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Captur G, Moon JC, Topriceanu CC, Joy G, Swadling L, Hallqvist J, Doykov I, Patel N, Spiewak J, Baldwin T, Hamblin M, Menacho K, Fontana M, Treibel TA, Manisty C, O'Brien B, Gibbons JM, Pade C, Brooks T, Altmann DM, Boyton RJ, McKnight Á, Maini MK, Noursadeghi M, Mills K, Heywood WE. Plasma proteomic signature predicts who will get persistent symptoms following SARS-CoV-2 infection. EBioMedicine 2022; 85:104293. [PMID: 36182629 PMCID: PMC9515404 DOI: 10.1016/j.ebiom.2022.104293] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/27/2022] [Accepted: 09/16/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The majority of those infected by ancestral Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) during the UK first wave (starting March 2020) did not require hospitalisation. Most had a short-lived mild or asymptomatic infection, while others had symptoms that persisted for weeks or months. We hypothesized that the plasma proteome at the time of first infection would reflect differences in the inflammatory response that linked to symptom severity and duration. METHODS We performed a nested longitudinal case-control study and targeted analysis of the plasma proteome of 156 healthcare workers (HCW) with and without lab confirmed SARS-CoV-2 infection. Targeted proteomic multiple-reaction monitoring analysis of 91 pre-selected proteins was undertaken in uninfected healthcare workers at baseline, and in infected healthcare workers serially, from 1 week prior to 6 weeks after their first confirmed SARS-CoV-2 infection. Symptom severity and antibody responses were also tracked. Questionnaires at 6 and 12 months collected data on persistent symptoms. FINDINGS Within this cohort (median age 39 years, interquartile range 30-47 years), 54 healthcare workers (44% male) had PCR or antibody confirmed infection, with the remaining 102 (38% male) serving as uninfected controls. Following the first confirmed SARS-CoV-2 infection, perturbation of the plasma proteome persisted for up to 6 weeks, tracking symptom severity and antibody responses. Differentially abundant proteins were mostly coordinated around lipid, atherosclerosis and cholesterol metabolism pathways, complement and coagulation cascades, autophagy, and lysosomal function. The proteomic profile at the time of seroconversion associated with persistent symptoms out to 12 months. Data are available via ProteomeXchange with identifier PXD036590. INTERPRETATION Our findings show that non-severe SARS-CoV-2 infection perturbs the plasma proteome for at least 6 weeks. The plasma proteomic signature at the time of seroconversion has the potential to identify which individuals are more likely to suffer from persistent symptoms related to SARS-CoV-2 infection. FUNDING INFORMATION The COVIDsortium is supported by funding donated by individuals, charitable Trusts, and corporations including Goldman Sachs, Citadel and Citadel Securities, The Guy Foundation, GW Pharmaceuticals, Kusuma Trust, and Jagclif Charitable Trust, and enabled by Barts Charity with support from University College London Hospitals (UCLH) Charity. This work was additionally supported by the Translational Mass Spectrometry Research Group and the Biomedical Research Center (BRC) at Great Ormond Street Hospital.
