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Aschenbrenner D, Nassiri I, Venkateswaran S, Pandey S, Page M, Drowley L, Armstrong M, Kugathasan S, Fairfax B, Uhlig HH. An isoform quantitative trait locus in SBNO2 links genetic susceptibility to Crohn's disease with defective antimicrobial activity. Nat Commun 2024; 15:4529. [PMID: 38806456 PMCID: PMC11133462 DOI: 10.1038/s41467-024-47218-3] [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: 05/05/2023] [Accepted: 03/25/2024] [Indexed: 05/30/2024] Open
Abstract
Despite major advances in linking single genetic variants to single causal genes, the significance of genetic variation on transcript-level regulation of expression, transcript-specific functions, and relevance to human disease has been poorly investigated. Strawberry notch homolog 2 (SBNO2) is a candidate gene in a susceptibility locus with different variants associated with Crohn's disease and bone mineral density. The SBNO2 locus is also differentially methylated in Crohn's disease but the functional mechanisms are unknown. Here we show that the isoforms of SBNO2 are differentially regulated by lipopolysaccharide and IL-10. We identify Crohn's disease associated isoform quantitative trait loci that negatively regulate the expression of the noncanonical isoform 2 corresponding with the methylation signals at the isoform 2 promoter in IBD and CD. The two isoforms of SBNO2 drive differential gene networks with isoform 2 dominantly impacting antimicrobial activity in macrophages. Our data highlight the role of isoform quantitative trait loci to understand disease susceptibility and resolve underlying mechanisms of disease.
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Affiliation(s)
- Dominik Aschenbrenner
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
- Immunology Disease Area, Novartis Biomedical Research, Basel, CH, Switzerland.
| | - Isar Nassiri
- Oxford-GSK Institute of Molecular and Computational Medicine (IMCM), Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Psychiatry, University of Oxford, Oxford, UK
| | | | - Sumeet Pandey
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- GSK Immunology Network, GSK Medicines Research Center, Stevenage, UK
| | - Matthew Page
- Translational Bioinformatics, UCB Pharma, Slough, UK
| | | | | | | | - Benjamin Fairfax
- MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford & Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
- Department of Paediatrics, University of Oxford, Oxford, UK.
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2
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Domínguez-Barragán J, Fernández-Sanlés A, Hernáez Á, Llauradó-Pont J, Marrugat J, Robinson O, Tzoulaki I, Elosua R, Lassale C. Blood DNA methylation signature of diet quality and association with cardiometabolic traits. Eur J Prev Cardiol 2024; 31:191-202. [PMID: 37793095 PMCID: PMC10809172 DOI: 10.1093/eurjpc/zwad317] [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: 05/30/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/06/2023]
Abstract
AIMS Diet quality might influence cardiometabolic health through epigenetic changes, but this has been little investigated in adults. Our aims were to identify cytosine-phosphate-guanine (CpG) dinucleotides associated with diet quality by conducting an epigenome-wide association study (EWAS) based on blood DNA methylation (DNAm) and to assess how diet-related CpGs associate with inherited susceptibility to cardiometabolic traits: body mass index (BMI), systolic blood pressure (SBP), triglycerides, type 2 diabetes (T2D), and coronary heart disease (CHD). METHODS AND RESULTS Meta-EWAS including 5274 participants in four cohorts from Spain, the USA, and the UK. We derived three dietary scores (exposures) to measure adherence to a Mediterranean diet, to a healthy plant-based diet, and to the Dietary Approaches to Stop Hypertension. Blood DNAm (outcome) was assessed with the Infinium arrays Human Methylation 450K BeadChip and MethylationEPIC BeadChip. For each diet score, we performed linear EWAS adjusted for age, sex, blood cells, smoking and technical variables, and BMI in a second set of models. We also conducted Mendelian randomization analyses to assess the potential causal relationship between diet-related CpGs and cardiometabolic traits. We found 18 differentially methylated CpGs associated with dietary scores (P < 1.08 × 10-7; Bonferroni correction), of which 12 were previously associated with cardiometabolic traits. Enrichment analysis revealed overrepresentation of diet-associated genes in pathways involved in inflammation and cardiovascular disease. Mendelian randomization analyses suggested that genetically determined methylation levels corresponding to lower diet quality at cg02079413 (SNORA54), cg02107842 (MAST4), and cg23761815 (SLC29A3) were causally associated with higher BMI and at cg05399785 (WDR8) with greater SBP, and methylation levels associated with higher diet quality at cg00711496 (PRMT1) with lower BMI, T2D risk, and CHD risk and at cg0557921 (AHRR) with lower CHD risk. CONCLUSION Diet quality in adults was related to differential methylation in blood at 18 CpGs, some of which related to cardiometabolic health.
