STATEMENT: In a mouse model of precursor B-cell acute lymphoblastic leukemia associated with high levels of reactive oxygen species, treatment with N-acetylcysteine did not delay disease progression but instead selected for leukemic clones with activating R653H mutations in Janus kinase 3.
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Affiliation(s)
- Mia P Sams
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
| | - James Iansavitchous
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
| | - Madeline Astridge
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
| | - Heidi Rysan
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
| | - Li S Xu
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
| | - Bruno Rodrigues de Oliveira
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
| | - Rodney P DeKoter
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
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Mathies LD, Kim AC, Soukup EM, Thomas AE, Bettinger JC. PBRM-1/PBAF-regulated genes in a multipotent progenitor in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2024; 14:jkad297. [PMID: 38150396 PMCID: PMC10917506 DOI: 10.1093/g3journal/jkad297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
The Caenorhabditis elegans somatic gonadal precursors (SGPs) are multipotent progenitors that generate all somatic cells of the adult reproductive system. The 2 SGPs originate in the mesodermal layer and are born through a division that produces one SGP and one head mesodermal cell (hmc). One hmc terminally differentiates, and the other dies by programmed cell death. The polybromo-associated BAF (PBAF) chromatin remodeling complex promotes the multipotent SGP fate. The complete loss of PBAF causes lethality, so we used a combination of Cre/lox recombination and GFP nanobody-directed protein degradation to eliminate PBRM-1, the signature subunit of the PBAF complex, from 83 mesodermal cells, including SGPs, body muscles, and the hmc. We used RNA sequencing to identify genes acting downstream of PBAF in these cells and identified 1,955 transcripts that were significantly differentially expressed between pbrm-1(-) and pbrm-1(+) in the mesoderm of L1 larvae. We found that genes involved in muscle cell function were overrepresented; most of these genes had lower expression in the absence of PBRM-1, suggesting that PBAF promotes muscle differentiation. Among the differentially expressed genes were 125 that are normally expressed at higher levels in SGP vs hmc and positively regulated by pbrm-1 and 53 that are normally expressed at higher levels in hmc vs SGP and are negatively regulated by pbrm-1; these are candidate regulators of the SGP/hmc fate decision. We validated one candidate gene using a fluorescent reporter; the hsp-12.3 reporter was derepressed in SGPs in pbrm-1 mutants, suggesting that hsp-12.3 expression is normally repressed by pbrm-1 in SGPs.
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Affiliation(s)
- Laura D Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Andrew C Kim
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Evan M Soukup
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Alan’da E Thomas
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
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Huang S, Rao Y, Ju AL, Ker DFE, Blocki AM, Wang DM, Tuan RS. Non-collagenous proteins, rather than the collagens, are key biochemical factors that mediate tenogenic bioactivity of tendon extracellular matrix. Acta Biomater 2024; 176:99-115. [PMID: 38142795 DOI: 10.1016/j.actbio.2023.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Despite the growing clinical use of extracellular matrix (ECM)-based biomaterials for tendon repair, undesired healing outcomes or complications have frequently been reported. A major scientific challenge has been the limited understanding of their functional compositions and mechanisms of action due to the complex nature of tendon ECM. Previously, we have reported a soluble ECM fraction from bovine tendons (tECM) by urea extraction, which exhibited strong, pro-tenogenic bioactivity on human adipose-derived stem cells (hASCs). In this study, to advance our previous findings and gain insights into the biochemical nature of its pro-tenogenesis activity, tECM was fractionated using (i) an enzymatic digestion approach (pepsin, hyaluronidase, and chondroitinase) to yield various enzyme-digested tECM fractions; and (ii) a gelation-based approach to yield collagen matrix-enriched (CM) and non-collagenous matrix-enriched (NCM) fractions. Their tenogenic bioactivity on hASCs was assessed. Our results collectively indicated that non-collagenous tECM proteins, rather than collagens, are likely the important biochemical factors responsible for tECM pro-tenogenesis bioactivity. Mechanistically, RNA-seq analysis revealed that tECM and its non-collagenous portion induced similar transcriptional profiles of hASCs, particularly genes associated with cell proliferation, collagen synthesis, and tenogenic differentiation, which were distinct from transcriptome induced by its collagenous portion. From an application perspective, the enhanced solubility of the non-collagenous tECM, compared to tECM, should facilitate its combination with various water-soluble biomaterials for tissue engineering protocols. Our work provides insight into the molecular characterization of native tendon ECM, which will help to effectively translate their functional components into the design of well-defined, ECM biomaterials for tendon regeneration. STATEMENT OF SIGNIFICANCE: Significant progress has been made in extracellular matrix (ECM)-based biomaterials for tendon repair. However, their effectiveness remains debated, with conflicting research and clinical findings. Understanding the functional composition and mechanisms of action of ECM is crucial for developing safe and effective bioengineered scaffolds. Expanding on our previous work with bovine tendon ECM extracts (tECM) exhibiting strong pro-tenogenesis activity, we fractionated tECM to evaluate its bioactive moieties. Our findings indicate that the non-collagenous matrix within tECM, rather than the collagenous portions, plays a major role in the pro-tenogenesis bioactivity on human adipose-derived stem cells. These insights will drive further optimization of ECM-based biomaterials, including our advanced method for preparing highly soluble, non-collagenous matrix-enriched tendon ECM for effective tendon repair.
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Affiliation(s)
- Shuting Huang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China; Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Center for Neuromusculoskeletal Restorative Medicine, Science Park, Hong Kong SAR, China.
| | - Ying Rao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China; Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Adler Leigh Ju
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China; Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Dai Fei Elmer Ker
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China; Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Ministry of Education Key Laboratory for Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Center for Neuromusculoskeletal Restorative Medicine, Science Park, Hong Kong SAR, China
| | - Anna M Blocki
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China; Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Center for Neuromusculoskeletal Restorative Medicine, Science Park, Hong Kong SAR, China
| | - Dan Michelle Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China; Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Ministry of Education Key Laboratory for Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Center for Neuromusculoskeletal Restorative Medicine, Science Park, Hong Kong SAR, China.
| | - Rocky S Tuan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China; Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Center for Neuromusculoskeletal Restorative Medicine, Science Park, Hong Kong SAR, China.
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Andreyev AY, Yang H, Doulias P, Dolatabadi N, Zhang X, Luevanos M, Blanco M, Baal C, Putra I, Nakamura T, Ischiropoulos H, Tannenbaum SR, Lipton SA. Metabolic Bypass Rescues Aberrant S-nitrosylation-Induced TCA Cycle Inhibition and Synapse Loss in Alzheimer's Disease Human Neurons. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306469. [PMID: 38235614 PMCID: PMC10966553 DOI: 10.1002/advs.202306469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/29/2023] [Indexed: 01/19/2024]
Abstract
In Alzheimer's disease (AD), dysfunctional mitochondrial metabolism is associated with synaptic loss, the major pathological correlate of cognitive decline. Mechanistic insight for this relationship, however, is still lacking. Here, comparing isogenic wild-type and AD mutant human induced pluripotent stem cell (hiPSC)-derived cerebrocortical neurons (hiN), evidence is found for compromised mitochondrial energy in AD using the Seahorse platform to analyze glycolysis and oxidative phosphorylation (OXPHOS). Isotope-labeled metabolic flux experiments revealed a major block in activity in the tricarboxylic acid (TCA) cycle at the α-ketoglutarate dehydrogenase (αKGDH)/succinyl coenzyme-A synthetase step, metabolizing α-ketoglutarate to succinate. Associated with this block, aberrant protein S-nitrosylation of αKGDH subunits inhibited their enzyme function. This aberrant S-nitrosylation is documented not only in AD-hiN but also in postmortem human AD brains versus controls, as assessed by two separate unbiased mass spectrometry platforms using both SNOTRAP identification of S-nitrosothiols and chemoselective-enrichment of S-nitrosoproteins. Treatment with dimethyl succinate, a cell-permeable derivative of a TCA substrate downstream to the block, resulted in partial rescue of mitochondrial bioenergetic function as well as reversal of synapse loss in AD-hiN. These findings have therapeutic implications that rescue of mitochondrial energy metabolism can ameliorate synaptic loss in hiPSC-based models of AD.
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Affiliation(s)
- Alexander Y. Andreyev
- Department of Molecular Medicine and Neurodegeneration New Medicines CenterThe Scripps Research InstituteLa JollaCA92037USA
| | - Hongmei Yang
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMA02139USA
- Northeast Asia Institute of Chinese MedicineChangchun University of Chinese MedicineChangchun130021China
- Present address:
The Public Experiment CenterChangchun University of Chinese MedicineChangchun130117China
| | - Paschalis‐Thomas Doulias
- Children's Hospital of Philadelphia Research Institute and Departments of Pediatrics and PharmacologyRaymond and Ruth Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaPA19104USA
- Department of Chemistry and Institute of BiosciencesUniversity Research Center of IoanninaUniversity of IoanninaIoannina45110Greece
| | - Nima Dolatabadi
- Department of Molecular Medicine and Neurodegeneration New Medicines CenterThe Scripps Research InstituteLa JollaCA92037USA
| | - Xu Zhang
- Department of Molecular Medicine and Neurodegeneration New Medicines CenterThe Scripps Research InstituteLa JollaCA92037USA
| | - Melissa Luevanos
- Department of Molecular Medicine and Neurodegeneration New Medicines CenterThe Scripps Research InstituteLa JollaCA92037USA
| | - Mayra Blanco
- Department of Molecular Medicine and Neurodegeneration New Medicines CenterThe Scripps Research InstituteLa JollaCA92037USA
| | - Christine Baal
- Department of Molecular Medicine and Neurodegeneration New Medicines CenterThe Scripps Research InstituteLa JollaCA92037USA
| | - Ivan Putra
- Department of Molecular Medicine and Neurodegeneration New Medicines CenterThe Scripps Research InstituteLa JollaCA92037USA
| | - Tomohiro Nakamura
- Department of Molecular Medicine and Neurodegeneration New Medicines CenterThe Scripps Research InstituteLa JollaCA92037USA
| | - Harry Ischiropoulos
- Children's Hospital of Philadelphia Research Institute and Departments of Pediatrics and PharmacologyRaymond and Ruth Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaPA19104USA
| | - Steven R. Tannenbaum
- Northeast Asia Institute of Chinese MedicineChangchun University of Chinese MedicineChangchun130021China
| | - Stuart A. Lipton
- Department of Molecular Medicine and Neurodegeneration New Medicines CenterThe Scripps Research InstituteLa JollaCA92037USA
- Department of NeurosciencesSchool of MedicineUniversity of California at San DiegoLa JollaCA92093USA
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Álvarez-Rodríguez M, Martinez-Serrano CA, Gardela J, Nieto H, de Mercado E, Rodríguez-Martínez H. MicroRNA expression in specific segments of the pig periovulatory internal genital tract is differentially regulated by semen or by seminal plasma. Res Vet Sci 2024; 168:105134. [PMID: 38194892 DOI: 10.1016/j.rvsc.2023.105134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/30/2023] [Accepted: 12/30/2023] [Indexed: 01/11/2024]
Abstract
microRNAs play pivotal roles during mammalian reproduction, including the cross-talk between gametes, embryos and the maternal genital tract. Mating induces changes in the expression of mRNA transcripts in the female, but whether miRNAs are involved remains to be elucidated. In the current study, we mapped 181 miRNAs in the porcine peri-ovulatory female reproductive tract: Cervix (Cvx), distal and proximal uterus (Dist-Ut, Prox-Ut), Utero-tubal-junction (UTJ), isthmus (Isth), ampulla (Amp), and infundibulum (Inf) when exposed to semen (natural mating (NM) or artificial insemination (AI-P1)) or to infusions of sperm-free seminal plasma (SP): the first 10 mL of the sperm rich fraction (SP-P1) or the entire ejaculate (SP-E). Among the most interesting findings, NM decreased mir-671, implicated in uterine development and pregnancy loss prior to embryo implantation, in Cvx, Dist-UT, Prox-UT, Isth, and Inf, while it increased in Amp. NM and SP-E induced the downregulation of miR-let7A-1 (Dist-UT, Prox-UT), a regulator of immunity during pregnancy. miR-34C-1, a regulator of endometrial receptivity gene expression, was increased in Dist-UT, UTJ and Amp (NM), in Prox-UT (AI-P1), and in Amp (SP-P1). miR-296, a modulator of the inflammatory response and apoptosis, was upregulated in the UTJ (all treatments). NM elicited the highest miRNA activity in the sperm reservoir (UTJ), suggesting that key-regulators such as miR-34c or miR-296 may modulate the metabolic processes linked to the adequate preparation for gamete encounter in the oviduct. Our results suggest that SP should be maintained in AI to warrant miRNA regulation within the female genital tract for reproductive success.
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Affiliation(s)
- Manuel Álvarez-Rodríguez
- Department of Animal Reproduction, Spanish National Institute for Agricultural and Food Research and Technology (INIA-CSIC), 28040 Madrid, Spain; Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynecology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Cristina A Martinez-Serrano
- Department of Animal Reproduction, Spanish National Institute for Agricultural and Food Research and Technology (INIA-CSIC), 28040 Madrid, Spain; Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynecology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Jaume Gardela
- Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynecology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain; Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain
| | - Helena Nieto
- Department of Animal Reproduction, Spanish National Institute for Agricultural and Food Research and Technology (INIA-CSIC), 28040 Madrid, Spain
| | - Eduardo de Mercado
- Department of Animal Reproduction, Spanish National Institute for Agricultural and Food Research and Technology (INIA-CSIC), 28040 Madrid, Spain
| | - Heriberto Rodríguez-Martínez
- Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynecology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden.