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Affiliation(s)
- Gabriella Captur
- UCL MRC Unit for Lifelong Health and Ageing, 33 Bedford Place, London WC1B 5JU, UK; Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; The Royal Free Hospital, Center for Inherited Heart Muscle Conditions, Cardiology Department, Pond Street, Hampstead, London NW3 2QG, UK
| | - James C Moon
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; Barts Heart Center, The Cardiovascular Magnetic Resonance Imaging Unit and The Inherited Cardiovascular Diseases Unit, St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - Constantin-Cristian Topriceanu
- UCL MRC Unit for Lifelong Health and Ageing, 33 Bedford Place, London WC1B 5JU, UK; Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK
| | - George Joy
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; Barts Heart Center, The Cardiovascular Magnetic Resonance Imaging Unit and The Inherited Cardiovascular Diseases Unit, St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - Leo Swadling
- Division of Infection and Immunity, University College London, London WC1E 6JF, UK
| | - Jenny Hallqvist
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Ivan Doykov
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Nina Patel
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Justyna Spiewak
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Tomas Baldwin
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Matt Hamblin
- Barts Heart Center, The Cardiovascular Magnetic Resonance Imaging Unit and The Inherited Cardiovascular Diseases Unit, St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - Katia Menacho
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; Barts Heart Center, The Cardiovascular Magnetic Resonance Imaging Unit and The Inherited Cardiovascular Diseases Unit, St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - Marianna Fontana
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; The Royal Free Hospital, Cardiac MRI Unit, Pond Street, Hampstead, London NW3 2QG, UK
| | - Thomas A Treibel
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; Barts Heart Center, The Cardiovascular Magnetic Resonance Imaging Unit and The Inherited Cardiovascular Diseases Unit, St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - Charlotte Manisty
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; Barts Heart Center, The Cardiovascular Magnetic Resonance Imaging Unit and The Inherited Cardiovascular Diseases Unit, St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - Ben O'Brien
- Department of Perioperative Medicine, St. Bartholomew's Hospital, Barts Health NHS Trust, West Smithfield, London EC1A 7BE, UK; Department of Cardiac Anesthesiology and Intensive Care Medicine, German Heart Center, Augustenburger Platz 1, 13353 Berlin, Germany; Department of Cardiac Anesthesiology and Intensive Care Medicine, Charité Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Outcomes Research Consortium, Department of Outcomes Research, The Cleveland Clinic, 9500 Euclid Ave P77, Cleveland, OH 44195, USA
| | - Joseph M Gibbons
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Corrina Pade
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Tim Brooks
- National Infection Service, Public Health England, Porton Down, UK
| | - Daniel M Altmann
- Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - Rosemary J Boyton
- Department of Infectious Disease, Imperial College London, London SW7 2AZ, UK; Lung Division, Royal Brompton Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London SW3 6NP, UK
| | - Áine McKnight
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Mala K Maini
- Division of Infection and Immunity, University College London, London WC1E 6JF, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London WC1E 6JF, UK
| | - Kevin Mills
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Wendy E Heywood
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK.
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Ooka T, Raita Y, Fujiogi M, Freishtat RJ, Gerszten RE, Mansbach JM, Zhu Z, Camargo CA, Hasegawa K. Proteomics endotyping of infants with severe bronchiolitis and risk of childhood asthma. Allergy 2022; 77:3350-3361. [PMID: 35620861 PMCID: PMC9617778 DOI: 10.1111/all.15390] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/10/2022] [Accepted: 05/18/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND Bronchiolitis is the leading cause of hospitalization in U.S. infants and a major risk factor for childhood asthma. Growing evidence supports clinical heterogeneity within bronchiolitis. We aimed to identify endotypes of infant bronchiolitis by integrating clinical, virus, and serum proteome data, and examine their relationships with asthma development. METHODS This is a multicenter prospective cohort study of infants hospitalized for physician-diagnosis of bronchiolitis. We identified bronchiolitis endotypes by applying unsupervised machine learning (clustering) approaches to integrated clinical, virus (respiratory syncytial virus [RSV], rhinovirus [RV]), and serum proteome data measured at hospitalization. We then examined their longitudinal association with the risk for developing asthma by age 6 years. RESULTS In 140 infants hospitalized with bronchiolitis, we identified three endotypes: (1) clinicalatopic virusRV proteomeNFκB-dysregulated , (2) clinicalnon-atopic virusRSV/RV proteomeTNF-dysregulated , and (3) clinicalclassic virusRSV proteomeNFκB/TNF-regulated endotypes. Endotype 1 infants were characterized by high proportion of IgE sensitization and RV infection. These endotype 1 infants also had dysregulated NFκB pathways (FDR < 0.001) and significantly higher risks for developing asthma (53% vs. 22%; adjOR 4.04; 95% CI, 1.49-11.0; p = 0.006), compared with endotype 3 (clinically resembling "classic" bronchiolitis). Likewise, endotype 2 infants were characterized by low proportion of IgE sensitization and high proportion of RSV or RV infection. These endotype 2 infants had dysregulated tumor necrosis factor (TNF)-mediated signaling pathway (FDR <0.001) and significantly higher risks for developing asthma (44% vs. 22%; adjOR 2.71; 95% CI, 1.03-7.11, p = 0.04). CONCLUSION In this multicenter cohort, integrated clustering of clinical, virus, and proteome data identified biologically distinct endotypes of bronchiolitis that have differential risks of asthma development.