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Affiliation(s)
- Jorge Domínguez-Barragán
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
| | - Alba Fernández-Sanlés
- MRC Unit for Lifelong Health and Ageing, University College London, London WC1E 7HB, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Álvaro Hernáez
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo 0463, Norway
- Blanquerna School of Health Sciences, Universitat Ramon Llull, 08025 Barcelona, Spain
- Consortium for Biomedical Research—Pathophysiology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, Monforte de Lemos 3-5, 08029 Madrid, Spain
| | - Joana Llauradó-Pont
- Barcelona Institute of Global Health (ISGlobal), Dr Aiguader 88, 08003, Barcelona, Spain
| | - Jaume Marrugat
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Oliver Robinson
- μedical Research Council Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Ioanna Tzoulaki
- Centre for Systems Biology, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Roberto Elosua
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, University of Vic—Central University of Catalunya, Ctra. de Roda, 70, 08500 Vic, Spain
| | - Camille Lassale
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Pathophysiology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, Monforte de Lemos 3-5, 08029 Madrid, Spain
- Barcelona Institute of Global Health (ISGlobal), Dr Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003, Barcelona, Spain
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Jo D, Arjunan A, Choi S, Jung YS, Park J, Jo J, Kim OY, Song J. Oligonol ameliorates liver function and brain function in the 5 × FAD mouse model: transcriptional and cellular analysis. Food Funct 2023; 14:9650-9670. [PMID: 37843873 DOI: 10.1039/d3fo03451h] [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: 10/17/2023]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disease worldwide and is accompanied by memory deficits, personality changes, anxiety, depression, and social difficulties. For treatment of AD, many researchers have attempted to find medicinal resources with high effectiveness and without side effects. Oligonol is a low molecular weight polypeptide derived from lychee fruit extract. We investigated the effects of oligonol in 5 × FAD transgenic AD mice, which developed severe amyloid pathology, through behavioral tests (Barnes maze, marble burying, and nestle shredding) and molecular experiments. Oligonol treatment attenuated blood glucose levels and increased the antioxidant response in the livers of 5 × FAD mice. Moreover, the behavioral score data showed improvements in anxiety, depressive behavior, and cognitive impairment following a 2-month course of orally administered oligonol. Oligonol treatment not only altered the circulating levels of cytokines and adipokines in 5 × FAD mice, but also significantly enhanced the mRNA and protein levels of antioxidant enzymes and synaptic plasticity in the brain cortex and hippocampus. Therefore, we highlight the therapeutic potential of oligonol to attenuate neuropsychiatric problems and improve memory deficits in the early stage of AD.
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Affiliation(s)
- Danbi Jo
- Department of Anatomy, Chonnam National University Medical School, Seoyangro 264, Hwasun 58128, Republic of Korea.
- Biomedical Science Graduate Program (BMSGP), Chonnam National University, Seoyangro 264, Hwasun 58128, Republic of Korea
| | - Archana Arjunan
- Department of Anatomy, Chonnam National University Medical School, Seoyangro 264, Hwasun 58128, Republic of Korea.
| | - Seoyoon Choi
- Department of Anatomy, Chonnam National University Medical School, Seoyangro 264, Hwasun 58128, Republic of Korea.
- Biomedical Science Graduate Program (BMSGP), Chonnam National University, Seoyangro 264, Hwasun 58128, Republic of Korea
| | - Yoon Seok Jung
- Department of Anatomy, Chonnam National University Medical School, Seoyangro 264, Hwasun 58128, Republic of Korea.
| | - Jihyun Park
- Department of Food Science and Nutrition, Dong-A University, Nakdong-daero 550 beon-gil, Saha-gu, Busan, 49315, Republic of Korea.
- Department of Health Sciences, Graduate School of Dong-A University, Nakdong-daero 550 beon-gil, Saha-gu, Busan, 49315, Republic of Korea
| | - Jihoon Jo
- Department of Biomedical Science, Chonnam National University Medical School, Seoyangro 264, Hwasun 58128, Republic of Korea.
| | - Oh Yoen Kim
- Department of Food Science and Nutrition, Dong-A University, Nakdong-daero 550 beon-gil, Saha-gu, Busan, 49315, Republic of Korea.
- Department of Health Sciences, Graduate School of Dong-A University, Nakdong-daero 550 beon-gil, Saha-gu, Busan, 49315, Republic of Korea
| | - Juhyun Song
- Department of Anatomy, Chonnam National University Medical School, Seoyangro 264, Hwasun 58128, Republic of Korea.
- Biomedical Science Graduate Program (BMSGP), Chonnam National University, Seoyangro 264, Hwasun 58128, Republic of Korea
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Brandstoetter T, Schmoellerl J, Grausenburger R, Kollmann S, Doma E, Huuhtanen J, Klampfl T, Eder T, Grebien F, Hoermann G, Zuber J, Mustjoki S, Maurer B, Sexl V. SBNO2 is a critical mediator of STAT3-driven hematological malignancies. Blood 2023; 141:1831-1845. [PMID: 36630607 PMCID: PMC10646773 DOI: 10.1182/blood.2022018494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/12/2022] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Gain-of-function mutations in the signal transducer and activator of transcription 3 (STAT3) gene are recurrently identified in patients with large granular lymphocytic leukemia (LGLL) and in some cases of natural killer (NK)/T-cell and adult T-cell leukemia/lymphoma. To understand the consequences and molecular mechanisms contributing to disease development and oncogenic transformation, we developed murine hematopoietic stem and progenitor cell models that express mutated STAT3Y640F. These cells show accelerated proliferation and enhanced self-renewal potential. We integrated gene expression analyses and chromatin occupancy profiling of STAT3Y640F-transformed cells with data from patients with T-LGLL. This approach uncovered a conserved set of direct transcriptional targets of STAT3Y640F. Among these, strawberry notch homolog 2 (SBNO2) represents an essential transcriptional target, which was identified by a comparative genome-wide CRISPR/Cas9-based loss-of-function screen. The STAT3-SBNO2 axis is also present in NK-cell leukemia, T-cell non-Hodgkin lymphoma, and NPM-ALK-rearranged T-cell anaplastic large cell lymphoma (T-ALCL), which are driven by STAT3-hyperactivation/mutation. In patients with NPM-ALK+ T-ALCL, high SBNO2 expression correlates with shorter relapse-free and overall survival. Our findings identify SBNO2 as a potential therapeutic intervention site for STAT3-driven hematopoietic malignancies.