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Gonzalez Galofre ZN, Kilpatrick AM, Marques M, Sá da Bandeira D, Ventura T, Gomez Salazar M, Bouilleau L, Marc Y, Barbosa AB, Rossi F, Beltran M, van de Werken HJG, van IJcken WFJ, Henderson NC, Forbes SJ, Crisan M. Runx1+ vascular smooth muscle cells are essential for hematopoietic stem and progenitor cell development in vivo. Nat Commun 2024; 15:1653. [PMID: 38395882 PMCID: PMC10891074 DOI: 10.1038/s41467-024-44913-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 01/09/2024] [Indexed: 02/25/2024] Open
Abstract
Hematopoietic stem cells (HSCs) produce all essential cellular components of the blood. Stromal cell lines supporting HSCs follow a vascular smooth muscle cell (vSMC) differentiation pathway, suggesting that some hematopoiesis-supporting cells originate from vSMC precursors. These pericyte-like precursors were recently identified in the aorta-gonad-mesonephros (AGM) region; however, their role in the hematopoietic development in vivo remains unknown. Here, we identify a subpopulation of NG2+Runx1+ perivascular cells that display a sclerotome-derived vSMC transcriptomic profile. We show that deleting Runx1 in NG2+ cells impairs the hematopoietic development in vivo and causes transcriptional changes in pericytes/vSMCs, endothelial cells and hematopoietic cells in the murine AGM. Importantly, this deletion leads also to a significant reduction of HSC reconstitution potential in the bone marrow in vivo. This defect is developmental, as NG2+Runx1+ cells were not detected in the adult bone marrow, demonstrating the existence of a specialised pericyte population in the HSC-generating niche, unique to the embryo.
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Affiliation(s)
- Zaniah N Gonzalez Galofre
- Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Alastair M Kilpatrick
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Madalena Marques
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Diana Sá da Bandeira
- Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Telma Ventura
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Mario Gomez Salazar
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Léa Bouilleau
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Yvan Marc
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Ana B Barbosa
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Fiona Rossi
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Mariana Beltran
- Centre for Inflammation Research/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, 3000 CA, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, 3000 CA, Rotterdam, The Netherlands
- Department of Immunology, Erasmus MC Cancer Institute, University Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Center for Biomics, Department of Cell Biology, Erasmus MC University Medical Centre, 3015 GE, Rotterdam, The Netherlands
| | - Neil C Henderson
- Centre for Inflammation Research/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Stuart J Forbes
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Mihaela Crisan
- Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK.
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK.
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65
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Hornstein ED, Charles M, Franklin M, Edwards B, Vintila S, Kleiner M, Sederoff H. IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss. PLANT MOLECULAR BIOLOGY 2024; 114:21. [PMID: 38368585 PMCID: PMC10874911 DOI: 10.1007/s11103-024-01422-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/20/2024] [Indexed: 02/19/2024]
Abstract
Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana. To explore if elements of this apparently beneficial trait are still present and could be reactivated we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis, and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state, which partially mimics AMF exposure in non-inoculated plants. Our results indicate that molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.
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Affiliation(s)
- Eli D Hornstein
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Melodi Charles
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Megan Franklin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Brianne Edwards
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Heike Sederoff
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
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Lukomska A, Theune WC, Frost MP, Xing J, Kearney A, Trakhtenberg EF. Upregulation of developmentally-downregulated miR-1247-5p promotes neuroprotection and axon regeneration in vivo. Neurosci Lett 2024; 823:137662. [PMID: 38286398 PMCID: PMC10923146 DOI: 10.1016/j.neulet.2024.137662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
Numerous micro-RNAs (miRNAs) affect neurodevelopment and neuroprotection, but potential roles of many miRNAs in regulating these processes are still unknown. Here, we used the retinal ganglion cell (RGC) central nervous system (CNS) projection neuron and optic nerve crush (ONC) injury model, to optimize a mature miRNA arm-specific quantification method for characterizing the developmental regulation of miR-1247-5p in RGCs, investigated whether injury affects its expression, and tested whether upregulating miR-1247-5p-mimic in RGCs promotes neuroprotection and axon regeneration. We found that, miR-1247-5p is developmentally-downregulated in RGCs, and is further downregulated after ONC. Importantly, RGC-specific upregulation of miR-1247-5p promoted neuroprotection and axon regeneration after injury in vivo. To gain insight into the underlying mechanisms, we analyzed by bulk-mRNA-seq embryonic and adult RGCs, along with adult RGCs transduced by miR-1247-5p-expressing viral vector, and identified developmentally-regulated cilial and mitochondrial biological processes, which were reinstated to their embryonic levels in adult RGCs by upregulation of miR-1247-5p. Since axon growth is also a developmentally-regulated process, in which mitochondrial dynamics play important roles, it is possible that miR-1247-5p promoted neuroprotection and axon regeneration through regulating mitochondrial functions.
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Affiliation(s)
- Agnieszka Lukomska
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - William C Theune
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Matthew P Frost
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Jian Xing
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Anja Kearney
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Ephraim F Trakhtenberg
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA.
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Öling S, Struck E, Noreen-Thorsen M, Zwahlen M, von Feilitzen K, Odeberg J, Pontén F, Lindskog C, Uhlén M, Dusart P, Butler LM. A human stomach cell type transcriptome atlas. BMC Biol 2024; 22:36. [PMID: 38355543 PMCID: PMC10865703 DOI: 10.1186/s12915-024-01812-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND The identification of cell type-specific genes and their modification under different conditions is central to our understanding of human health and disease. The stomach, a hollow organ in the upper gastrointestinal tract, provides an acidic environment that contributes to microbial defence and facilitates the activity of secreted digestive enzymes to process food and nutrients into chyme. In contrast to other sections of the gastrointestinal tract, detailed descriptions of cell type gene enrichment profiles in the stomach are absent from the major single-cell sequencing-based atlases. RESULTS Here, we use an integrative correlation analysis method to predict human stomach cell type transcriptome signatures using unfractionated stomach RNAseq data from 359 individuals. We profile parietal, chief, gastric mucous, gastric enteroendocrine, mitotic, endothelial, fibroblast, macrophage, neutrophil, T-cell, and plasma cells, identifying over 1600 cell type-enriched genes. CONCLUSIONS We uncover the cell type expression profile of several non-coding genes strongly associated with the progression of gastric cancer and, using a sex-based subset analysis, uncover a panel of male-only chief cell-enriched genes. This study provides a roadmap to further understand human stomach biology.
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Affiliation(s)
- S Öling
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
| | - E Struck
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
| | - M Noreen-Thorsen
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
| | - M Zwahlen
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
| | - K von Feilitzen
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
| | - J Odeberg
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
- The University Hospital of North Norway (UNN), 9019, Tromsø, Norway
- Department of Haematology, Coagulation Unit, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - F Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 752 37, Uppsala, Sweden
| | - C Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 752 37, Uppsala, Sweden
| | - M Uhlén
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
| | - P Dusart
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
- Clinical Chemistry and Blood Coagulation Research, Department of Molecular Medicine and Surgery, Karolinska Institute, 171 76, Stockholm, Sweden
- Clinical Chemistry, Karolinska University Laboratory, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - L M Butler
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway.
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden.
- Clinical Chemistry and Blood Coagulation Research, Department of Molecular Medicine and Surgery, Karolinska Institute, 171 76, Stockholm, Sweden.
- Clinical Chemistry, Karolinska University Laboratory, Karolinska University Hospital, 171 76, Stockholm, Sweden.
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Esteban-Medina M, Loucera C, Rian K, Velasco S, Olivares-González L, Rodrigo R, Dopazo J, Peña-Chilet M. The mechanistic functional landscape of retinitis pigmentosa: a machine learning-driven approach to therapeutic target discovery. J Transl Med 2024; 22:139. [PMID: 38321543 PMCID: PMC10848380 DOI: 10.1186/s12967-024-04911-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/20/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Retinitis pigmentosa is the prevailing genetic cause of blindness in developed nations with no effective treatments. In the pursuit of unraveling the intricate dynamics underlying this complex disease, mechanistic models emerge as a tool of proven efficiency rooted in systems biology, to elucidate the interplay between RP genes and their mechanisms. The integration of mechanistic models and drug-target interactions under the umbrella of machine learning methodologies provides a multifaceted approach that can boost the discovery of novel therapeutic targets, facilitating further drug repurposing in RP. METHODS By mapping Retinitis Pigmentosa-related genes (obtained from Orphanet, OMIM and HPO databases) onto KEGG signaling pathways, a collection of signaling functional circuits encompassing Retinitis Pigmentosa molecular mechanisms was defined. Next, a mechanistic model of the so-defined disease map, where the effects of interventions can be simulated, was built. Then, an explainable multi-output random forest regressor was trained using normal tissue transcriptomic data to learn causal connections between targets of approved drugs from DrugBank and the functional circuits of the mechanistic disease map. Selected target genes involvement were validated on rd10 mice, a murine model of Retinitis Pigmentosa. RESULTS A mechanistic functional map of Retinitis Pigmentosa was constructed resulting in 226 functional circuits belonging to 40 KEGG signaling pathways. The method predicted 109 targets of approved drugs in use with a potential effect over circuits corresponding to nine hallmarks identified. Five of those targets were selected and experimentally validated in rd10 mice: Gabre, Gabra1 (GABARα1 protein), Slc12a5 (KCC2 protein), Grin1 (NR1 protein) and Glr2a. As a result, we provide a resource to evaluate the potential impact of drug target genes in Retinitis Pigmentosa. CONCLUSIONS The possibility of building actionable disease models in combination with machine learning algorithms to learn causal drug-disease interactions opens new avenues for boosting drug discovery. Such mechanistically-based hypotheses can guide and accelerate the experimental validations prioritizing drug target candidates. In this work, a mechanistic model describing the functional disease map of Retinitis Pigmentosa was developed, identifying five promising therapeutic candidates targeted by approved drug. Further experimental validation will demonstrate the efficiency of this approach for a systematic application to other rare diseases.
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Affiliation(s)
- Marina Esteban-Medina
- Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Systems and Computational Medicine Group, Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain
| | - Carlos Loucera
- Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Systems and Computational Medicine Group, Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain
| | - Kinza Rian
- Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Systems and Computational Medicine Group, Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain
| | - Sheyla Velasco
- Group of Pathophysiology and Therapies for Vision Disorders, Príncipe Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Lorena Olivares-González
- Group of Pathophysiology and Therapies for Vision Disorders, Príncipe Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Regina Rodrigo
- Group of Pathophysiology and Therapies for Vision Disorders, Príncipe Felipe Research Center (CIPF), 46012, Valencia, Spain
- Biomedical Research Networking Center in Rare Diseases (CIBERER), Health Institute Carlos III, 28029, Madrid, Spain
- Department of Physiology, University of Valencia (UV), 46100, Burjassot, Spain
- Department of Anatomy and Physiology, Catholic University of Valencia San Vicente Mártir, 46001, Valencia, Spain
- Joint Research Unit on Endocrinology, Nutrition and Clinical Dietetics UV-IIS La Fe, 46026, Valencia, Spain
| | - Joaquin Dopazo
- Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain.
- Systems and Computational Medicine Group, Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain.
- Biomedical Research Networking Center in Rare Diseases (CIBERER), Health Institute Carlos III, 28029, Madrid, Spain.
| | - Maria Peña-Chilet
- Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain.
- Systems and Computational Medicine Group, Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain.
- Biomedical Research Networking Center in Rare Diseases (CIBERER), Health Institute Carlos III, 28029, Madrid, Spain.
- BigData, AI, Biostatistics & Bioinformatics Platform, Health Research Institute La Fe (IISLaFe), 46026, Valencia, Spain.
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VanBuren R, Nguyen A, Marks RA, Mercado C, Pardo A, Pardo J, Schuster J, Aubin BS, Wilson ML, Rhee SY. Variability in drought gene expression datasets highlight the need for community standardization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578814. [PMID: 38370805 PMCID: PMC10871248 DOI: 10.1101/2024.02.04.578814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Physiologically relevant drought stress is difficult to apply consistently, and the heterogeneity in experimental design, growth conditions, and sampling schemes make it challenging to compare water deficit studies in plants. Here, we re-analyzed hundreds of drought gene expression experiments across diverse model and crop species and quantified the variability across studies. We found that drought studies are surprisingly uncomparable, even when accounting for differences in genotype, environment, drought severity, and method of drying. Many studies, including most Arabidopsis work, lack high-quality phenotypic and physiological datasets to accompany gene expression, making it impossible to assess the severity or in some cases the occurrence of water deficit stress events. From these datasets, we developed supervised learning classifiers that can accurately predict if RNA-seq samples have experienced a physiologically relevant drought stress, and suggest this can be used as a quality control for future studies. Together, our analyses highlight the need for more community standardization, and the importance of paired physiology data to quantify stress severity for reproducibility and future data analyses.