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Affiliation(s)
- Tadao Ooka
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Health Science, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Yoshihiko Raita
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michimasa Fujiogi
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Robert J. Freishtat
- Center for Genetic Medicine Research and Division of Emergency Medicine Children’s National Hospital. Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine and Cardiovascular Institute, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Jonathan M. Mansbach
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Carlos A. Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Tiwari R, Bommi PV, Gao P, Schipma MJ, Zhou Y, Quaggin SE, Chandel NS, Kapitsinou PP. Chemical inhibition of oxygen-sensing prolyl hydroxylases impairs angiogenic competence of human vascular endothelium through metabolic reprogramming. iScience 2022; 25:105086. [PMID: 36157579 PMCID: PMC9494243 DOI: 10.1016/j.isci.2022.105086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/24/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Endothelial cell (EC) metabolism has emerged as a driver of angiogenesis. While hypoxia inactivates the oxygen sensors prolyl-4 hydroxylase domain-containing proteins 1-3 (PHD1-3) and stimulates angiogenesis, the effects of PHDs on EC functions remain poorly defined. Here, we investigated the impact of chemical PHD inhibition by dimethyloxalylglycine (DMOG) on angiogenic competence and metabolism of human vascular ECs. DMOG reduced EC proliferation, migration, and tube formation capacities, responses that were associated with an unfavorable metabolic reprogramming. While glycolytic genes were induced, multiple genes encoding sub-units of mitochondrial complex I were suppressed with concurrent decline in nicotinamide adenine dinucleotide (NAD+) levels. Importantly, the DMOG-induced defects in EC migration could be partially rescued by augmenting NAD+ levels through nicotinamide riboside or citrate supplementation. In summary, by integrating functional assays, transcriptomics, and metabolomics, we provide insights into the effects of PHD inhibition on angiogenic competence and metabolism of human vascular ECs.
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Affiliation(s)
- Ratnakar Tiwari
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, 303 East Superior Street, SQBRC 8-408, Chicago, 60611 IL, USA
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Prashant V. Bommi
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, 303 East Superior Street, SQBRC 8-408, Chicago, 60611 IL, USA
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Peng Gao
- Department of Medicine and Robert H. Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Matthew J. Schipma
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yalu Zhou
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, 303 East Superior Street, SQBRC 8-408, Chicago, 60611 IL, USA
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Susan E. Quaggin
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, 303 East Superior Street, SQBRC 8-408, Chicago, 60611 IL, USA
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Navdeep S. Chandel
- Department of Medicine and Robert H. Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pinelopi P. Kapitsinou
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, 303 East Superior Street, SQBRC 8-408, Chicago, 60611 IL, USA
- Division of Nephrology & Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Medicine and Robert H. Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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154
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Banimfreg BH, Shamayleh A, Alshraideh H. Survey for Computer-Aided Tools and Databases in Metabolomics. Metabolites 2022; 12:metabo12101002. [PMID: 36295904 PMCID: PMC9610953 DOI: 10.3390/metabo12101002] [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: 09/10/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/14/2022] Open
Abstract
Metabolomics has advanced from innovation and functional genomics tools and is currently a basis in the big data-led precision medicine era. Metabolomics is promising in the pharmaceutical field and clinical research. However, due to the complexity and high throughput data generated from such experiments, data mining and analysis are significant challenges for researchers in the field. Therefore, several efforts were made to develop a complete workflow that helps researchers analyze data. This paper introduces a review of the state-of-the-art computer-aided tools and databases in metabolomics established in recent years. The paper provides computational tools and resources based on functionality and accessibility and provides hyperlinks to web pages to download or use. This review aims to present the latest computer-aided tools, databases, and resources to the metabolomics community in one place.