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Affiliation(s)
- Tania Brandstoetter
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Reinhard Grausenburger
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sebastian Kollmann
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Eszter Doma
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Thorsten Klampfl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Eder
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- ICAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Barbara Maurer
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
- University of Innsbruck, Innsbruck, Austria
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Pavlou MAS, Singh K, Ravichandran S, Halder R, Nicot N, Birck C, Grandbarbe L, Del Sol A, Michelucci A. Transcriptional and Chromatin Accessibility Profiling of Neural Stem Cells Differentiating into Astrocytes Reveal Dynamic Signatures Affected under Inflammatory Conditions. Cells 2023; 12:cells12060948. [PMID: 36980289 PMCID: PMC10047363 DOI: 10.3390/cells12060948] [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: 01/18/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Astrocytes arise from multipotent neural stem cells (NSCs) and represent the most abundant cell type of the central nervous system (CNS), playing key roles in the developing and adult brain. Since the differentiation of NSCs towards a gliogenic fate is a precisely timed and regulated process, its perturbation gives rise to dysfunctional astrocytic phenotypes. Inflammation, which often underlies neurological disorders, including neurodevelopmental disorders and brain tumors, disrupts the accurate developmental process of NSCs. However, the specific consequences of an inflammatory environment on the epigenetic and transcriptional programs underlying NSCs' differentiation into astrocytes is unexplored. Here, we address this gap by profiling in mice glial precursors from neural tissue derived from early embryonic stages along their astrocytic differentiation trajectory in the presence or absence of tumor necrosis factor (TNF), a master pro-inflammatory cytokine. By using a combination of RNA- and ATAC-sequencing approaches, together with footprint and integrated gene regulatory network analyses, we here identify key differences during the differentiation of NSCs into astrocytes under physiological and inflammatory settings. In agreement with its role to turn cells resistant to inflammatory challenges, we detect Nrf2 as a master transcription factor supporting the astrocytic differentiation under TNF exposure. Further, under these conditions, we unravel additional transcriptional regulatory hubs, including Stat3, Smad3, Cebpb, and Nfkb2, highlighting the interplay among pathways underlying physiological astrocytic developmental processes and those involved in inflammatory responses, resulting in discrete astrocytic phenotypes. Overall, our study reports key transcriptional and epigenetic changes leading to the identification of molecular regulators of astrocytic differentiation. Furthermore, our analyses provide a valuable resource for understanding inflammation-induced astrocytic phenotypes that might contribute to the development and progression of CNS disorders with an inflammatory component.
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Affiliation(s)
- Maria Angeliki S Pavlou
- Department of Life Sciences and Medicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210 Luxembourg, Luxembourg
| | - Kartikeya Singh
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Srikanth Ravichandran
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Rashi Halder
- Scientific Central Services, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Nathalie Nicot
- Translational Medicine Operations Hub, Luxembourg Institute of Health, L-3555 Dudelange, Luxembourg
- LuxGen Genome Center, Luxembourg Institute of Health & Laboratoire National de Santé, L-3555 Dudelange, Luxembourg
| | - Cindy Birck
- Department of Life Sciences and Medicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Luc Grandbarbe
- Department of Life Sciences and Medicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
- Computational Biology Group, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Alessandro Michelucci
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210 Luxembourg, Luxembourg
- Scientific Central Services, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
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Coppieters N, Scalisi J, Digregorio M, Leparc L, Velazquez Saez L, Lombard A, Rogister B, Neirinckx V. Study of Strawberry Notch homolog 1 and 2 expression in human glioblastoma. J Neurooncol 2023; 161:515-523. [PMID: 36695974 DOI: 10.1007/s11060-023-04240-7] [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: 12/07/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023]
Abstract
PURPOSE In this work, we aimed to comprehensively document the expression of Strawberry Notch homolog (SBNO) 1 and 2 in glioblastoma (GBM) tissue and patient-derived GBM stem-like cell (GSC) cultures. METHODS We investigated SBNO1 and SBNO2 expression at the RNA and protein levels in glioma patient tissue and GSCs, respectively by performing immunostainings and qPCR analyses. We also used publicly-available datasets for assessing SBNO1 and SBNO2 gene expression and related copy number alterations. We used lentiviral transduction of SBNO2 to analyze the effect of its expression in patient-derived GSCs. RESULTS We observed that SBNO2 expression is increased in GBM tissue samples compared to non tumoral brain, or lower-grade gliomas, whereas SBNO1 expression remains unchanged. We hypothesized that such SBNO2 high expression might be linked to copy-number alterations at the level of the 19p13 chromosome section. We located SBNO1 and SBNO2 in different subcellular compartments. Finally, we observed that SBNO2 overexpression induces different phenotypes in different patient-derived GSCs. CONCLUSION These results provide the first characterization of SBNO1 and SBNO2 expression in glioma tissue, and indicate SBNO2 as highly expressed in GBM.