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Wayhelova M, Vallova V, Broz P, Mikulasova A, Smetana J, Dynkova Filkova H, Machackova D, Handzusova K, Gaillyova R, Kuglik P. Exome sequencing improves the molecular diagnostics of paediatric unexplained neurodevelopmental disorders. Orphanet J Rare Dis 2024; 19:41. [PMID: 38321498 PMCID: PMC10845791 DOI: 10.1186/s13023-024-03056-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) and/or associated multiple congenital abnormalities (MCAs) represent a genetically heterogeneous group of conditions with an adverse prognosis for the quality of intellectual and social abilities and common daily functioning. The rapid development of exome sequencing (ES) techniques, together with trio-based analysis, nowadays leads to up to 50% diagnostic yield. Therefore, it is considered as the state-of-the-art approach in these diagnoses. RESULTS In our study, we present the results of ES in a cohort of 85 families with 90 children with severe NDDs and MCAs. The interconnection of the in-house bioinformatic pipeline and a unique algorithm for variant prioritization resulted in a diagnostic yield of up to 48.9% (44/90), including rare and novel causative variants (41/90) and intragenic copy-number variations (CNVs) (3/90). Of the total number of 47 causative variants, 53.2% (25/47) were novel, highlighting the clinical benefit of ES for unexplained NDDs. Moreover, trio-based ES was verified as a reliable tool for the detection of rare CNVs, ranging from intragenic exon deletions (GRIN2A, ZC4H2 genes) to a 6-Mb duplication. The functional analysis using PANTHER Gene Ontology confirmed the involvement of genes with causative variants in a wide spectrum of developmental processes and molecular pathways, which form essential structural and functional components of the central nervous system. CONCLUSION Taken together, we present one of the first ES studies of this scale from the central European region. Based on the high diagnostic yield for paediatric NDDs in this study, 48.9%, we confirm trio-based ES as an effective and reliable first-tier diagnostic test in the genetic evaluation of children with NDDs.
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Affiliation(s)
- Marketa Wayhelova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic.
| | - Vladimira Vallova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic
| | - Petr Broz
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University Prague and University Hospital Motol, Prague, Czech Republic
| | - Aneta Mikulasova
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Jan Smetana
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hana Dynkova Filkova
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic
| | - Dominika Machackova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristina Handzusova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Renata Gaillyova
- Department of Medical Genetics and Genomics, University Hospital Brno, Brno, Czech Republic
| | - Petr Kuglik
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic
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71
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Durkin SM, Ballinger MA, Nachman MW. Tissue-specific and cis-regulatory changes underlie parallel, adaptive gene expression evolution in house mice. PLoS Genet 2024; 20:e1010892. [PMID: 38306396 PMCID: PMC10866503 DOI: 10.1371/journal.pgen.1010892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/14/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Changes in gene regulation have long been appreciated as a driving force of adaptive evolution, however the relative contributions of cis- and trans-acting changes to gene regulation over short evolutionary timescales remain unclear. Instances of recent, parallel phenotypic evolution provide an opportunity to assess whether parallel patterns are seen at the level of gene expression, and to assess the relative contribution of cis- and trans- changes to gene regulation in the early stages of divergence. Here, we studied gene expression in liver and brown adipose tissue in two wild-derived strains of house mice that independently adapted to cold, northern environments, and we compared them to a strain of house mice from a warm, tropical environment. To investigate gene regulatory evolution, we studied expression in parents and allele-specific expression in F1 hybrids of crosses between warm-adapted and cold-adapted strains. First, we found that the different cold-adapted mice showed both unique and shared changes in expression, but that the proportion of shared changes (i.e. parallelism) was greater than expected by chance. Second, we discovered that expression evolution occurred largely at tissue-specific and cis-regulated genes, and that these genes were over-represented in parallel cases of evolution. Finally, we integrated the expression data with scans for selection in natural populations and found substantial parallelism in the two northern populations for genes under selection. Furthermore, selection outliers were associated with cis-regulated genes more than expected by chance; cis-regulated genes under selection influenced phenotypes such as body size, immune functioning, and activity level. These results demonstrate that parallel patterns of gene expression in mice that have independently adapted to cold environments are driven largely by tissue-specific and cis-regulatory changes, providing insight into the mechanisms of adaptive gene regulatory evolution at the earliest stages of divergence.
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Affiliation(s)
- Sylvia M. Durkin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Mallory A. Ballinger
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Michael W. Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
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Nascimento-Gonçalves E, Seixas F, Palmeira C, Martins G, Fonseca C, Duarte JA, Faustino-Rocha AI, Colaço B, Pires MJ, Neuparth MJ, Moreira-Gonçalves D, Fardilha M, Henriques MC, Patrício D, Pelech S, Ferreira R, Oliveira PA. Lifelong exercise training promotes the remodelling of the immune system and prostate signalome in a rat model of prostate carcinogenesis. GeroScience 2024; 46:817-840. [PMID: 37171559 PMCID: PMC10828357 DOI: 10.1007/s11357-023-00806-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
This work aimed to understand how lifelong exercise training promotes the remodelling of the immune system and prostate signalome in a rat model of PCa. Fifty-five male Wistar rats were divided into four groups: control sedentary, control exercised, induced PCa sedentary and induced PCa exercised. Exercised animals were trained in a treadmill for 53 weeks. Pca induction consisted on the sequential administration of flutamide, N-methyl-N-nitrosourea and testosterone propionate implants. Serum concentrations of C-reactive protein (CRP) and tumor necrosis factor (TNF)-like weak inducer of apoptosis (TWEAK) were not different among groups. Peripheral levels of γδ T cells were higher in Pca exercised group than in the PCa sedentary group (p < 0.05). Exercise training also induced Oestrogen Receptor (ESR1) upregulation and Mitogen-activated Protein Kinase 13 (MAPK13) downregulation, changed the content of the phosphorylated (at Ser-104) form of this receptor (coded by the gene ESR1) and seemed to increase Erα phosphorylation and activity in exercised PCa rats when compared with sedentary PCa rats. Our data highlight the exercise-induced remodelling of peripheral lymphocyte subpopulations and lymphocyte infiltration in prostate tissue. Moreover, exercise training promotes the remodelling prostate signalome in this rat model of prostate carcinogenesis.
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Affiliation(s)
- Elisabete Nascimento-Gonçalves
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, 5000-801, Vila Real, Portugal
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro (UA), 3810-193, Aveiro, Portugal
| | - Fernanda Seixas
- Animal and Veterinary Research Centre (CECAV), Associate Laboratory for Animal and Veterinary Science - AL4AnimalS, UTAD, 5000-801, Vila Real, Portugal
- Department of Veterinary Sciences, University of Trás-Os-Montes and Alto Douro, 5000-801, Vila Real, Portugal
| | - Carlos Palmeira
- Clinical Pathology Department, Portuguese Institute of Oncology of Porto, 4200-072, Porto, Portugal
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-072, Porto, Portugal
- School of Health Science Fernando Pessoa and FP-i3iD, 4200-253, Porto, Portugal
| | - Gabriela Martins
- Clinical Pathology Department, Portuguese Institute of Oncology of Porto, 4200-072, Porto, Portugal
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-072, Porto, Portugal
| | - Carolina Fonseca
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, 5000-801, Vila Real, Portugal
| | - José Alberto Duarte
- CIAFEL, Research Centre in Physical Activity, Health and Leisure, Faculty of Sport, University of Porto, 4200-450, Porto, Portugal
| | - Ana I Faustino-Rocha
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, 5000-801, Vila Real, Portugal
- Department of Zootechnics, School of Sciences and Technology, University of Évora, 7004-516, Évora, Portugal
- Comprehensive Health Research Centre, 7004-516, Évora, Portugal
| | - Bruno Colaço
- Animal and Veterinary Research Centre (CECAV), Associate Laboratory for Animal and Veterinary Science - AL4AnimalS, UTAD, 5000-801, Vila Real, Portugal
- Department of Zootechnics, University of Trás-Os-Montes and Alto Douro, 5000-801, Vila Real, Portugal
| | - Maria João Pires
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, 5000-801, Vila Real, Portugal
- Department of Veterinary Sciences, University of Trás-Os-Montes and Alto Douro, 5000-801, Vila Real, Portugal
| | - Maria João Neuparth
- Research Center in Physical Activity, Health and Leisure (CIAFEL)-Faculty of Sports-University of Porto (FADEUP), Portugal and Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
- TOXRUN - Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116, Gandra, Portugal
| | - Daniel Moreira-Gonçalves
- Research Center in Physical Activity, Health and Leisure (CIAFEL)-Faculty of Sports-University of Porto (FADEUP), Portugal and Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - Margarida Fardilha
- Department of Medical Sciences, iBiMED - Institute of Biomedicine, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Magda C Henriques
- Department of Medical Sciences, iBiMED - Institute of Biomedicine, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Daniela Patrício
- Department of Medical Sciences, iBiMED - Institute of Biomedicine, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Steven Pelech
- Department of Medicine, University of British Columbia, Vancouver, B.C, Canada
- Kinexus Bioinformatics Corporation, Suite 1 - 8755 Ash Street, Vancouver, BC, V6P 6T3, Canada
| | - Rita Ferreira
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Paula A Oliveira
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal.
- Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, 5000-801, Vila Real, Portugal.
- Department of Veterinary Sciences, University of Trás-Os-Montes and Alto Douro, 5000-801, Vila Real, Portugal.
- Clinical Academic Center of Trás-Os-Montes and Alto Douro, University of Trás-Os-Montes and Alto Douro, 5000-801, Vila Real, Portugal.
- University of Trás-os-Montes and Alto Douro, Quinta dos Prados, 5001-801, Vila Real, Portugal.
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73
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Kim EJ, Jeon D, Park YJ, Woo H, Eyun SI. Dietary exposure of the water flea Daphnia galeata to microcystin-LR. Anim Cells Syst (Seoul) 2024; 28:25-36. [PMID: 38298818 PMCID: PMC10829830 DOI: 10.1080/19768354.2024.2302529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/01/2024] [Indexed: 02/02/2024] Open
Abstract
Harmful substances like the cyanotoxin microcystin-leucine-arginine (MC-LR) are commonly found in eutrophic freshwater environments, posing risks to aquatic organisms. The water flea, Daphnia, is a well-established model organism for environmental toxicology research. Nevertheless, there is currently insufficient research on the genes that respond to MC-LR in Daphnia galeata. This study aimed to gain insights into the notable genes that react significantly to MC-LR. In this study, we generated an extensive RNA-Seq sequences isolated from the D. galeata HK strain, Han River in Korea. This strain was nourished with a diet of the green microalga Chlorella vulgaris and treated with pure MC-LR at a concentration of 36 ug/L. The transcriptome profile in response to the MC-LR treatment was obtained and 336 differentially expressed genes were subjected to Gene Ontology (GO) and euKaryotic Orthologous Groups of proteins analyses. GO enrichment analysis showed that chemical stimulus, amino sugar metabolic and catabolic process, oxidative stress, and detoxification were highly enriched, in reverse, proteolysis and fucosylation were underpresented. Detoxification process related genes such as peroxidase-like, chorion, and thyroid peroxidase-like were enriched for eliminating or neutralizing MC_LR from an organism's body. Furthermore, functional protein classification revealed an upregulation of lipid and inorganic ion transport processes, while amino acid and carbohydrate transport processes were found to be downregulated. These findings offer insights into how organisms respond to ecotoxic stimuli, providing valuable information for understanding adaptation or defense pathways.
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Affiliation(s)
- Eun-jeong Kim
- Department of Life Science, Chung-ang University, Seoul, Korea
| | - Donggu Jeon
- Department of Life Science, Chung-ang University, Seoul, Korea
| | - Yeon-jeong Park
- Water Environmental Management Department, Korea Water Resources Corporation (K-water), Daejeon, Korea
| | - Hyunmin Woo
- Department of Life Science, Chung-ang University, Seoul, Korea
| | - Seong-il Eyun
- Department of Life Science, Chung-ang University, Seoul, Korea
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74
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Islam M, Behura SK. Single-Cell Transcriptional Response of the Placenta to the Ablation of Caveolin-1: Insights into the Adaptive Regulation of Brain-Placental Axis in Mice. Cells 2024; 13:215. [PMID: 38334607 PMCID: PMC10854826 DOI: 10.3390/cells13030215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Caveolin-1 (Cav1) is a major plasma membrane protein that plays important functions in cellular metabolism, proliferation, and senescence. Mice lacking Cav1 show abnormal gene expression in the fetal brain. Though evidence for placental influence on brain development is emerging, whether the ablation of Cav1 affects the regulation of the brain-placental axis remains unexamined. The current study tests the hypothesis that gene expression changes in specific cells of the placenta and the fetal brain are linked to the deregulation of the brain-placental axis in Cav1-null mice. By performing single-nuclei RNA sequencing (snRNA-seq) analyses, we show that the abundance of the extravillious trophoblast (EVT) and stromal cells, but not the cytotrophoblast (CTB) or syncytiotrophoblast (STB), are significantly impacted due to Cav1 ablation in mice. Interestingly, specific genes related to brain development and neurogenesis were significantly differentially expressed in trophoblast cells due to Cav1 deletion. Comparison of single-cell gene expression between the placenta and the fetal brain further showed that specific genes such as plexin A1 (Plxna1), phosphatase and actin regulator 1 (Phactr1) and amyloid precursor-like protein 2 (Aplp2) were differentially expressed between the EVT and STB cells of the placenta, and also, between the radial glia and ependymal cells of the fetal brain. Bulk RNA-seq analysis of the whole placenta and the fetal brain further identified genes differentially expressed in a similar manner between the placenta and the fetal brain due to the absence of Cav1. The deconvolution of reference cell types from the bulk RNA-seq data further showed that the loss of Cav1 impacted the abundance of EVT cells relative to the stromal cells in the placenta, and that of the glia cells relative to the neuronal cells in the fetal brain. Together, the results of this study suggest that the ablation of Cav1 causes deregulated gene expression in specific cell types of the placenta and the fetal brain in mice.