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Emerald BS, Al Jailani MA, Ibrahim MF, Kumar CA, Allouh MZ. Cellular and Molecular Variations in Male and Female Murine Skeletal Muscle after Long-Term Feeding with a High-Fat Diet. Int J Mol Sci 2022; 23:ijms23179547. [PMID: 36076943 PMCID: PMC9455932 DOI: 10.3390/ijms23179547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Current information regarding the effects of a high-fat diet (HFD) on skeletal muscle is contradictory. This study aimed to investigate the effects of a long-term HFD on skeletal muscle in male and female mice at the morphological, cellular, and molecular levels. Adult mice of the C57BL/6 strain were fed standard chow or an HFD for 20 weeks. The tibialis anterior muscles were dissected, weighed, and processed for cellular and molecular analyses. Immunocytochemical and morphometric techniques were applied to quantify fiber size, satellite cells (SCs), and myonuclei. Additionally, PCR array and RT-qPCR tests were performed to determine the expression levels of key muscle genes. Muscles from HFD mice showed decreases in weight, SCs, and myonuclei, consistent with the atrophic phenotype. This atrophy was associated with a decrease in the percentage of oxidative fibers within the muscle. These findings were further confirmed by molecular analyses that showed significant reductions in the expression of Pax7, Myh1, and Myh2 genes and increased Mstn gene expression. Male and female mice showed similar trends in response to HFD-induced obesity. These findings indicate that the long-term effects of obesity on skeletal muscle resemble those of age-related sarcopenia.
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156
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Zhou W, Jiang X, Tan X, Li D, Wang H, You J, Li X, Zhang M. Transcriptome analysis provides novel insights into the soil amendments induced response in continuously cropped Codonopsis tangshen. FRONTIERS IN PLANT SCIENCE 2022; 13:972804. [PMID: 36035706 PMCID: PMC9413139 DOI: 10.3389/fpls.2022.972804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Codonopsis tangshen Oliv (C. tangshen) is an important Chinese traditional medicinal plant with various health benefits. However, the growth of C. tangshen are seriously affected by continuous cropping, which led to the decrease of the yield and quality. A field experiment was conducted to learn the effects of soil amendments on the growth of C. tangshen under continuous cropping condition, and the biological events which occurred at molecular level were investigated. The results indicated that the content of chlorophyll a (Chl a), chlorophyll b (Chl b), and carotenoid (Car) was significantly higher in SCPM (silicon-calcium-potassium-magnesium fertilizer), SCPMA (SCPM combined with azoxystrobin) and SCPMAOM (SCPM combined with azoxystrobin and organic manure) treatments. Moreover, the yield and the levels of alkaloid, polysaccharide, flavone and total protein in the treatments of SCPM, SCPMA and SCPMAOM were significantly higher than those in the control, and these indexes were all highest in the SCPMAOM treatment. RNA-sequencing (RNA-Seq) is an economical and efficient method to obtain genetic information for species with or without available genome data. In this study, RNA-Seq was performed to understand how continuously cropped C. tangshen responded to the soil amendments at the transcriptome level. The number of differentially expressed genes (DEGs) were as follows: CK vs. SCPM (719 up- and 1456 down-), CK vs. SCPMA (1302 up- and 1748 down-), CK vs. SCPMAOM (1274 up- and 1678 down-). The soil amendments affected the growth of C. tangshen mainly by regulating the genes involved in pathways of 'photosynthesis,' 'plant hormone signal transduction,' 'biosynthesis of unsaturated fatty acids,' 'phenylpropanoid biosynthesis,' and 'starch and sucrose metabolism,' etc. qRT-PCR was performed to validate the expressions of 10 target genes such as CP26, PsaF, and POX, etc., which verified the reliability of RNA-Seq results. Overall, this study revealed the roles and underlying mechanisms of the soil amendments in regulating the growth of continuously cropped C. tangshen at transcriptome level. These findings are beneficial for improving the continuous cropping tolerance and may be valuable for future genetic improvement of C. tangshen.