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Affiliation(s)
- Natacha Coppieters
- Laboratory of Nervous System Diseases and Therapy, GIGA Neuroscience, GIGA Institute, University of Liège, Liège, Belgium
| | - Joshua Scalisi
- Laboratory of Nervous System Diseases and Therapy, GIGA Neuroscience, GIGA Institute, University of Liège, Liège, Belgium
| | - Marina Digregorio
- Laboratory of Nervous System Diseases and Therapy, GIGA Neuroscience, GIGA Institute, University of Liège, Liège, Belgium
| | - Louise Leparc
- Laboratory of Nervous System Diseases and Therapy, GIGA Neuroscience, GIGA Institute, University of Liège, Liège, Belgium
| | - Laetitia Velazquez Saez
- Laboratory of Nervous System Diseases and Therapy, GIGA Neuroscience, GIGA Institute, University of Liège, Liège, Belgium
| | - Arnaud Lombard
- Laboratory of Nervous System Diseases and Therapy, GIGA Neuroscience, GIGA Institute, University of Liège, Liège, Belgium
- Neurosurgery Department, University Hospital, University of Liège, Liège, Belgium
| | - Bernard Rogister
- Laboratory of Nervous System Diseases and Therapy, GIGA Neuroscience, GIGA Institute, University of Liège, Liège, Belgium
- Neurology Department, University Hospital, University of Liège, Liège, Belgium
| | - Virginie Neirinckx
- Laboratory of Nervous System Diseases and Therapy, GIGA Neuroscience, GIGA Institute, University of Liège, Liège, Belgium.
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Syme TE, Grill M, Hayashida E, Viengkhou B, Campbell IL, Hofer MJ. Strawberry notch homolog 2 regulates the response to interleukin-6 in the central nervous system. J Neuroinflammation 2022; 19:126. [PMID: 35624480 PMCID: PMC9145108 DOI: 10.1186/s12974-022-02475-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cytokine interleukin-6 (IL-6) modulates a variety of inflammatory processes and, context depending, can mediate either pro- or anti-inflammatory effects. Excessive IL-6 signalling in the brain is associated with chronic inflammation resulting in neurodegeneration. Strawberry notch homolog 2 (Sbno2) is an IL-6-regulated gene whose function is largely unknown. Here we aimed to address this issue by investigating the impact of Sbno2 disruption in mice with IL-6-mediated neuroinflammation. METHODS Mice with germline disruption of Sbno2 (Sbno2-/-) were generated and crossed with transgenic mice with chronic astrocyte production of IL-6 (GFAP-IL6). Phenotypic, molecular and transcriptomic analyses were performed on tissues and primary cell cultures to clarify the role of SBNO2 in IL-6-mediated neuroinflammation. RESULTS We found Sbno2-/- mice to be viable and overtly normal. By contrast GFAP-IL6 × Sbno2-/- mice had more severe disease compared with GFAP-IL6 mice. This was evidenced by exacerbated neuroinflammation and neurodegeneration and enhanced IL-6-responsive gene expression. Cell culture experiments on primary astrocytes from Sbno2-/- mice further showed elevated and sustained transcript levels of a number of IL-6 stimulated genes. Notably, despite enhanced disease in vivo and gene expression both in vivo and in vitro, IL-6-stimulated gp130 pathway activation was reduced when Sbno2 is disrupted. CONCLUSION Based on these results, we propose a role for SBNO2 as a novel negative feedback regulator of IL-6 that restrains the excessive inflammatory actions of this cytokine in the brain.
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Affiliation(s)
- Taylor E Syme
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Magdalena Grill
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, 8010, Graz, Austria
- Division of Phoniatrics, Department of Otorhinolaryngology, Medical University of Graz, 8036, Graz, Austria
| | - Emina Hayashida
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Barney Viengkhou
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Iain L Campbell
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Markus J Hofer
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
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Methylation at CpG sites related to growth differentiation factor-15 was not prospectively associated with cardiovascular death in discordant monozygotic twins. Sci Rep 2022; 12:4410. [PMID: 35292700 PMCID: PMC8924170 DOI: 10.1038/s41598-022-08369-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/07/2022] [Indexed: 11/29/2022] Open
Abstract
Myocardial infarction patients had decreased methylation at four growth differentiating factor-15 (GDF-15) related CpG sites (cg13033858, cg16936953, cg17150809, and cg18608055). These sites had not been studied for their association with cardiovascular disease (CVD) deaths. Thus, we aimed to assess the associations independent of genes, shared environment, and traditional CVD risk factors. Nineteen white, male, monozygotic twin pairs discordant for CVD deaths were included from the National Heart, Lung and Blood Institute Twin Study (NHLBI) initiated in 1969. Data on vital status was collected through December 31, 2014. Methylation of buffy coat DNA at exam 3 (1986–87) was measured using the Illumina HumanMethylation450 BeadChip. Principal component analysis was used to generate a score representing blood leukocyte composition and baseline CVD risk factors and predominated with natural killer cells, CD4+ T cells, and Framingham risk score. Conditional logistic regression demonstrated that methylation at the four CpG sites was not associated with CVD deaths before (all p > 0.05, bootstrapped p > 0.05) and after adjustment for the score (all p > 0.05). Joint influences of cg16936953 and the score were statistically significant (p < 0.05). In conclusion, joint influences of methylation at the site cg16936953 and the score are prospectively associated with CVD deaths independent of germline and common environment. ClinicalTrials.gov Identifier for NHLBI Twin Study: NCT00005124.