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Affiliation(s)
- Maliha Islam
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA;
| | - Susanta K. Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA;
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Reproduction and Health Group, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO 65211, USA
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75
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Falco JA, Wynia-Smith SL, McCoy J, Smith BC, Weerapana E. Identification of Protein Targets of S-Nitroso-Coenzyme A-Mediated S-Nitrosation Using Chemoproteomics. ACS Chem Biol 2024; 19:193-207. [PMID: 38159293 PMCID: PMC11154738 DOI: 10.1021/acschembio.3c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
S-Nitrosation is a cysteine post-translational modification fundamental to cellular signaling. This modification regulates protein function in numerous biological processes in the nervous, cardiovascular, and immune systems. Small molecule or protein nitrosothiols act as mediators of NO signaling by transferring the NO group (formally NO+) to a free thiol on a target protein through a transnitrosation reaction. The protein targets of specific transnitrosating agents and the extent and functional effects of S-nitrosation on these target proteins have been poorly characterized. S-nitroso-coenzyme A (CoA-SNO) was recently identified as a mediator of endogenous S-nitrosation. Here, we identified direct protein targets of CoA-SNO-mediated transnitrosation using a competitive chemical-proteomic approach that quantified the extent of modification on 789 cysteine residues in response to CoA-SNO. A subset of cysteines displayed high susceptibility to modification by CoA-SNO, including previously uncharacterized sites of S-nitrosation. We further validated and functionally characterized the functional effects of S-nitrosation on the protein targets phosphofructokinase (platelet type), ATP citrate synthase, and ornithine aminotransferase.
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Affiliation(s)
- Julia A. Falco
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Sarah L. Wynia-Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - James McCoy
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Brian C. Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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76
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Powers J, Zhang X, Reyes AV, Zavaliev R, Xu SL, Dong X. Next-generation mapping of the salicylic acid signaling hub and transcriptional cascade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574047. [PMID: 38260692 PMCID: PMC10802274 DOI: 10.1101/2024.01.03.574047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
For over 60 years, salicylic acid (SA) has been known as a plant immune signal required for both basal and systemic acquired resistance (SAR). SA activates these immune responses by reprogramming up to 20% of the transcriptome through the function of NPR1. However, components in the NPR1-signaling hub, which appears as nuclear condensates, and the NPR1- signaling cascade remained elusive due to difficulties in studying transcriptional cofactors whose chromatin associations are often indirect and transient. To overcome this challenge, we applied TurboID to divulge the NPR1-proxiome, which detected almost all known NPR1-interactors as well as new components of transcription-related complexes. Testing of new components showed that chromatin remodeling and histone demethylation contribute to SA-induced resistance. Globally, NPR1-proxiome shares a striking similarity to GBPL3-proxiome involved in SA synthesis, except associated transcription factors (TFs), suggesting that common regulatory modules are recruited to reprogram specific transcriptomes by transcriptional cofactors, like NPR1, through binding to unique TFs. Stepwise greenCUT&RUN analyses showed that, upon SA-induction, NPR1 initiates the transcriptional cascade primarily through association with TGA TFs to induce expression of secondary TFs, predominantly WRKYs. WRKY54 and WRKY70 then play a major role in inducing immune-output genes without interacting with NPR1 at the chromatin. Moreover, a loss of NPR1 condensate formation decreases its chromatin-association and transcriptional activity, indicating the importance of condensates in organizing the NPR1- signaling hub and initiating the transcriptional cascade. This study demonstrates how combinatorial applications of TurboID and stepwise greenCUT&RUN transcend traditional genetic methods to globally map signaling hubs and transcriptional cascades.
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Affiliation(s)
- Jordan Powers
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Xing Zhang
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Andres V. Reyes
- Carnegie Institute for Science, Stanford University, Stanford, CA 94305, USA
| | - Raul Zavaliev
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Shou-Ling Xu
- Carnegie Institute for Science, Stanford University, Stanford, CA 94305, USA
| | - Xinnian Dong
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
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Kwon S, Safer J, Nguyen DT, Hoksza D, May P, Arbesfeld JA, Rubin AF, Campbell AJ, Burgin A, Iqbal S. Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573913. [PMID: 38260256 PMCID: PMC10802383 DOI: 10.1101/2024.01.02.573913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics technologies have enabled the detection and generation of variants at an unprecedented scale. However, efficient tools and resources are needed to link these two disparate data types - to "map" variants onto protein structures, to better understand how the variation causes disease and thereby design therapeutics. Here we present the Genomics 2 Proteins Portal (G2P; g2p.broadinstitute.org/): a human proteome-wide resource that maps 19,996,443 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the G2P portal generalizes the capability of linking genomics to proteins beyond databases by allowing users to interactively upload protein residue-wise annotations (variants, scores, etc.) as well as the protein structure to establish the connection. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure-function relationship between natural or synthetic variations and their molecular phenotype.
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78
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Torres JR, Botto JF, Sanchez DH. Canonical transcriptional gene silencing may contribute to long-term heat response and recovery through MOM1. PLANT, CELL & ENVIRONMENT 2024; 47:372-382. [PMID: 37712454 DOI: 10.1111/pce.14722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/28/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
Abstract
Plant canonical transcriptional gene silencing (TGS) is involved in epigenetic mechanisms that mediate genomic imprinting and the suppression of transposable elements (TEs). It has been recognised that long-term heat disrupts epigenetic silencing, with the ensuing activation of TEs. However, the physiological involvement of the TGS machinery under prolonged high temperatures has not yet been established. Here, we performed non-lethal extended periodic heat stress and recovery treatments on Arabidopsis thaliana lines mutated on key TGS factors, analysing transcriptomic changes of coding-protein genes and TEs. Plants bearing MET1, DRM2 and CMT3, and MOM1 mutated alleles showed novel transcriptional properties compatible with functionalities concerning the induction/repression of partially shared or private heat-triggered transcriptome networks. Certain observations supported the idea that some responses are based on thermal de-silencing. TEs transcriptional activation uncovered the interaction with specific epigenetic layers, which may play dedicated suppressing roles under determinate physiological conditions such as heat. Furthermore, physiological experimentation suggested that MOM1 is required to resume growth after stress. Our data thus provide initial evidence that at least one canonical TGS factor may contribute to plant acclimation and recovery from non-lethal long-term heat despite the stress-induced epigenetic disturbance.
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Affiliation(s)
- José Roberto Torres
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Javier F Botto
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Diego H Sanchez
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
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79
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Corral-Lopez A, Bloch NI, van der Bijl W, Cortazar-Chinarro M, Szorkovszky A, Kotrschal A, Darolti I, Buechel SD, Romenskyy M, Kolm N, Mank JE. Functional convergence of genomic and transcriptomic architecture underlies schooling behaviour in a live-bearing fish. Nat Ecol Evol 2024; 8:98-110. [PMID: 37985898 PMCID: PMC10781616 DOI: 10.1038/s41559-023-02249-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023]
Abstract
The organization and coordination of fish schools provide a valuable model to investigate the genetic architecture of affiliative behaviours and dissect the mechanisms underlying social behaviours and personalities. Here we used replicate guppy selection lines that vary in schooling propensity and combine quantitative genetics with genomic and transcriptomic analyses to investigate the genetic basis of sociability phenotypes. We show that consistent with findings in collective motion patterns, experimental evolution of schooling propensity increased the sociability of female, but not male, guppies when swimming with unfamiliar conspecifics. This finding highlights a relevant link between coordinated motion and sociability for species forming fission-fusion societies in which both group size and the type of social interactions are dynamic across space and time. We further show that alignment and attraction, the two major traits forming the sociability personality axis in this species, showed heritability estimates at the upper end of the range previously described for social behaviours, with important variation across sexes. The results from both Pool-seq and RNA-seq data indicated that genes involved in neuron migration and synaptic function were instrumental in the evolution of sociability, highlighting a crucial role of glutamatergic synaptic function and calcium-dependent signalling processes in the evolution of schooling.
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Affiliation(s)
- Alberto Corral-Lopez
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Zoology/Ethology, Stockholm University, Stockholm, Sweden.
- Division of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| | - Natasha I Bloch
- Department of Biomedical Engineering, University of Los Andes, Bogota, Colombia
| | - Wouter van der Bijl
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Maria Cortazar-Chinarro
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- MEMEG Department of Biology, Lund University, Lund, Sweden
| | - Alexander Szorkovszky
- RITMO Centre for Interdisciplinary Studies in Rhythm, Time and Motion, University of Oslo, Oslo, Norway
| | - Alexander Kotrschal
- Behavioural Ecology, Wageningen University and Research, Wageningen, the Netherlands
| | - Iulia Darolti
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Severine D Buechel
- Behavioural Ecology, Wageningen University and Research, Wageningen, the Netherlands
| | - Maksym Romenskyy
- Department of Zoology/Ethology, Stockholm University, Stockholm, Sweden
| | - Niclas Kolm
- Department of Zoology/Ethology, Stockholm University, Stockholm, Sweden
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Hayward SJ, Chesnaye NC, Hole B, Aylward R, Meuleman Y, Torino C, Porto G, Szymczak M, Drechsler C, Dekker FW, Evans M, Jager KJ, Wanner C, Caskey FJ. Protein Biomarkers and Major Cardiovascular Events in Older People With Advanced CKD: The European Quality (EQUAL) Study. Kidney Med 2024; 6:100745. [PMID: 38162538 PMCID: PMC10757029 DOI: 10.1016/j.xkme.2023.100745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Abstract
Rationale & Objective Cardiovascular disease is the leading cause of morbidity and mortality in chronic kidney disease (CKD). We investigated 184 inflammatory and cardiovascular proteins to determine their potential as biomarkers for major cardiovascular events (MACEs). Study Design The European Quality (EQUAL) is an observational cohort study that enrolled people aged ≥65 years with an estimated glomerular filtration rate ≤20 mL/min/1.73 m2. Setting & Participants Recruited participants were split into the discovery (n = 611) and replication cohorts (n = 292). Exposure Levels of 184 blood proteins were measured at the baseline visit, and each protein was analyzed individually. Outcome MACE. Analytical Approach Cox proportional hazard models adjusted for age, sex, estimated glomerular filtration rate, previous MACE, and country were used to determine the risk of MACE. Proteins with false discovery rate adjusted P values of <0.05 in the discovery cohort were tested in the replication cohort. Sensitivity analyses were performed by adjusting for traditional risk factors, CKD-specific risk factors, and level of proteinuria and segregating atherosclerotic and nonatherosclerotic MACE. Results During a median follow-up of 2.9 years, 349 people (39%) experienced a MACE. Forty-eight proteins were associated with MACE in the discovery cohort; 9 of these were reproduced in the replication cohort. Three of these proteins maintained a strong association with MACE after adjustment for traditional and CKD-specific risk factors and proteinuria. Tenascin (TNC), fibroblast growth factor-23 (FGF-23), and V-set and immunoglobulin domain-containing protein 2 (VSIG2) were associated with both atherosclerotic and nonatherosclerotic MACE. All replicated proteins except carbonic anhydrase 1 and carbonic anhydrase 3 were associated with nonatherosclerotic MACE. Limitations Single protein concentration measurements and limited follow-up time. Conclusions Our findings corroborate previously reported relationships between FGF-23, vascular cell adhesion protein-1, TNC, and placental growth factor with cardiovascular outcomes in CKD. We identify 5 proteins not previously linked with MACE in CKD that may be targets for future therapies. Plain-Language Summary Kidney disease increases the risk of heart disease, stroke, and other vascular conditions. Blood tests that predict the likelihood of these problems may help to guide treatment, but studies are needed in people with kidney disease. We analyzed blood tests from older people with kidney disease, looking for proteins associated with higher risk of these conditions. Nine proteins were identified, of which 3 showed a strong effect after all other information was considered. This work supports previous research regarding 4 of these proteins and identifies 5 additional proteins that may be associated with higher risk. Further work is needed to confirm our findings and to determine whether these proteins can be used to guide treatment.