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Floudas A, Smith CM, Tynan O, Neto N, Krishna V, Wade SM, Hanlon M, Cunningham C, Marzaioli V, Canavan M, Fletcher JM, Mullan RH, Cole S, Hao LY, Monaghan MG, Nagpal S, Veale DJ, Fearon U. Distinct stromal and immune cell interactions shape the pathogenesis of rheumatoid and psoriatic arthritis. Ann Rheum Dis 2022; 81:1224-1242. [PMID: 35701153 DOI: 10.1136/annrheumdis-2021-221761] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/12/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Immune and stromal cell communication is central in the pathogenesis of rheumatoid arthritis (RA) and psoriatic arthritis (PsA), however, the nature of these interactions in the synovial pathology of the two pathotypes can differ. Identifying immune-stromal cell crosstalk at the site of inflammation in RA and PsA is challenging. This study creates the first global transcriptomic analysis of the RA and PsA inflamed joint and investigates immune-stromal cell interactions in the pathogenesis of synovial inflammation. METHODS Single cell transcriptomic profiling of 178 000 synovial tissue cells from five patients with PsA and four patients with RA, importantly, without prior sorting of immune and stromal cells. This approach enabled the transcriptomic analysis of the intact synovial tissue and identification of immune and stromal cell interactions. State of the art data integration and annotation techniques identified and characterised 18 stromal and 14 immune cell clusters. RESULTS Global transcriptomic analysis of synovial cell subsets identifies actively proliferating synovial T cells and indicates that due to differential λ and κ immunoglobulin light chain usage, synovial plasma cells are potentially not derived from the local memory B cell pool. Importantly, we report distinct fibroblast and endothelial cell transcriptomes indicating abundant subpopulations in RA and PsA characterised by differential transcription factor usage. Using receptor-ligand interactions and downstream target characterisation, we identify RA-specific synovial T cell-derived transforming growth factor (TGF)-β and macrophage interleukin (IL)-1β synergy in driving the transcriptional profile of FAPα+THY1+ invasive synovial fibroblasts, expanded in RA compared with PsA. In vitro characterisation of patient with RA synovial fibroblasts showed metabolic switch to glycolysis, increased adhesion intercellular adhesion molecules 1 expression and IL-6 secretion in response to combined TGF-β and IL-1β treatment. Disrupting specific immune and stromal cell interactions offers novel opportunities for targeted therapeutic intervention in RA and PsA.