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Xia Y, Brewer A, Bell JT. DNA methylation signatures of incident coronary heart disease: findings from epigenome-wide association studies. Clin Epigenetics 2021; 13:186. [PMID: 34627379 PMCID: PMC8501606 DOI: 10.1186/s13148-021-01175-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/19/2021] [Indexed: 12/12/2022] Open
Abstract
Coronary heart disease (CHD) is a type of cardiovascular disease (CVD) that affects the coronary arteries, which provide oxygenated blood to the heart. It is a major cause of mortality worldwide. Various prediction methods have been developed to assess the likelihood of developing CHD, including those based on clinical features and genetic variation. Recent epigenome-wide studies have identified DNA methylation signatures associated with the development of CHD, indicating that DNA methylation may play a role in predicting future CHD. This narrative review summarises recent findings from DNA methylation studies of incident CHD (iCHD) events from epigenome-wide association studies (EWASs). The results suggest that DNA methylation signatures may identify new mechanisms involved in CHD progression and could prove a useful adjunct for the prediction of future CHD.
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Affiliation(s)
- Yujing Xia
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, SE1 7EH, UK
| | - Alison Brewer
- School of Cardiovascular Medicine and Sciences, James Black Centre, King's College London British Heart Foundation Centre of Excellence, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, SE1 7EH, UK.
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Mayneris-Perxachs J, Cardellini M, Hoyles L, Latorre J, Davato F, Moreno-Navarrete JM, Arnoriaga-Rodríguez M, Serino M, Abbott J, Barton RH, Puig J, Fernández-Real X, Ricart W, Tomlinson C, Woodbridge M, Gentileschi P, Butcher SA, Holmes E, Nicholson JK, Pérez-Brocal V, Moya A, Clain DM, Burcelin R, Dumas ME, Federici M, Fernández-Real JM. Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome. MICROBIOME 2021; 9:104. [PMID: 33962692 PMCID: PMC8106161 DOI: 10.1186/s40168-021-01052-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/18/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND The gut microbiome and iron status are known to play a role in the pathophysiology of non-alcoholic fatty liver disease (NAFLD), although their complex interaction remains unclear. RESULTS Here, we applied an integrative systems medicine approach (faecal metagenomics, plasma and urine metabolomics, hepatic transcriptomics) in 2 well-characterised human cohorts of subjects with obesity (discovery n = 49 and validation n = 628) and an independent cohort formed by both individuals with and without obesity (n = 130), combined with in vitro and animal models. Serum ferritin levels, as a markers of liver iron stores, were positively associated with liver fat accumulation in parallel with lower gut microbial gene richness, composition and functionality. Specifically, ferritin had strong negative associations with the Pasteurellaceae, Leuconostocaceae and Micrococcaea families. It also had consistent negative associations with several Veillonella, Bifidobacterium and Lactobacillus species, but positive associations with Bacteroides and Prevotella spp. Notably, the ferritin-associated bacterial families had a strong correlation with iron-related liver genes. In addition, several bacterial functions related to iron metabolism (transport, chelation, heme and siderophore biosynthesis) and NAFLD (fatty acid and glutathione biosynthesis) were also associated with the host serum ferritin levels. This iron-related microbiome signature was linked to a transcriptomic and metabolomic signature associated to the degree of liver fat accumulation through hepatic glucose metabolism. In particular, we found a consistent association among serum ferritin, Pasteurellaceae and Micrococcacea families, bacterial functions involved in histidine transport, the host circulating histidine levels and the liver expression of GYS2 and SEC24B. Serum ferritin was also related to bacterial glycine transporters, the host glycine serum levels and the liver expression of glycine transporters. The transcriptomic findings were replicated in human primary hepatocytes, where iron supplementation also led to triglycerides accumulation and induced the expression of lipid and iron metabolism genes in synergy with palmitic acid. We further explored the direct impact of the microbiome on iron metabolism and liver fact accumulation through transplantation of faecal microbiota into recipient's mice. In line with the results in humans, transplantation from 'high ferritin donors' resulted in alterations in several genes related to iron metabolism and fatty acid accumulation in recipient's mice. CONCLUSIONS Altogether, a significant interplay among the gut microbiome, iron status and liver fat accumulation is revealed, with potential significance for target therapies. Video abstract.
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Affiliation(s)
- Jordi Mayneris-Perxachs
- Department of Endocrinology, Diabetes and Nutrition, Hospital of Girona "Dr Josep Trueta", Girona, Spain
- Departament de Ciències Mèdiques, University of Girona, Girona and Biomedical Research Institute of Girona (IdibGi), Girona, Spain
- CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Girona, Spain
| | - Marina Cardellini
- Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133, Rome, Italy
| | - Lesley Hoyles
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
- Department of Bioscience, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Jèssica Latorre
- Department of Endocrinology, Diabetes and Nutrition, Hospital of Girona "Dr Josep Trueta", Girona, Spain
- Departament de Ciències Mèdiques, University of Girona, Girona and Biomedical Research Institute of Girona (IdibGi), Girona, Spain
- CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Girona, Spain
| | - Francesca Davato
- Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133, Rome, Italy
| | - José Maria Moreno-Navarrete
- Department of Endocrinology, Diabetes and Nutrition, Hospital of Girona "Dr Josep Trueta", Girona, Spain
- Departament de Ciències Mèdiques, University of Girona, Girona and Biomedical Research Institute of Girona (IdibGi), Girona, Spain
- CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Girona, Spain
| | - María Arnoriaga-Rodríguez
- Department of Endocrinology, Diabetes and Nutrition, Hospital of Girona "Dr Josep Trueta", Girona, Spain
- Departament de Ciències Mèdiques, University of Girona, Girona and Biomedical Research Institute of Girona (IdibGi), Girona, Spain
- CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Girona, Spain
| | - Matteo Serino
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
- Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR) 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Team 2: 'Intestinal Risk Factors, Diabetes, Dyslipidemia, and Heart Failure', 31432, Toulouse Cedex 4, France