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Affiliation(s)
- Samantha J.L. Hayward
- Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom
| | - Nicholas C. Chesnaye
- Amsterdam UMC, University of Amsterdam, ERA Registry, Medical Informatics, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Quality of Care, Amsterdam, The Netherlands
| | - Barnaby Hole
- Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Ryan Aylward
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Yvette Meuleman
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia Torino
- Institute of Clinical Physiology, National Research Council, Reggio Calabria, Italy
| | - Gaetana Porto
- GOM Bianchi Melacrino Morelli, Reggio Calabria, Italy
| | - Maciej Szymczak
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | | | - Friedo W. Dekker
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marie Evans
- Department of Clinical Sciences Intervention and Technology, Karolinska Institutet and Karolinska, Stockholm, Sweden
| | - Kitty J. Jager
- Amsterdam UMC, University of Amsterdam, ERA Registry, Medical Informatics, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Quality of Care, Amsterdam, The Netherlands
| | - Christoph Wanner
- Division of Nephrology, University Hospital of Wurzburg, Wurzburg, Germany
| | - Fergus J. Caskey
- Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - EQUAL investigators
- Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom
- Amsterdam UMC, University of Amsterdam, ERA Registry, Medical Informatics, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Quality of Care, Amsterdam, The Netherlands
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Institute of Clinical Physiology, National Research Council, Reggio Calabria, Italy
- GOM Bianchi Melacrino Morelli, Reggio Calabria, Italy
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
- Division of Nephrology, University Hospital of Wurzburg, Wurzburg, Germany
- Department of Clinical Sciences Intervention and Technology, Karolinska Institutet and Karolinska, Stockholm, Sweden
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Tuncel T, Metintas M, Güntülü AK, Güneş HV. Whole-Genome Comparative Copy Number Alteration Profiling between Malignant Pleural Mesothelioma and Asbestos-Induced Chronic Pleuritis. J Environ Pathol Toxicol Oncol 2024; 43:31-44. [PMID: 37824368 DOI: 10.1615/jenvironpatholtoxicoloncol.2023047755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
Malignant pleural mesothelioma (MPM) is rare and aggressive cancer. The most important risk factor for MPM is exposure to asbestos. In this study, we scanned the genomes of individuals MPM and asbestos-induced chronic pleuritis (AICP) to compare and determine copy number alterations (CNAs) between two asbestos-related diseases. We used high-resolution SNP arrays to compare CNA profiles between MPM (n = 55) and AICP (n = 18). DNAs extracted from pleural tissues in both groups. SNP array analysis revealed common losses at 1p, 3p, 6q, 9p, 13q, 14q, 15q, 16q, 22q and frequent gains at chromosomes 1, 3, 5, 7, 8, and 6p, 12q, 15q, 17p, 20q in MPMs (frequencies max 67%-min 30%; these alterations were not detected in AICPs. Besides detecting well-known MPM-associated CNAs, our high -resolution copy number profiling also detected comparatively rare CNAs for MPMs including losses like 9q33.3, 16q and gains of 1p, 1q, 3p, 3q, 6p, 7q, 15q, 12q, 17p, 20q at significant frequencies in the MPM cohort. We also observed Copy Number gains clustered on the NF2 locus in AICPs, whereas this region was commonly deleted in MPMs. According to this distinct genomic profiles between the two groups, AICPs genomes can be clearly distinguished from highly altered MPM genomes. Hence, we can suggest that SNP arrays can be used as a supporting diagnostic tool in terms of discriminating asbestos-related malignant disease such as MPM and benign pleural lesions, which can be challenging in most instances.
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Affiliation(s)
- Tunç Tuncel
- Health Institutes of Turkey, Turkish Biotechnology Institute, Ankara, Turkey
| | - Muzaffer Metintas
- Eskisehir Osmangazi University Medical Faculty, Department of Chest Diseases, Lung and Pleural Cancers Research and Clinical Center, Eskisehir, Turkey
| | - A K Güntülü
- Eskisehir Osmangazi University Medical Faculty, Department of Chest Diseases, Lung and Pleural Cancers Research and Clinical Center, Eskisehir, Turkey
| | - Hasan Veysi Güneş
- Eskisehir Osmangazi University Medical Faculty, Department of Medical Biology, Eskisehir, Turkey
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Akhmetshina A, Bianco V, Bradić I, Korbelius M, Pirchheim A, Kuentzel KB, Eichmann TO, Hinteregger H, Kolb D, Habisch H, Liesinger L, Madl T, Sattler W, Radović B, Sedej S, Birner-Gruenberger R, Vujić N, Kratky D. Loss of lysosomal acid lipase results in mitochondrial dysfunction and fiber switch in skeletal muscles of mice. Mol Metab 2024; 79:101869. [PMID: 38160938 PMCID: PMC7615526 DOI: 10.1016/j.molmet.2023.101869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024] Open
Abstract
OBJECTIVE Lysosomal acid lipase (LAL) is the only enzyme known to hydrolyze cholesteryl esters (CE) and triacylglycerols in lysosomes at an acidic pH. Despite the importance of lysosomal hydrolysis in skeletal muscle (SM), research in this area is limited. We hypothesized that LAL may play an important role in SM development, function, and metabolism as a result of lipid and/or carbohydrate metabolism disruptions. RESULTS Mice with systemic LAL deficiency (Lal-/-) had markedly lower SM mass, cross-sectional area, and Feret diameter despite unchanged proteolysis or protein synthesis markers in all SM examined. In addition, Lal-/- SM showed increased total cholesterol and CE concentrations, especially during fasting and maturation. Regardless of increased glucose uptake, expression of the slow oxidative fiber marker MYH7 was markedly increased in Lal-/-SM, indicating a fiber switch from glycolytic, fast-twitch fibers to oxidative, slow-twitch fibers. Proteomic analysis of the oxidative and glycolytic parts of the SM confirmed the transition between fast- and slow-twitch fibers, consistent with the decreased Lal-/- muscle size due to the "fiber paradox". Decreased oxidative capacity and ATP concentration were associated with reduced mitochondrial function of Lal-/- SM, particularly affecting oxidative phosphorylation, despite unchanged structure and number of mitochondria. Impairment in muscle function was reflected by increased exhaustion in the treadmill peak effort test in vivo. CONCLUSION We conclude that whole-body loss of LAL is associated with a profound remodeling of the muscular phenotype, manifested by fiber type switch and a decline in muscle mass, most likely due to dysfunctional mitochondria and impaired energy metabolism, at least in mice.
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Affiliation(s)
- Alena Akhmetshina
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Valentina Bianco
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Ivan Bradić
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Melanie Korbelius
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Anita Pirchheim
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Katharina B Kuentzel
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; Department of Biomedical Science, University of Copenhagen, Copenhagen, Denmark
| | - Thomas O Eichmann
- Institute of Molecular Biosciences, University of Graz, Graz, Austria; Core Facility Mass Spectrometry, Center for Medical Research, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Helga Hinteregger
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Dagmar Kolb
- BioTechMed-Graz, Graz, Austria; Core Facility Ultrastructural Analysis, Medical University of Graz, Graz, Austria; Gottfried Schatz Research Center, Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Hansjoerg Habisch
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Laura Liesinger
- Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Wolfgang Sattler
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Branislav Radović
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Simon Sedej
- BioTechMed-Graz, Graz, Austria; Department of Internal Medicine, Division of Cardiology, Medical University of Graz, Graz, Austria; Institute of Physiology, Faculty of Medicine, University of Maribor, Slovenia
| | - Ruth Birner-Gruenberger
- BioTechMed-Graz, Graz, Austria; Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria; Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Nemanja Vujić
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Dagmar Kratky
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria.
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Gohel D, Zhang P, Gupta AK, Li Y, Chiang CW, Li L, Hou Y, Pieper AA, Cummings J, Cheng F. Sildenafil as a Candidate Drug for Alzheimer's Disease: Real-World Patient Data Observation and Mechanistic Observations from Patient-Induced Pluripotent Stem Cell-Derived Neurons. J Alzheimers Dis 2024; 98:643-657. [PMID: 38427489 PMCID: PMC10977448 DOI: 10.3233/jad-231391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 03/03/2024]
Abstract
Background Alzheimer's disease (AD) is a chronic neurodegenerative disease needing effective therapeutics urgently. Sildenafil, one of the approved phosphodiesterase-5 inhibitors, has been implicated as having potential effect in AD. Objective To investigate the potential therapeutic benefit of sildenafil on AD. Methods We performed real-world patient data analysis using the MarketScan® Medicare Supplemental and the Clinformatics® databases. We conducted propensity score-stratified analyses after adjusting confounding factors (i.e., sex, age, race, and comorbidities). We used both familial and sporadic AD patient induced pluripotent stem cells (iPSC) derived neurons to evaluate the sildenafil's mechanism-of-action. Results We showed that sildenafil usage is associated with reduced likelihood of AD across four new drug compactor cohorts, including bumetanide, furosemide, spironolactone, and nifedipine. For instance, sildenafil usage is associated with a 54% reduced incidence of AD in MarketScan® (hazard ratio [HR] = 0.46, 95% CI 0.32- 0.66) and a 30% reduced prevalence of AD in Clinformatics® (HR = 0.70, 95% CI 0.49- 1.00) compared to spironolactone. We found that sildenafil treatment reduced tau hyperphosphorylation (pTau181 and pTau205) in a dose-dependent manner in both familial and sporadic AD patient iPSC-derived neurons. RNA-sequencing data analysis of sildenafil-treated AD patient iPSC-derived neurons reveals that sildenafil specifically target AD related genes and pathobiological pathways, mechanistically supporting the beneficial effect of sildenafil in AD. Conclusions These real-world patient data validation and mechanistic observations from patient iPSC-derived neurons further suggested that sildenafil is a potential repurposable drug for AD. Yet, randomized clinical trials are warranted to validate the causal treatment effects of sildenafil in AD.
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Affiliation(s)
- Dhruv Gohel
- Genomic Medicine Institute,Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Pengyue Zhang
- Department of Biostatistics and Health Data Science, Indiana University, Indianapolis, IN, USA
| | - Amit Kumar Gupta
- Genomic Medicine Institute,Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yichen Li
- Genomic Medicine Institute,Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Chien-Wei Chiang
- Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH, USA
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH, USA
| | - Yuan Hou
- Genomic Medicine Institute,Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Andrew A. Pieper
- Brain Health Medicines Center, Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Department of Psychiatry, Case Western Reserve University, Cleveland, OH, USA
- Geriatric Psychiatry, GRECC, Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA
- Institute for Transformative Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
| | - Jeffrey Cummings
- Department of Brain Health, School of Integrated Health Sciences, Chambers-Grundy Center for Transformative Neuroscience, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Feixiong Cheng
- Genomic Medicine Institute,Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
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Zeng V, Uauy C, Chen Y. Identification of a novel SNP in the miR172 binding site of Q homoeolog AP2L-D5 is associated with spike compactness and agronomic traits in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:13. [PMID: 38142253 DOI: 10.1007/s00122-023-04514-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/23/2023] [Indexed: 12/25/2023]
Abstract
KEY MESSAGE This study found that the compact spike locus of ANK-15 is on chromosome 5D instead of 2B. We have identified a new allele of AP2L-D5 as the candidate causal polymorphism. Spike architecture is a key determinant of wheat yield, a crop which supports much of the human diet but whose yield gains are stagnating. Spike architecture mutants offer opportunities to identify genetic factors contributing to inflorescence development. Here, we investigate the locus underlying the compact spike phenotype of mutant line ANK-15 by conducting mRNA-sequencing and genetic mapping using ANK-15 and its non-compact spike near-isogenic line Novosibirskaya 67 (N67). Previous literature has placed the compact spike locus of ANK-15 to chromosome 2B. However, based on the single nucleotide polymorphisms (SNPs) identified using mRNA-seq data, we were unable to detect polymorphisms between N67 and ANK-15 in the putative chromosome 2B region. We performed differential expression analysis of developing rachis and found that AP2L-D5, the D homoeolog of the domestication Q gene, is upregulated in ANK-15 in comparison to N67. ANK-15 carries a SNP in the microRNA172 binding site of AP2L-D5, which is predicted to lead to higher expression of AP2L-D5 due to decreased miRNA172-mediated degradation. Furthermore, we performed genetic mapping using an ANK-15 × N67 F2 population and found a single quantitative trait locus on chromosome 5D coinciding with the position of AP2L-D5. This result suggests that AP2L-D5 is likely the underlying causal gene for the compact spike phenotype in ANK-15. We performed a field trial to investigate the effect of the AP2L-D5 allele on agronomic traits and found that the AP2L-D5 allele from ANK-15 is associated with a significant reduction in height, increased thousand grain weight (TGW), and increased grain width.
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Affiliation(s)
- Victoria Zeng
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yi Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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85
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Weiner L, Fitzgerald A, Maynard R, Marcisak E, Nasir A, Glasgow E, Jablonski S, Van Der Veken P, Pearson G, Eisman S, Mace E, Fertig E. Fibroblast activation protein regulates natural killer cell migration, extravasation and tumor infiltration. RESEARCH SQUARE 2023:rs.3.rs-3706465. [PMID: 38196606 PMCID: PMC10775390 DOI: 10.21203/rs.3.rs-3706465/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Natural killer (NK) cells play a critical role in physiologic and pathologic conditions such as pregnancy, infection, autoimmune disease and cancer. In cancer, numerous strategies have been designed to exploit the cytolytic properties of NK cells, with variable success. A major hurdle to NK-cell focused therapies is NK cell recruitment and infiltration into tumors. While the chemotaxis pathways regulating NK recruitment to different tissues are well delineated, the mechanisms human NK cells employ to physically migrate are ill-defined. We show for the first time that human NK cells express fibroblast activation protein (FAP), a cell surface protease previously thought to be primarily expressed by activated fibroblasts. FAP degrades the extracellular matrix to facilitate cell migration and tissue remodeling. We used novel in vivo zebrafish and in vitro 3D culture models to demonstrate that FAP knock out and pharmacologic inhibition restrict NK cell migration, extravasation, and invasion through tissue matrix. Notably, forced overexpression of FAP promotes NK cell invasion through matrix in both transwell and tumor spheroid assays, ultimately increasing tumor cell lysis. Additionally, FAP overexpression enhances NK cells invasion into a human tumor in immunodeficient mice. These findings demonstrate the necessity of FAP in NK cell migration and present a new approach to modulate NK cell trafficking and enhance cell-based therapy in solid tumors.