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Affiliation(s)
- Achilleas Floudas
- Molecular Rheumatology, Clinical Medicine, Trinity Biomedical Science Institute, Dublin, Ireland
- Eular Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, Univeristy College Dublin, Dublin, Ireland
| | - Conor M Smith
- Translational Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Orla Tynan
- Molecular Rheumatology, Clinical Medicine, Trinity Biomedical Science Institute, Dublin, Ireland
- Eular Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, Univeristy College Dublin, Dublin, Ireland
| | - Nuno Neto
- Department of Mechanical and Manufacturing Engineering, Trinity College Dublin, Dublin, Ireland
| | - Vinod Krishna
- Immunology, Janssen Research & Development, Spring House, PA, USA
| | - Sarah M Wade
- Molecular Rheumatology, Clinical Medicine, Trinity Biomedical Science Institute, Dublin, Ireland
- Eular Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, Univeristy College Dublin, Dublin, Ireland
| | - Megan Hanlon
- Molecular Rheumatology, Clinical Medicine, Trinity Biomedical Science Institute, Dublin, Ireland
- Eular Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, Univeristy College Dublin, Dublin, Ireland
| | - Clare Cunningham
- Molecular Rheumatology, Clinical Medicine, Trinity Biomedical Science Institute, Dublin, Ireland
- Eular Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, Univeristy College Dublin, Dublin, Ireland
| | - Viviana Marzaioli
- Molecular Rheumatology, Clinical Medicine, Trinity Biomedical Science Institute, Dublin, Ireland
- Eular Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, Univeristy College Dublin, Dublin, Ireland
| | - Mary Canavan
- Molecular Rheumatology, Clinical Medicine, Trinity Biomedical Science Institute, Dublin, Ireland
- Eular Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, Univeristy College Dublin, Dublin, Ireland
| | - Jean M Fletcher
- Translational Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Ronan H Mullan
- Department of Rheumatology, Tallaght University Hospital, Trinity College Dublin, Dublin, Ireland
| | - Suzanne Cole
- Immunology, Janssen Research & Development, Spring House, PA, USA
| | - Ling-Yang Hao
- Immunology, Janssen Research & Development, Spring House, PA, USA
| | - Michael G Monaghan
- Department of Mechanical and Manufacturing Engineering, Trinity College Dublin, Dublin, Ireland
| | - Sunil Nagpal
- Immunology, Janssen Research & Development, Spring House, PA, USA
| | - Douglas J Veale
- Eular Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, Univeristy College Dublin, Dublin, Ireland
| | - Ursula Fearon
- Molecular Rheumatology, Clinical Medicine, Trinity Biomedical Science Institute, Dublin, Ireland
- Eular Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, Univeristy College Dublin, Dublin, Ireland
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Palazzo A, Hernandez-Vargas H, Goehrig D, Médard JJ, Vindrieux D, Flaman JM, Bernard D. Transformed cells after senescence give rise to more severe tumor phenotypes than transformed non-senescent cells. Cancer Lett 2022; 546:215850. [DOI: 10.1016/j.canlet.2022.215850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022]
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Signaling Pathways Associated with Chronic Wound Progression: A Systems Biology Approach. Antioxidants (Basel) 2022; 11:antiox11081506. [PMID: 36009225 PMCID: PMC9404828 DOI: 10.3390/antiox11081506] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022] Open
Abstract
Previously we have shown that several oxidative stress-driven pathways in cutaneous chronic wounds are dysregulated in the first 48 h post-wounding. Here, we performed an RNASeq analysis of tissues collected up to day 20 after wounding, when we have determined full chronicity is established. Weighted Gene Correlation Network Analysis was performed in R segregating the genes into 14 modules. Genes in the modules significantly correlated (p < 0.05) to early and full chronicity were used for pathway analysis using pathfindR. In early chronicity, we observed enrichment of several pathways. Dysregulation of Ephrin/Eph signaling leads to growth cone collapse and impairs neuronal regeneration. Adra2b and Adra2a overexpression in early and full chronicity, respectively, decreased cAMP production and impaired re-epithelialization and granulation tissue formation. Several pathways involving a Smooth-muscle-actin (Acta1) were also enriched with Acta1 overexpression contributing to impaired angiogenesis. During full chronicity, the ‘JAK-STAT’ pathway was suppressed undermining host defenses against infection. Wnt signaling was also suppressed, impairing re-epithelialization and granulation tissue formation. Biomarkers of cancer such as overexpression of SDC1 and constitutive activation of ErbB2/HER2 were also identified. In conclusion, we show that during progression to full chronicity, numerous signaling pathways are dysregulated, including some related to carcinogenesis, suggesting that chronic wounds behave much like cancer. Experimental verification in vivo could identify candidates for treatment of chronic wounds.