| | - James Abbott
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Richard H Barton
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Josep Puig
- Department of Endocrinology, Diabetes and Nutrition, Hospital of Girona "Dr Josep Trueta", Girona, Spain
- Departament de Ciències Mèdiques, University of Girona, Girona and Biomedical Research Institute of Girona (IdibGi), Girona, Spain
- CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Girona, Spain
| | | | - Wifredo Ricart
- Department of Endocrinology, Diabetes and Nutrition, Hospital of Girona "Dr Josep Trueta", Girona, Spain
- Departament de Ciències Mèdiques, University of Girona, Girona and Biomedical Research Institute of Girona (IdibGi), Girona, Spain
- CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Girona, Spain
| | - Christopher Tomlinson
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Mark Woodbridge
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | | | - Sarah A Butcher
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Elaine Holmes
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Jeremy K Nicholson
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Vicente Pérez-Brocal
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) and Instituto de Biología Integrativa de Sistemas, Universitat de València and Consejo Superior de Investigaciones Científicas (CSIC), València, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Andrés Moya
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) and Instituto de Biología Integrativa de Sistemas, Universitat de València and Consejo Superior de Investigaciones Científicas (CSIC), València, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Donald Mc Clain
- Department of Internal Medicine, Wake Forest School of Medicine, Winston Salem, NC, 27157, USA
- The W. G. Hefner Veterans Affairs Medical Center, Salisbury, NC, 28144, USA
| | - Rémy Burcelin
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
- Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR) 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Team 2: 'Intestinal Risk Factors, Diabetes, Dyslipidemia, and Heart Failure', 31432, Toulouse Cedex 4, France
| | - Marc-Emmanuel Dumas
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
- Section of Genomic and Environmental Medicine, National Heart & Lung Institute, Imperial College London, Dovehouse Street, London, SW3 6LY, UK
- European Genomic Institute for Diabetes, CNRS UMR 8199, INSERM UMR 1283, Institut Pasteur de Lille, Lille University Hospital, University of Lille, 59045, Lille, France
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montréal, QC, H3A 0G1, Canada
| | - Massimo Federici
- Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133, Rome, Italy
| | - José-Manuel Fernández-Real
- Department of Endocrinology, Diabetes and Nutrition, Hospital of Girona "Dr Josep Trueta", Girona, Spain.
- Departament de Ciències Mèdiques, University of Girona, Girona and Biomedical Research Institute of Girona (IdibGi), Girona, Spain.
- CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Girona, Spain.
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Systematic Identification of Key Functional Modules and Genes in Gastric Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8853348. [PMID: 33282955 PMCID: PMC7685902 DOI: 10.1155/2020/8853348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/14/2020] [Accepted: 10/28/2020] [Indexed: 11/24/2022]
Abstract
Gastric cancer (GC) is associated with high incidence and mortality rates worldwide. Differentially expressed gene (DEG) analysis and weighted gene coexpression network analysis (WGCNA) are important bioinformatic methods for screening core genes. In our study, DEG analysis and WGCNA were combined to screen the hub genes, and pathway enrichment analyses were performed on the DEGs. SBNO2 was identified as the hub gene based on the intersection between the DEGs and the purple module in WGCNA. The expression and prognostic value of SBNO2 were verified in UALCAN, GEPIA2, Human Cancer Metastasis Database, Kaplan–Meier plotter, and TIMER. We identified 1974 DEGs, and 28 modules were uncovered via WGCNA. The purple module was identified as the hub module in WGCNA. SBNO2 was identified as the hub gene, which was upregulated in tumour tissues. Moreover, patients with GC and higher SBNO2 expression had worse prognoses. In addition, SBNO2 was suggested to play an important role in immune cell infiltration. In summary, based on DEGs and key modules related to GC, we identified SBNO2 as a hub gene, thereby offering novel insights into the development and treatment of GC.
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Perron IJ, Keenan BT, Chellappa K, Lahens NF, Yohn NL, Shockley KR, Pack AI, Veasey SC. Dietary challenges differentially affect activity and sleep/wake behavior in mus musculus: Isolating independent associations with diet/energy balance and body weight. PLoS One 2018; 13:e0196743. [PMID: 29746501 PMCID: PMC5945034 DOI: 10.1371/journal.pone.0196743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 04/18/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND AND AIMS Associated with numerous metabolic and behavioral abnormalities, obesity is classified by metrics reliant on body weight (such as body mass index). However, overnutrition is the common cause of obesity, and may independently contribute to these obesity-related abnormalities. Here, we use dietary challenges to parse apart the relative influence of diet and/or energy balance from body weight on various metabolic and behavioral outcomes. MATERIALS AND METHODS Seventy male mice (mus musculus) were subjected to the diet switch feeding paradigm, generating groups with various body weights and energetic imbalances. Spontaneous activity patterns, blood metabolite levels, and unbiased gene expression of the nutrient-sensing ventral hypothalamus (using RNA-sequencing) were measured, and these metrics were compared using standardized multivariate linear regression models. RESULTS Spontaneous activity patterns were negatively related to body weight (p<0.0001) but not diet/energy balance (p = 0.63). Both body weight and diet/energy balance predicted circulating glucose and insulin levels, while body weight alone predicted plasma leptin levels. Regarding gene expression within the ventral hypothalamus, only two genes responded to diet/energy balance (neuropeptide y [npy] and agouti-related peptide [agrp]), while others were related only to body weight. CONCLUSIONS Collectively, these results demonstrate that individual components of obesity-specifically obesogenic diets/energy imbalance and elevated body mass-can have independent effects on metabolic and behavioral outcomes. This work highlights the shortcomings of using body mass-based indices to assess metabolic health, and identifies novel associations between blood biomarkers, neural gene expression, and animal behavior following dietary challenges.