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Affiliation(s)
| | - Allison Fitzgerald
- Lombardi Comprehensive Cancer Center, Georgetown University Medial Center, Washington
| | | | - Emily Marcisak
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine
| | | | | | | | | | | | | | - Emily Mace
- Columbia University Irving Medical Center
| | - Elana Fertig
- Johns Hopkins Convergence Institute, Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Department of Biomedical Engineeri
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86
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Ahmad N, Samoylenko A, Abene I, Abdelrady E, Zhyvolozhnyi A, Makieieva O, Bart G, Skovorodkin I, Vainio SJ. Generation of novel in vitro flexible kidney organoid model to investigate the role of extracellular vesicles in induction of nephrogenesis. Cell Commun Signal 2023; 21:358. [PMID: 38110951 PMCID: PMC10726558 DOI: 10.1186/s12964-023-01374-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 10/29/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND During kidney organogenesis, metanephric mesenchyme (MM) and ureteric bud (UB) interact reciprocally to form nephrons. Signaling stimuli involved in these interactions include Wnts, growth factors and nano/micro particles. How UB and MM are interacting is not completely understood. Our study investigated the signaling and communication via extracellular vesicles (EVs) during nephrogenesis. Embryonic day (E) 11.5 mouse kidney UB and MM produce very low number of primary cells that have limited ability for proliferation in culture. Such limitations obstruct studying the role of EVs in induction of nephrogenesis. These issues necessitate to generate a nephrogenesis model allowing to study the comprehensive role of EVs during nephrogenesis. RESULTS Our study generated a UB derived cell line-based in vitro flexible model of nephrogenesis allowing expandable cell culturing, in addition to performing characterization, tracking and blocking of EVs. UB cell line aggregation with E11.5 MM cells induced the formation of segmented nephrons. Most efficient nephrogenesis was obtained by the co-culturing of 30,000 cells of UB cell line with 50,000 MM cells. Results revealed that both the UB and the MM secrete EVs during nephrogenesis. UB cell line derived EVs were characterized by their size, morphology and expression of markers (CD63, TSG101, CD9 and CD81). Furthermore, proteomics data of UB cell line-derived EVs revealed large number of proteins involved in nephrogenesis-related signaling pathways. Palmitoylated GFP-tagged EVs from UB cell line were found in the nephron formation zone in the developing kidney organoid. UB cell line derived EVs did not induce nephrogenesis in MM cells but significantly contributed to the survival and nephrogenesis-competency of MM cells. The secretion of EVs was continuously inhibited during the ongoing nephrogenesis by the knockdown of RalA and RalB gene expression using short hairpin RNAs. This inhibition partially impaired the ability of UB cell line to induce nephrogenesis. Moreover, impaired nephrogenesis was partially rescued by the addition of EVs. CONCLUSION Our study established a novel in vitro flexible model of nephrogenesis that solved the limitations of primary embryonic kidney cells and mouse embryonic stem cell kidney organoids for the EV research. EVs were found to be an integral part of nephrogenesis process. Video Abstract.
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Affiliation(s)
- Naveed Ahmad
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland.
| | - Anatoliy Samoylenko
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland
| | - Ichrak Abene
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland
| | - Eslam Abdelrady
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland
| | - Artem Zhyvolozhnyi
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland
| | - Olha Makieieva
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland
| | - Geneviève Bart
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland
| | - Ilya Skovorodkin
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland
| | - Seppo J Vainio
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland.
- Infotech Oulu, University of Oulu, 90014, Oulu, Finland.
- Flagship GeneCellNano, University of Oulu, 90220, Oulu, Finland.
- Kvantum Institute, University of Oulu, 90014, Oulu, Finland.
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Strawn M, Safranski TJ, Behura SK. Does DNA methylation in the fetal brain leave an epigenetic memory in the blood? Gene 2023; 887:147788. [PMID: 37696423 DOI: 10.1016/j.gene.2023.147788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/23/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023]
Abstract
Epigenetic memory is an emerging concept that refers to the process in which epigenetic changes occurring early-in life can lead to long-term programs of gene regulation in time and space. By leveraging neural network regression modeling of DNA methylation data in pigs, we show that specific methylations in the adult blood can reliably predict methylation changes that occurred in the fetal brain. Genes associated with these methylations represented known markers of specific cell types of blood including bone marrow hematopoietic progenitor cells, and ependymal and oligodendrocyte cells of brain. This suggested that methylation changes that occurred in the developing brain were maintained as an epigenetic memory in the blood through the adult life.
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Affiliation(s)
- Monica Strawn
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Timothy J Safranski
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States; MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, United States; Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO 65211, United States.
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88
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Huertas-Abril PV, Jurado J, Prieto-Álamo MJ, García-Barrera T, Abril N. Proteomic analysis of the hepatic response to a pollutant mixture in mice. The protective action of selenium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166558. [PMID: 37633382 DOI: 10.1016/j.scitotenv.2023.166558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Metals and pharmaceuticals contaminate water and food worldwide, forming mixtures where they can interact to enhance their individual toxicity. Here we use a shotgun proteomic approach to evaluate the toxicity of a pollutant mixture (PM) of metals (As, Cd, Hg) and pharmaceuticals (diclofenac, flumequine) on mice liver proteostasis. These pollutants are abundant in the environment, accumulate in the food chain, and are toxic to humans primarily through oxidative damage. Thus, we also evaluated the putative antagonistic effect of low-dose dietary supplementation with the antioxidant trace element selenium. A total of 275 proteins were affected by PM treatment. Functional analyses revealed an increased abundance of proteins involved in the integrated stress response that promotes translation, the inflammatory response, carbohydrate and lipid metabolism, and the sustained expression of the antioxidative response mediated by NRF2. As a consequence, a reductive stress situation arises in the cell that inhibits the RICTOR pathway, thus activating the early stage of autophagy, impairing xenobiotic metabolism, and potentiating lipid biosynthesis and steatosis. PM exposure-induced hepato-proteostatic alterations were significantly reduced in Se supplemented mice, suggesting that the use of this trace element as a dietary supplement may at least partially ameliorate liver damage caused by exposure to environmental mixtures.
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Affiliation(s)
- Paula V Huertas-Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - Juan Jurado
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - María-José Prieto-Álamo
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - Tamara García-Barrera
- Research Center of Natural Resources, Health, and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, Campus El Carmen, University of Huelva, Fuerzas Armadas Ave., 21007 Huelva, Spain
| | - Nieves Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain.
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89
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Nilsson EE, McBirney M, De Santos S, King SE, Beck D, Greeley C, Holder LB, Skinner MK. Multiple generation distinct toxicant exposures induce epigenetic transgenerational inheritance of enhanced pathology and obesity. ENVIRONMENTAL EPIGENETICS 2023; 9:dvad006. [PMID: 38162685 PMCID: PMC10756336 DOI: 10.1093/eep/dvad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/12/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
Three successive multiple generations of rats were exposed to different toxicants and then bred to the transgenerational F5 generation to assess the impacts of multiple generation different exposures. The current study examines the actions of the agricultural fungicide vinclozolin on the F0 generation, followed by jet fuel hydrocarbon mixture exposure of the F1 generation, and then pesticide dichlorodiphenyltrichloroethane on the F2 generation gestating females. The subsequent F3 and F4 generations and F5 transgenerational generation were obtained and F1-F5 generations examined for male sperm epigenetic alterations and pathology in males and females. Significant impacts on the male sperm differential DNA methylation regions were observed. The F3-F5 generations were similar in ∼50% of the DNA methylation regions. The pathology of each generation was assessed in the testis, ovary, kidney, and prostate, as well as the presence of obesity and tumors. The pathology used a newly developed Deep Learning, artificial intelligence-based histopathology analysis. Observations demonstrated compounded disease impacts in obesity and metabolic parameters, but other pathologies plateaued with smaller increases at the F5 transgenerational generation. Observations demonstrate that multiple generational exposures, which occur in human populations, appear to increase epigenetic impacts and disease susceptibility.
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Affiliation(s)
- Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Margaux McBirney
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Sarah De Santos
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Stephanie E King
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Colin Greeley
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA
| | - Lawrence B Holder
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
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90
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Nomura M, Murad NF, Madhavan SS, Eap B, Garcia TY, Aguirre CG, Verdin E, Ellerby L, Furman D, Newman JC. A ketogenic diet reduces age-induced chronic neuroinflammation in mice Running title: ketogenic diet and brain inflammaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569598. [PMID: 38106160 PMCID: PMC10723274 DOI: 10.1101/2023.12.01.569598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Beta-hydroxybutyrate (BHB) is a ketone body synthesized during fasting or strenuous exercise. Our previous study demonstrated that a cyclic ketogenic diet (KD), which induces BHB levels similar to fasting every other week, reduces midlife mortality and improves memory in aging mice. BHB actively regulates gene expression and inflammatory activation through non-energetic signaling pathways. Neither of these activities has been well-characterized in the brain and they may represent mechanisms by which BHB affects brain function during aging. First, we analyzed hepatic gene expression in an aging KD-treated mouse cohort using bulk RNA-seq. In addition to the downregulation of TOR pathway activity, cyclic KD reduces inflammatory gene expression in the liver. We observed via flow cytometry that KD also modulates age-related systemic T cell functions. Next, we investigated whether BHB affects brain cells transcriptionally in vitro. Gene expression analysis in primary human brain cells (microglia, astrocytes, neurons) using RNA-seq shows that BHB causes a mild level of inflammation in all three cell types. However, BHB inhibits the more pronounced LPS-induced inflammatory gene activation in microglia. Furthermore, we confirmed that BHB similarly reduces LPS-induced inflammation in primary mouse microglia and bone marrow-derived macrophages (BMDMs). BHB is recognized as an inhibitor of histone deacetylase (HDAC), an inhibitor of NLRP3 inflammasome, and an agonist of the GPCR Hcar2. Nevertheless, in microglia, BHB's anti-inflammatory effects are independent of these known mechanisms. Finally, we examined the brain gene expression of 12-month-old male mice fed with one-week and one-year cyclic KD. While a one-week KD increases inflammatory signaling, a one-year cyclic KD reduces neuroinflammation induced by aging. In summary, our findings demonstrate that BHB mitigates the microglial response to inflammatory stimuli, like LPS, possibly leading to decreased chronic inflammation in the brain after long-term KD treatment in aging mice.
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Affiliation(s)
| | | | - Sidharth S Madhavan
- Buck Institute for Research on Aging, Novato, CA, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Brenda Eap
- Buck Institute for Research on Aging, Novato, CA, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | | | - Carlos Galicia Aguirre
- Buck Institute for Research on Aging, Novato, CA, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Lisa Ellerby
- Buck Institute for Research on Aging, Novato, CA, USA
| | - David Furman
- Buck Institute for Research on Aging, Novato, CA, USA
| | - John C Newman
- Buck Institute for Research on Aging, Novato, CA, USA
- Division of Geriatrics, University of California, San Francisco, San Francisco, CA, USA
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91
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Zhang C, Atanasov KE, Murillo E, Vives-Peris V, Zhao J, Deng C, Gómez-Cadenas A, Alcázar R. Spermine deficiency shifts the balance between jasmonic acid and salicylic acid-mediated defence responses in Arabidopsis. PLANT, CELL & ENVIRONMENT 2023; 46:3949-3970. [PMID: 37651604 DOI: 10.1111/pce.14706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023]
Abstract
Polyamines are small aliphatic polycations present in all living organisms. In plants, the most abundant polyamines are putrescine (Put), spermidine (Spd) and spermine (Spm). Polyamine levels change in response to different pathogens, including Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). However, the regulation of polyamine metabolism and their specific contributions to defence are not fully understood. Here we report that stimulation of Put biosynthesis by Pst DC3000 is dependent on coronatine (COR) perception and jasmonic acid (JA) signalling, independently of salicylic acid (SA). Conversely, lack of Spm in spermine synthase (spms) mutant stimulated galactolipids and JA biosynthesis, and JA signalling under basal conditions and during Pst DC3000 infection, whereas compromised SA-pathway activation and defence outputs through SA-JA antagonism. The dampening of SA responses correlated with COR and Pst DC3000-inducible deregulation of ANAC019 expression and its key SA-metabolism gene targets. Spm deficiency also led to enhanced disease resistance to the necrotrophic fungal pathogen Botrytis cinerea and stimulated endoplasmic reticulum (ER) stress signalling in response to Pst DC3000. Overall, our findings provide evidence for the integration of polyamine metabolism in JA- and SA-mediated defence responses, as well as the participation of Spm in buffering ER stress during defence.