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Autin P, Deshayes S, Lea J, Boisgerault N, Dupré E, Labarrière N, Leguevel R, Fonteneau JF, Blanquart C, Fradin D. The DCMU Herbicide Shapes T-cell Functions By Modulating Micro-RNA Expression Profiles. Front Immunol 2022; 13:925241. [PMID: 35967413 PMCID: PMC9366666 DOI: 10.3389/fimmu.2022.925241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/21/2022] [Indexed: 11/25/2022] Open
Abstract
DCMU [N-(3,4-dichlorophenyl)-N-dimethylurea] or diuron is a widely used herbicide, which can cause adverse effects on human, especially on immune cells, due to their intrinsic properties and wide distribution. These cells are important for fighting not only against virus or bacteria but also against neoplastic cell development. We developed an approach that combines functional studies and miRNA and RNA sequencing data to evaluate the effects of DCMU on the human immune response against cancer, particularly the one carried out by CD8+ T cells. We found that DCMU modulates the expression of miRNA in a dose-dependent manner, leading to a specific pattern of gene expression and consequently to a diminished cytokine and granzyme B secretions. Using mimics or anti-miRs, we identified several miRNA, such as hsa-miR-3135b and hsa-miR-21-5p, that regulate these secretions. All these changes reduce the CD8+ T cells’ cytotoxic activity directed against cancer cells, in vitro and in vivo in a zebrafish model. To conclude, our study suggests that DCMU reduces T-cell abilities, participating thus to the establishment of an environment conducive to cancer development.
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Affiliation(s)
- Pierre Autin
- Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d’Angers, CRCI2NA, Nantes, France
| | - Sophie Deshayes
- Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d’Angers, CRCI2NA, Nantes, France
| | - Juliette Lea
- Université de Rennes, ImPACcell Plateform, BIOSIT, Rennes, France
| | - Nicolas Boisgerault
- Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d’Angers, CRCI2NA, Nantes, France
| | - Emilie Dupré
- Nantes Université, Univ Angers, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes, France
| | - Nathalie Labarrière
- Nantes Université, Univ Angers, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes, France
| | - Rémy Leguevel
- Université de Rennes, ImPACcell Plateform, BIOSIT, Rennes, France
| | - Jean-François Fonteneau
- Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d’Angers, CRCI2NA, Nantes, France
| | - Christophe Blanquart
- Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d’Angers, CRCI2NA, Nantes, France
| | - Delphine Fradin
- Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d’Angers, CRCI2NA, Nantes, France
- *Correspondence: Delphine Fradin,
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Cremonesi P, Capra E, Turri F, Lazzari B, Chessa S, Battelli G, Colombini S, Rapetti L, Castiglioni B. Effect of Diet Enriched With Hemp Seeds on Goat Milk Fatty Acids, Transcriptome, and miRNAs. FRONTIERS IN ANIMAL SCIENCE 2022. [DOI: 10.3389/fanim.2022.909271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In dairy ruminants, a diet supplemented with feed rich in unsaturated fatty acids can be an effective medium to increase the health-promoting properties of milk, although their effect on the pathways/genes involved in these processes has not been properly and completely defined to date. To improve our knowledge of the cell’s activity in specific conditions, next-generation RNA-sequencing technology was used to allow whole transcriptome characterization under given conditions. In addition to this, microRNAs (miRNAs) have recently been known as post-transcriptional regulators in fatty acid and cholesterol metabolism by targeting lipid metabolism genes. In this study, to analyze the transcriptome and miRNAs in goat milk after a supplemental diet enriched with linoleic acid (hemp seeds), next-generation RNA-sequencing was used in order to point out the general biological mechanisms underlying the effects related to milk fat metabolism. Ten pluriparous Alpine goats were fed with the same pretreatment diet for 40 days; then, they were arranged to two dietary treatments consisting of control (C) and hemp seed (H)-supplemented diets. Milk samples were collected at 40 (time point = T0) and 140 days of lactation (time point = T1). Milk fatty acid (FA) profiles revealed a significant effect of hemp seeds that determined a strong increment in the preformed FA, causing a reduction in the concentration of de-novo FA. Monounsaturated and polyunsaturated n−3 FAs were increased by hemp treatment, determining a reduction in the n−6/n−3 ratio. After removing milk fats and proteins, RNA was extracted from the milk cells and transcriptomic analysis was conducted using Illumina RNA-sequencing. A total of 3,835 genes were highly differentially expressed (p-value < 0.05, fold change > 1.5, and FDR < 0.05) in the H group. Functional analyses evidenced changes in metabolism, immune, and inflammatory responses. Furthermore, modifications in feeding strategies affected also key transcription factors regulating the expression of several genes involved in milk fat metabolism, such as peroxisome proliferator-activated receptors (PPARs). Moreover, 38 (15 known and 23 novel) differentially expressed miRNAs were uncovered in the H group and their potential functions were also predicted. This study gives the possibility to improve our knowledge of the molecular changes occurring after a hemp seed supplementation in the goat diet and increase our understanding of the relationship between nutrient variation and phenotypic effects.