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Affiliation(s)
- Isaac J. Perron
- Center for Sleep and Circadian Neurobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: ,
| | - Brendan T. Keenan
- Center for Sleep and Circadian Neurobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Karthikeyani Chellappa
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nicholas F. Lahens
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nicole L. Yohn
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Keith R. Shockley
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Allan I. Pack
- Center for Sleep and Circadian Neurobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sigrid C. Veasey
- Center for Sleep and Circadian Neurobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Shi LL, Zhang N, Xie XM, Chen YJ, Wang R, Shen L, Zhou JS, Hu JG, Lü HZ. Transcriptome profile of rat genes in injured spinal cord at different stages by RNA-sequencing. BMC Genomics 2017; 18:173. [PMID: 28201982 PMCID: PMC5312572 DOI: 10.1186/s12864-017-3532-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 02/01/2017] [Indexed: 12/15/2022] Open
Abstract
Background Spinal cord injury (SCI) results in fatal damage and currently has no effective treatment. The pathological mechanisms of SCI remain unclear. In this study, genome-wide transcriptional profiling of spinal cord samples from injured rats at different time points after SCI was performed by RNA-Sequencing (RNA-Seq). The transcriptomes were systematically characterized to identify the critical genes and pathways that are involved in SCI pathology. Results RNA-Seq results were obtained from total RNA harvested from the spinal cords of sham control rats and rats in the acute, subacute, and chronic phases of SCI (1 day, 6 days and 28 days after injury, respectively; n = 3 in every group). Compared with the sham-control group, the number of differentially expressed genes was 1797 in the acute phase (1223 upregulated and 574 downregulated), 6590 in the subacute phase (3460 upregulated and 3130 downregulated), and 3499 in the chronic phase (1866 upregulated and 1633 downregulated), with an adjusted P-value <0.05 by DESeq. Gene ontology (GO) enrichment analysis showed that differentially expressed genes were most enriched in immune response, MHC protein complex, antigen processing and presentation, translation-related genes, structural constituent of ribosome, ion gated channel activity, small GTPase mediated signal transduction and cytokine and/or chemokine activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the most enriched pathways included ribosome, antigen processing and presentation, retrograde endocannabinoid signaling, axon guidance, dopaminergic synapses, glutamatergic synapses, GABAergic synapses, TNF, HIF-1, Toll-like receptor, NF-kappa B, NOD-like receptor, cAMP, calcium, oxytocin, Rap1, B cell receptor and chemokine signaling pathway. Conclusions This study has not only characterized changes in global gene expression through various stages of SCI progression in rats, but has also systematically identified the critical genes and signaling pathways in SCI pathology. These results will expand our understanding of the complex molecular mechanisms involved in SCI and provide a foundation for future studies of spinal cord tissue damage and repair. The sequence data from this study have been deposited into Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra; accession number PRJNA318311). Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3532-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ling-Ling Shi
- Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People's Republic of China.,Department of Immunology, Bengbu Medical College, Anhui, 233030, People's Republic of China
| | - Nan Zhang
- Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China
| | - Xiu-Mei Xie
- Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People's Republic of China.,Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China
| | - Yue-Juan Chen
- Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People's Republic of China.,Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China
| | - Rui Wang
- Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China
| | - Lin Shen
- Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People's Republic of China.,Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China
| | - Jian-Sheng Zhou
- Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China
| | - Jian-Guo Hu
- Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People's Republic of China. .,Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China.
| | - He-Zuo Lü
- Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People's Republic of China. .,Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Anhui, 233004, People's Republic of China. .,Department of Immunology, Bengbu Medical College, Anhui, 233030, People's Republic of China.
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Brzezinka K, Altmann S, Czesnick H, Nicolas P, Gorka M, Benke E, Kabelitz T, Jähne F, Graf A, Kappel C, Bäurle I. Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling. eLife 2016; 5:e17061. [PMID: 27680998 DOI: 10.7554/elife.17061.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/25/2016] [Indexed: 05/21/2023] Open
Abstract
Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that promotes a more efficient response to recurring stress. We show that this heat stress memory requires the activity of the FORGETTER1 (FGT1) locus, with fgt1 mutants displaying reduced maintenance of heat-induced gene expression. FGT1 encodes the Arabidopsis thaliana orthologue of Strawberry notch (Sno), and the protein globally associates with the promoter regions of actively expressed genes in a heat-dependent fashion. FGT1 interacts with chromatin remodelers of the SWI/SNF and ISWI families, which also display reduced heat stress memory. Genomic targets of the BRM remodeler overlap significantly with FGT1 targets. Accordingly, nucleosome dynamics at loci with altered maintenance of heat-induced expression are affected in fgt1. Together, our results suggest that by modulating nucleosome occupancy, FGT1 mediates stress-induced chromatin memory.