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Affiliation(s)
- Chi Zhang
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Kostadin E Atanasov
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Ester Murillo
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Vicente Vives-Peris
- Departamento de Biología, Bioquímica y Ciencias Naturales, Universitat Jaume I, Castelló de la Plana, Spain
| | - Jiaqi Zhao
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Cuiyun Deng
- Plant Synthetic Biology and Metabolic Engineering Program, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Cerdanyola, Barcelona, Spain
| | - Aurelio Gómez-Cadenas
- Departamento de Biología, Bioquímica y Ciencias Naturales, Universitat Jaume I, Castelló de la Plana, Spain
| | - Rubén Alcázar
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
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92
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Lebold KM, Cook M, Pincus AB, Nevonen KA, Davis BA, Carbone L, Calco GN, Pierce AB, Proskocil BJ, Fryer AD, Jacoby DB, Drake MG. Grandmaternal allergen sensitization reprograms epigenetic and airway responses to allergen in second-generation offspring. Am J Physiol Lung Cell Mol Physiol 2023; 325:L776-L787. [PMID: 37814791 PMCID: PMC11068409 DOI: 10.1152/ajplung.00103.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 10/11/2023] Open
Abstract
Asthma susceptibility is influenced by environmental, genetic, and epigenetic factors. DNA methylation is one form of epigenetic modification that regulates gene expression and is both inherited and modified by environmental exposures throughout life. Prenatal development is a particularly vulnerable time period during which exposure to maternal asthma increases asthma risk in offspring. How maternal asthma affects DNA methylation in offspring and what the consequences of differential methylation are in subsequent generations are not fully known. In this study, we tested the effects of grandmaternal house dust mite (HDM) allergen sensitization during pregnancy on airway physiology and inflammation in HDM-sensitized and challenged second-generation mice. We also tested the effects of grandmaternal HDM sensitization on tissue-specific DNA methylation in allergen-naïve and -sensitized second-generation mice. Descendants of both allergen- and vehicle-exposed grandmaternal founders exhibited airway hyperreactivity after HDM sensitization. However, grandmaternal allergen sensitization significantly potentiated airway hyperreactivity and altered the epigenomic trajectory in second-generation offspring after HDM sensitization compared with HDM-sensitized offspring from vehicle-exposed founders. As a result, biological processes and signaling pathways associated with epigenetic modifications were distinct between lineages. A targeted analysis of pathway-associated gene expression found that Smad3 was significantly dysregulated as a result of grandmaternal allergen sensitization. These data show that grandmaternal allergen exposure during pregnancy establishes a unique epigenetic trajectory that reprograms allergen responses in second-generation offspring and may contribute to asthma risk.NEW & NOTEWORTHY Asthma susceptibility is influenced by environmental, genetic, and epigenetic factors. This study shows that maternal allergen exposure during pregnancy promotes unique epigenetic trajectories in second-generation offspring at baseline and in response to allergen sensitization, which is associated with the potentiation of airway hyperreactivity. These effects are one mechanism by which maternal asthma may influence the inheritance of asthma risk.
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Affiliation(s)
- Katie M Lebold
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, United States
| | - Madeline Cook
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Alexandra B Pincus
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Kimberly A Nevonen
- Knight Cardiovascular Institute Epigenetics Consortium, Oregon Health and Science University, Portland, Oregon, United States
| | - Brett A Davis
- Knight Cardiovascular Institute Epigenetics Consortium, Oregon Health and Science University, Portland, Oregon, United States
| | - Lucia Carbone
- Knight Cardiovascular Institute Epigenetics Consortium, Oregon Health and Science University, Portland, Oregon, United States
- Department of Medicine, Oregon Health and Science University, Portland, Oregon, United States
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon, United States
| | - Gina N Calco
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Aubrey B Pierce
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Becky J Proskocil
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Allison D Fryer
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Oregon Health and Science University, Portland, Oregon, United States
| | - David B Jacoby
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Matthew G Drake
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Oregon Health and Science University, Portland, Oregon, United States
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93
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Zhang Z, Wei Z, Zhao L, Gu C, Meng Y. Assessing the clinical utility of multi-omics data for predicting serous ovarian cancer prognosis. J OBSTET GYNAECOL 2023; 43:2171778. [PMID: 36803381 DOI: 10.1080/01443615.2023.2171778] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Ovarian cancer (OC) is characterised by heterogeneity that complicates the prediction of patient survival and treatment outcomes. Here, we conducted analyses to predict the prognosis of patients from the Genomic Data Commons database and validated the predictions by fivefold cross-validation and by using an independent dataset in the International Cancer Genome Consortium database. We analysed the somatic DNA mutation, mRNA expression, DNA methylation, and microRNA expression data of 1203 samples from 599 serous ovarian cancer (SOC) patients. We found that principal component transformation (PCT) improved the predictive performance of the survival and therapeutic models. Deep learning algorithms also showed better predictive power than the decision tree (DT) and random forest (RF). Furthermore, we identified a series of molecular features and pathways that are associated with patient survival and treatment outcomes. Our study provides perspective on building reliable prognostic and therapeutic strategies and further illuminates the molecular mechanisms of SOC.Impact statementWhat is already known on this subject? Recent studies have focussed on predicting cancer outcomes based on omics data. But the limitation is the performance of single-platform genomic analyses or the small numbers of genomic analyses.What do the results of this study add? We analysed multi-omics data, found that principal component transformation (PCT) significantly improved the predictive performance of the survival and therapeutic models. Deep learning algorithms also showed better predictive power than did decision tree (DT) and random forest (RF). Furthermore, we identified a series of molecular features and pathways that are associated with patient survival and treatment outcomes.What are the implications of these findings for clinical practice and/or further research? Our study provides perspective on how to build reliable prognostic and therapeutic strategies and further illuminates the molecular mechanisms of SOC for future studies.
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Affiliation(s)
- Zhe Zhang
- Department of Obstetrics and Gynecology, Seventh Medical Center of Chinese, PLA General Hospital, Beijing, P.R. China
| | - Zhiyao Wei
- Department of Obstetrics and Gynecology, Seventh Medical Center of Chinese, PLA General Hospital, Beijing, P.R. China
| | - Luyang Zhao
- Department of Obstetrics and Gynecology, Seventh Medical Center of Chinese, PLA General Hospital, Beijing, P.R. China
| | - Chenglei Gu
- Department of Obstetrics and Gynecology, Seventh Medical Center of Chinese, PLA General Hospital, Beijing, P.R. China
| | - Yuanguang Meng
- Department of Obstetrics and Gynecology, Seventh Medical Center of Chinese, PLA General Hospital, Beijing, P.R. China
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94
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Duncan GE, Avery A, Maamar MB, Nilsson EE, Beck D, Skinner MK. Epigenome-wide association study of systemic effects of obesity susceptibility in human twins. Epigenetics 2023; 18:2268834. [PMID: 37871278 PMCID: PMC10595392 DOI: 10.1080/15592294.2023.2268834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/01/2023] [Indexed: 10/25/2023] Open
Abstract
The current study was designed to use an epigenome-wide association approach (EWAS) to identify potential systemic DNA methylation alterations that are associated with obesity using 22 discordant twin pairs. Buccal cells (from a cheek swab) were used as a non-obesity relevant purified marker cell for the epigenetic analysis. Analysis of differential DNA methylation regions (DMRs) was used to identify epigenetic associations with metabolic and dietary measures related to obesity with discordant twins. An edgeR analysis provided a DMR signature with p < 1e-04, but statistical significance was reduced due to low sample size and known multiple origins of obesity. A weighted gene coexpression network analysis (WGCNA) was performed and identified modules (p < 0.005) of epigenetic sites that correlated with different metabolic and dietary measures. The DMR and WGCNA epigenetic sites were near genes (e.g., CIDEC, SPP1, ZFPG9, and POMC) with previously identified obesity associated pathways (e.g., metabolism, cholesterol, and fat digestion). Observations demonstrate the feasibility of identifying systemic epigenetic biomarkers for obesity, which can be further investigated for clinical relevance in future research with larger sample sizes. The availability of a systemic epigenetic biomarker for obesity susceptibility may facilitate preventative medicine and clinical management of the disease early in life.
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Affiliation(s)
- Glen E. Duncan
- Department of Nutrition and Exercise Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Ally Avery
- Department of Nutrition and Exercise Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Eric E. Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
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95
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Wei CH, Wang EW, Ma L, Zhou Y, Zheng L, Hampel H, Shehayeb S, Lee S, Cohen J, Kohut A, Fan F, Rosen S, Wu X, Shen B, Zhao Y. POLD1 DEDD Motif Mutation Confers Hypermutation in Endometrial Cancer and Durable Response to Pembrolizumab. Cancers (Basel) 2023; 15:5674. [PMID: 38067377 PMCID: PMC10705788 DOI: 10.3390/cancers15235674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Mutations in the DNA polymerase delta 1 (POLD1) exonuclease domain cause DNA proofreading defects, hypermutation, hereditary colorectal and endometrial cancer, and are predictive of immunotherapy response. Exonuclease activity is carried out by two magnesium cations, bound to four highly conserved, negatively charged amino acids (AA) consisting of aspartic acid at amino acid position 316 (p.D316), glutamic acid at position 318 (p.E318), p.D402, and p.D515 (termed DEDD motif). Germline polymorphisms resulting in charge-discordant AA substitutions in the DEDD motif are classified as variants of uncertain significance (VUSs) by laboratories and thus would be considered clinically inactionable. We hypothesize this mutation class is clinically pathogenic. METHODS A review of clinical presentation was performed in our index patient with a POLD1(p.D402N) heterozygous proband with endometrial cancer. Implications of this mutation class were evaluated by a Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA)-guided systematic review, in silico analysis with orthogonal biochemical confirmation, and whole-exome and RNA sequencing analysis of the patient's tumor and engineered cell lines. RESULTS Our systematic review favored a Mendelian disease mutation class associated with endometrial and colorectal cancers. In silico analysis predicted defective protein function, confirmed by biochemical assay demonstrating loss of nuclease activity. A POLD1-specific mutational signature was found in both the patient's tumor and POLD1(p.D402N) overexpressing cell. Furthermore, paired whole-exome/transcriptome analysis of endometrial tumor demonstrated hypermutation and T cell-inflamed gene expression profile (GEP), which are joint predictive biomarkers for pembrolizumab. Our patient showed a deep, durable response to immune checkpoint inhibitor (ICI). CONCLUSION Charge-discordant AA substitution in the DEDD motif of POLD1 is detrimental to DNA proofreading and should be reclassified as likely pathogenic and possibly predictive of ICI sensitivity.
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Affiliation(s)
- Christina Hsiao Wei
- Department of Pathology, City of Hope Medical Center (COHNMC), Duarte, CA 91010, USA;
| | - Edward Wenge Wang
- Department of Oncology & Therapeutics Research, City of Hope Medical Center (COHNMC), Duarte, CA 91010, USA;
| | - Lingzi Ma
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute at City of Hope Medical Center (COHNMC), Duarte, CA 91010, USA; (L.M.); (Y.Z.); (L.Z.); (B.S.)
| | - Yajing Zhou
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute at City of Hope Medical Center (COHNMC), Duarte, CA 91010, USA; (L.M.); (Y.Z.); (L.Z.); (B.S.)
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute at City of Hope Medical Center (COHNMC), Duarte, CA 91010, USA; (L.M.); (Y.Z.); (L.Z.); (B.S.)
| | - Heather Hampel
- Clinical Cancer Genetics, City of Hope Medical Center (COHMC), Duarte, CA 91010, USA; (H.H.); (S.S.)
| | - Susan Shehayeb
- Clinical Cancer Genetics, City of Hope Medical Center (COHMC), Duarte, CA 91010, USA; (H.H.); (S.S.)
| | - Stephen Lee
- Division of Gynecologic Oncology and Surgery, City of Hope Medical Center (COHNMC), Duarte, CA 91010, USA; (S.L.); (J.C.); (A.K.)
| | - Joshua Cohen
- Division of Gynecologic Oncology and Surgery, City of Hope Medical Center (COHNMC), Duarte, CA 91010, USA; (S.L.); (J.C.); (A.K.)
| | - Adrian Kohut
- Division of Gynecologic Oncology and Surgery, City of Hope Medical Center (COHNMC), Duarte, CA 91010, USA; (S.L.); (J.C.); (A.K.)
| | - Fang Fan
- Department of Pathology, City of Hope Medical Center (COHNMC), Duarte, CA 91010, USA;
| | - Steven Rosen
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope Medical Center (COHNMC), Duarte, CA 91010, USA;
- Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (X.W.); (Y.Z.)
| | - Xiwei Wu
- Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (X.W.); (Y.Z.)
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute at City of Hope Medical Center (COHNMC), Duarte, CA 91010, USA; (L.M.); (Y.Z.); (L.Z.); (B.S.)
| | - Yuqi Zhao
- Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (X.W.); (Y.Z.)
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96
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Andrade-Brito DE, Núñez-Ríos DL, Martínez-Magaña JJ, Nagamatsu ST, Rompala G, Zillich L, Witt SH, Clark SL, Latig MC, Montalvo-Ortiz JL. Neuronal-specific methylome and hydroxymethylome analysis reveal replicated and novel loci associated with alcohol use disorder. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.28.23299094. [PMID: 38105948 PMCID: PMC10725575 DOI: 10.1101/2023.11.28.23299094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Alcohol use disorder (AUD) is a complex condition associated with adverse health consequences that affect millions of individuals worldwide. Epigenetic modifications, including DNA methylation (5mC), have been associated with AUD and other alcohol-related traits. Epigenome-wide association studies (EWAS) have identified differentially methylated genes associated with AUD in human peripheral and brain tissue. More recently, epigenetic studies of AUD have also evaluated DNA hydroxymethylation (5hmC) in the human brain. However, most of the epigenetic work in postmortem brain tissue has examined bulk tissue. In this study, we investigated neuronal-specific 5mC and 5hmC alterations at CpG sites associated with AUD in the human orbitofrontal cortex (OFC). Neuronal nuclei from the OFC were evaluated in 34 human postmortem brain samples (10 AUD, 24 non-AUD). Reduced representation oxidative bisulfite sequencing was used to assess 5mC and 5hmC at the genome-wide level. Differential 5mC and 5hmC were evaluated using the methylKit R package and significance was set at false discovery rate <0.05 and differential methylation >2. Functional enrichment analyses were performed and replication was evaluated replication in an independent dataset that assessed 5mC and 5hmC of AUD in bulk cortical tissue. We identified 417 5mC and 363 5hmC genome-wide significant differential CpG sites associated with AUD, with 59% in gene promoters. We also identified genes previously implicated in alcohol consumption, such as SYK, CHRM2, DNMT3A, and GATA4, for 5mC and GATA4, and GAD1, GATA4, DLX1 for 5hmC. Replication was observed for 28 CpG sites from a previous AUD 5mC and 5hmC study, including FOXP1. Lastly, GWAS enrichment analysis showed an association with AUD for differential 5mC genes. This study reveals neuronal-specific methylome and hydroxymethylome dysregulation associated with AUD. We replicated previous findings and identified novel associations with AUD for both 5mC and 5hmC marks within the OFC. Our findings provide new insights into the epigenomic dysregulation of AUD in the human brain.
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Affiliation(s)
- Diego E. Andrade-Brito
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- National Center of Post-Traumatic Stress Disorder, VA CT Healthcare, West Haven, CT, USA
| | - Diana L. Núñez-Ríos
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- National Center of Post-Traumatic Stress Disorder, VA CT Healthcare, West Haven, CT, USA
| | - José Jaime Martínez-Magaña
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- National Center of Post-Traumatic Stress Disorder, VA CT Healthcare, West Haven, CT, USA
| | - Sheila T. Nagamatsu
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- National Center of Post-Traumatic Stress Disorder, VA CT Healthcare, West Haven, CT, USA
| | - Gregory Rompala
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Stephanie H. Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Shaunna L. Clark
- Department of Psychiatry & Behavioral Sciences, Texas A&M University, College Station, Texas, USA
| | - Maria C. Latig
- Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia
| | | | - Janitza L. Montalvo-Ortiz
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- National Center of Post-Traumatic Stress Disorder, VA CT Healthcare, West Haven, CT, USA
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97
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Sahu SK, Liu M, Wang G, Chen Y, Li R, Fang D, Sahu DN, Mu W, Wei J, Liu J, Zhao Y, Zhang S, Lisby M, Liu X, Xu X, Li L, Wang S, Liu H, He C. Chromosome-scale genomes of commercially important mahoganies, Swietenia macrophylla and Khaya senegalensis. Sci Data 2023; 10:832. [PMID: 38007506 PMCID: PMC10676371 DOI: 10.1038/s41597-023-02707-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 10/31/2023] [Indexed: 11/27/2023] Open
Abstract
Mahogany species (family Meliaceae) are highly valued for their aesthetic and durable wood. Despite their economic and ecological importance, genomic resources for mahogany species are limited, hindering genetic improvement and conservation efforts. Here we perform chromosome-scale genome assemblies of two commercially important mahogany species: Swietenia macrophylla and Khaya senegalensis. By combining 10X sequencing and Hi-C data, we assemble high-quality genomes of 274.49 Mb (S. macrophylla) and 406.50 Mb (K. senegalensis), with scaffold N50 lengths of 8.51 Mb and 7.85 Mb, respectively. A total of 99.38% and 98.05% of the assembled sequences are anchored to 28 pseudo-chromosomes in S. macrophylla and K. senegalensis, respectively. We predict 34,129 and 31,908 protein-coding genes in S. macrophylla and K. senegalensis, respectively, of which 97.44% and 98.49% are functionally annotated. The chromosome-scale genome assemblies of these mahogany species could serve as a vital genetic resource, especially in understanding the properties of non-model woody plants. These high-quality genomes could support the development of molecular markers for breeding programs, conservation efforts, and the sustainable management of these valuable forest resources.
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Affiliation(s)
- Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150400, China
| | - Guanlong Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- College of Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Ruirui Li
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, Chongqing Normal University, Chongqing, 400047, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Durgesh Nandini Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Weixue Mu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Jinpu Wei
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Jie Liu
- Forestry Bureau of Ruili, Yunnan Dehong, Ruili, 678600, China
| | - Yuxian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Shouzhou Zhang
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518083, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150400, China.
| | - Chengzhong He
- Key Laboratory for Forest Genetic & Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China.
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98
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Gil-Jaramillo N, Aristizábal-Pachón AF, Luque Aleman MA, González Gómez V, Escobar Hurtado HD, Girón Pinto LC, Jaime Camacho JS, Rojas-Cruz AF, González-Giraldo Y, Pinzón A, González J. Competing endogenous RNAs in human astrocytes: crosstalk and interacting networks in response to lipotoxicity. Front Neurosci 2023; 17:1195840. [PMID: 38027526 PMCID: PMC10679742 DOI: 10.3389/fnins.2023.1195840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Neurodegenerative diseases (NDs) are characterized by a progressive deterioration of neuronal function, leading to motor and cognitive damage in patients. Astrocytes are essential for maintaining brain homeostasis, and their functional impairment is increasingly recognized as central to the etiology of various NDs. Such impairment can be induced by toxic insults with palmitic acid (PA), a common fatty acid, that disrupts autophagy, increases reactive oxygen species, and triggers inflammation. Although the effects of PA on astrocytes have been addressed, most aspects of the dynamics of this fatty acid remain unknown. Additionally, there is still no model that satisfactorily explains how astroglia goes from being neuroprotective to neurotoxic. Current incomplete knowledge needs to be improved by the growing field of non-coding RNAs (ncRNAs), which is proven to be related to NDs, where the complexity of the interactions among these molecules and how they control other RNA expressions need to be addressed. In the present study, we present an extensive competing endogenous RNA (ceRNA) network using transcriptomic data from normal human astrocyte (NHA) cells exposed to PA lipotoxic conditions and experimentally validated data on ncRNA interaction. The obtained network contains 7 lncRNA transcripts, 38 miRNAs, and 239 mRNAs that showed enrichment in ND-related processes, such as fatty acid metabolism and biosynthesis, FoxO and TGF-β signaling pathways, prion diseases, apoptosis, and immune-related pathways. In addition, the transcriptomic profile was used to propose 22 potential key controllers lncRNA/miRNA/mRNA axes in ND mechanisms. The relevance of five of these axes was corroborated by the miRNA expression data obtained in other studies. MEG3 (ENST00000398461)/hsa-let-7d-5p/ATF6B axis showed importance in Parkinson's and late Alzheimer's diseases, while AC092687.3/hsa-let-7e-5p/[SREBF2, FNIP1, PMAIP1] and SDCBP2-AS1 (ENST00000446423)/hsa-miR-101-3p/MAPK6 axes are probably related to Alzheimer's disease development and pathology. The presented network and axes will help to understand the PA-induced mechanisms in astrocytes, leading to protection or injury in the CNS under lipotoxic conditions as part of the intricated cellular regulation influencing the pathology of different NDs. Furthermore, the five corroborated axes could be considered study targets for new pharmacologic treatments or as possible diagnostic molecules, contributing to improving the quality of life of millions worldwide.
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Affiliation(s)
- Natalia Gil-Jaramillo
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | | | - María Alejandra Luque Aleman
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Valentina González Gómez
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Hans Deyvy Escobar Hurtado
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Laura Camila Girón Pinto
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Juan Sebastian Jaime Camacho
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Alexis Felipe Rojas-Cruz
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Andrés Pinzón
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
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99
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Imon RR, Aktar S, Morshed N, Nur SM, Mahtarin R, Rahman FA, Talukder MEK, Alam R, Karpiński TM, Ahammad F, Zamzami MA, Tan SC. Biological and clinical significance of the glypican-3 gene in human lung adenocarcinoma: An in silico analysis. Medicine (Baltimore) 2023; 102:e35347. [PMID: 37960765 PMCID: PMC10637541 DOI: 10.1097/md.0000000000035347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/01/2023] [Indexed: 11/15/2023] Open
Abstract
Glypican-3 (GPC3), a membrane-bound heparan sulfate proteoglycan, has long been found to be dysregulated in human lung adenocarcinomas (LUADs). Nevertheless, the function, mutational profile, epigenetic regulation, co-expression profile, and clinicopathological significance of the GPC3 gene in LUAD progression are not well understood. In this study, we analyzed cancer microarray datasets from publicly available databases using bioinformatics tools to elucidate the above parameters. We observed significant downregulation of GPC3 in LUAD tissues compared to their normal counterparts, and this downregulation was associated with shorter overall survival (OS) and relapse-free survival (RFS). Nevertheless, no significant differences in the methylation pattern of GPC3 were observed between LUAD and normal tissues, although lower promoter methylation was observed in male patients. GPC3 expression was also found to correlate significantly with infiltration of B cells, CD8+, CD4+, macrophages, neutrophils, and dendritic cells in LUAD. In addition, a total of 11 missense mutations were identified in LUAD patients, and ~1.4% to 2.2% of LUAD patients had copy number amplifications in GPC3. Seventeen genes, mainly involved in dopamine receptor-mediated signaling pathways, were frequently co-expressed with GPC3. We also found 11 TFs and 7 miRNAs interacting with GPC3 and contributing to disease progression. Finally, we identified 3 potential inhibitors of GPC3 in human LUAD, namely heparitin, gemcitabine and arbutin. In conclusion, GPC3 may play an important role in the development of LUAD and could serve as a promising biomarker in LUAD.
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Affiliation(s)
- Raihan Rahman Imon
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, Bangladesh
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Sharmin Aktar
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, Bangladesh
- Department of Microbiology, Faculty of Biological Science, University of Dhaka, Dhaka, Bangladesh
| | - Niaz Morshed
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, Bangladesh
- Department of Pharmacy, Faculty of Biological Science, University of Dhaka, Dhaka, Bangladesh
| | - Suza Mohammad Nur
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rumana Mahtarin
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, Bangladesh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Farazi Abinash Rahman
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, Bangladesh
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Enamul Kabir Talukder
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, Bangladesh
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Rahat Alam
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, Bangladesh
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Tomasz M. Karpiński
- Chair and Department of Medical Microbiology, Poznań University of Medical Sciences, Wieniawskiego, Poland
| | - Foysal Ahammad
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, Bangladesh
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mazin A. Zamzami
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Artificial Intelligence for Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shing Cheng Tan
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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100
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Dupouy G, Cashell R, Brychkova G, Tuteja R, McKeown PC, Spillane C. PICKLE RELATED 2 is a Neofunctionalized Gene Duplicate Under Positive Selection With Antagonistic Effects to the Ancestral PICKLE Gene on the Seed Transcriptome. Genome Biol Evol 2023; 15:evad191. [PMID: 37931037 PMCID: PMC10630071 DOI: 10.1093/gbe/evad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
The evolution and diversification of proteins capable of remodeling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodeling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis thaliana, yet the basis of this functional divergence remains unknown. In this study, we demonstrate that genes encoding the CHD3 proteins PICKLE (PKL) and PICKLE-RELATED 2 (PKR2) originated from a duplication event during the diversification of crown Brassicaceae, and that these homologs have undergone distinct evolutionary trajectories since this duplication, with PKR2 fast evolving under positive selection, while PKL is subject to purifying selection. We find that the rapid evolution of PKR2 under positive selection reduces the encoded protein's intrinsic disorder, possibly suggesting a tertiary structure configuration which differs from that of PKL. Our whole genome transcriptome analysis in seeds of pkr2 and pkl mutants reveals that they act antagonistically on the expression of specific sets of genes, providing a basis for their differing roles in seed development. Our results provide insights into how gene duplication and neofunctionalization can lead to differing and antagonistic selective pressures on transcriptomes during plant reproduction, as well as on the evolutionary diversification of the CHD3 family within seed plants.
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Affiliation(s)
- Gilles Dupouy
- Genetics and Biotechnology Lab, Agriculture & Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway H91 REW4, Ireland
| | - Ronan Cashell
- Genetics and Biotechnology Lab, Agriculture & Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway H91 REW4, Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Lab, Agriculture & Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway H91 REW4, Ireland
| | - Reetu Tuteja
- Genetics and Biotechnology Lab, Agriculture & Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway H91 REW4, Ireland
| | - Peter C McKeown
- Genetics and Biotechnology Lab, Agriculture & Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway H91 REW4, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Lab, Agriculture & Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway H91 REW4, Ireland
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