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Affiliation(s)
- Krzysztof Brzezinka
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Simone Altmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Hjördis Czesnick
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Philippe Nicolas
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michal Gorka
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Eileen Benke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Tina Kabelitz
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Felix Jähne
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Alexander Graf
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Brzezinka K, Altmann S, Czesnick H, Nicolas P, Gorka M, Benke E, Kabelitz T, Jähne F, Graf A, Kappel C, Bäurle I. Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling. eLife 2016; 5:e17061. [PMID: 27680998 DOI: 10.7554/elife.17061.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/25/2016] [Indexed: 05/24/2023] Open
Abstract
Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that promotes a more efficient response to recurring stress. We show that this heat stress memory requires the activity of the FORGETTER1 (FGT1) locus, with fgt1 mutants displaying reduced maintenance of heat-induced gene expression. FGT1 encodes the Arabidopsis thaliana orthologue of Strawberry notch (Sno), and the protein globally associates with the promoter regions of actively expressed genes in a heat-dependent fashion. FGT1 interacts with chromatin remodelers of the SWI/SNF and ISWI families, which also display reduced heat stress memory. Genomic targets of the BRM remodeler overlap significantly with FGT1 targets. Accordingly, nucleosome dynamics at loci with altered maintenance of heat-induced expression are affected in fgt1. Together, our results suggest that by modulating nucleosome occupancy, FGT1 mediates stress-induced chromatin memory.
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Affiliation(s)
- Krzysztof Brzezinka
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Simone Altmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Hjördis Czesnick
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Philippe Nicolas
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michal Gorka
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Eileen Benke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Tina Kabelitz
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Felix Jähne
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Alexander Graf
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Brzezinka K, Altmann S, Czesnick H, Nicolas P, Gorka M, Benke E, Kabelitz T, Jähne F, Graf A, Kappel C, Bäurle I. Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling. eLife 2016; 5. [PMID: 27680998 PMCID: PMC5040591 DOI: 10.7554/elife.17061] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/25/2016] [Indexed: 12/28/2022] Open
Abstract
Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that promotes a more efficient response to recurring stress. We show that this heat stress memory requires the activity of the FORGETTER1 (FGT1) locus, with fgt1 mutants displaying reduced maintenance of heat-induced gene expression. FGT1 encodes the Arabidopsis thaliana orthologue of Strawberry notch (Sno), and the protein globally associates with the promoter regions of actively expressed genes in a heat-dependent fashion. FGT1 interacts with chromatin remodelers of the SWI/SNF and ISWI families, which also display reduced heat stress memory. Genomic targets of the BRM remodeler overlap significantly with FGT1 targets. Accordingly, nucleosome dynamics at loci with altered maintenance of heat-induced expression are affected in fgt1. Together, our results suggest that by modulating nucleosome occupancy, FGT1 mediates stress-induced chromatin memory. DOI:http://dx.doi.org/10.7554/eLife.17061.001 In nature, plant growth is often limited by unfavourable conditions or disease. Plants have thus evolved sophisticated mechanisms to adapt to such stresses. In fact, brief exposure to stress can prime plants to be better prepared for a future stress following a period without stress. However, the molecular basis of this memory-like phenomenon is poorly understood. Now, Brzezinka, Altmann et al. have used priming by heat stress as a model to dissect the memory of environmental stresses in thale cress, Arabidopsis thaliana. First, a library of mutant plants were tested to identify a gene that is specifically required for heat stress memory but not for the initial responses to heat. Brzezinka, Altmann et al. identified one such gene and termed it FORGETTER1 (or FGT1 for short). Further experiments then revealed that the FGT1 protein binds directly to a specific class of heat-inducible genes that are relevant for heat stress memory. Brzezinka, Altmann et al. propose that the FGT1 protein makes sure that the heat-inducible genes are always accessible and active by modifying the way the DNA containing these genes is packaged. DNA is wrapped around protein complexes called nucleosomes and depending on how tightly the DNA of a gene is wrapped makes it more or less easy to activate the gene. In agreement with this model, FGT1 does interact with proteins that can reposition nucleosomes and leave the DNA more loosely packaged. Also, the fact that plants that lack a working FGT1 gene repackage the DNA of memory-related genes too early after experiencing heat stress provides further support for the model. Together these findings could lead to new approaches for breeding programmes to improve stress tolerance in crop plants. One future challenge will be to find out whether memories involving nucleosomes are also made in response to other stressful conditions, such as attack by pests and disease. DOI:http://dx.doi.org/10.7554/eLife.17061.002
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Affiliation(s)
- Krzysztof Brzezinka
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Simone Altmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Hjördis Czesnick
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Philippe Nicolas
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michal Gorka
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Eileen Benke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Tina Kabelitz
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Felix Jähne
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Alexander Graf
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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17
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Cai Z, Zhao B, Deng Y, Shangguan S, Zhou F, Zhou W, Li X, Li Y, Chen G. Notch signaling in cerebrovascular diseases (Review). Mol Med Rep 2016; 14:2883-98. [PMID: 27574001 PMCID: PMC5042775 DOI: 10.3892/mmr.2016.5641] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 07/22/2016] [Indexed: 12/30/2022] Open
Abstract
The Notch signaling pathway is a crucial regulator of numerous fundamental cellular processes. Increasing evidence suggests that Notch signaling is involved in inflammation and oxidative stress, and thus in the progress of cerebrovascular diseases. In addition, Notch signaling in cerebrovascular diseases is associated with apoptosis, angiogenesis and the function of blood-brain barrier. Despite the contradictory results obtained to date as to whether Notch signaling is harmful or beneficial, the regulation of Notch signaling may provide a novel strategy for the treatment of cerebrovascular diseases.
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Affiliation(s)
- Zhiyou Cai
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Bin Zhao
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Yanqing Deng
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Shouqin Shangguan
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Faming Zhou
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Wenqing Zhou
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Xiaoli Li
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Yanfeng Li
- Department of Neurology, Peking Union Medical College Hospital, Beijing 100730, P.R. China
| | - Guanghui Chen
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
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