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Tremmel R, Nies AT, van Eijck BAC, Handin N, Haag M, Winter S, Büttner FA, Kölz C, Klein F, Mazzola P, Hofmann U, Klein K, Hoffmann P, Nöthen MM, Gaugaz FZ, Artursson P, Schwab M, Schaeffeler E. Hepatic Expression of the Na+-Taurocholate Cotransporting Polypeptide Is Independent from Genetic Variation. Int J Mol Sci 2022; 23:ijms23137468. [PMID: 35806468 PMCID: PMC9267852 DOI: 10.3390/ijms23137468] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
The hepatic Na+-taurocholate cotransporting polypeptide NTCP/SLC10A1 is important for the uptake of bile salts and selected drugs. Its inhibition results in increased systemic bile salt concentrations. NTCP is also the entry receptor for the hepatitis B/D virus. We investigated interindividual hepatic SLC10A1/NTCP expression using various omics technologies. SLC10A1/NTCP mRNA expression/protein abundance was quantified in well-characterized 143 human livers by real-time PCR and LC-MS/MS-based targeted proteomics. Genome-wide SNP arrays and SLC10A1 next-generation sequencing were used for genomic analyses. SLC10A1 DNA methylation was assessed through MALDI-TOF MS. Transcriptomics and untargeted metabolomics (UHPLC-Q-TOF-MS) were correlated to identify NTCP-related metabolic pathways. SLC10A1 mRNA and NTCP protein levels varied 44-fold and 10.4-fold, respectively. Non-genetic factors (e.g., smoking, alcohol consumption) influenced significantly NTCP expression. Genetic variants in SLC10A1 or other genes do not explain expression variability which was validated in livers (n = 50) from The Cancer Genome Atlas. The identified two missense SLC10A1 variants did not impair transport function in transfectants. Specific CpG sites in SLC10A1 as well as single metabolic alterations and pathways (e.g., peroxisomal and bile acid synthesis) were significantly associated with expression. Inter-individual variability of NTCP expression is multifactorial with the contribution of clinical factors, DNA methylation, transcriptional regulation as well as hepatic metabolism, but not genetic variation.
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Affiliation(s)
- Roman Tremmel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Anne T. Nies
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
- iFIT Cluster of Excellence (EXC2180) “Image Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany
| | - Barbara A. C. van Eijck
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Niklas Handin
- Department of Pharmacy, Uppsala University, 75123 Uppsala, Sweden; (N.H.); (F.Z.G.); (P.A.)
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Florian A. Büttner
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Charlotte Kölz
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Franziska Klein
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Pascale Mazzola
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Kathrin Klein
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (P.H.); (M.M.N.)
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4001 Basel, Switzerland
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (P.H.); (M.M.N.)
- Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Fabienne Z. Gaugaz
- Department of Pharmacy, Uppsala University, 75123 Uppsala, Sweden; (N.H.); (F.Z.G.); (P.A.)
| | - Per Artursson
- Department of Pharmacy, Uppsala University, 75123 Uppsala, Sweden; (N.H.); (F.Z.G.); (P.A.)
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
- iFIT Cluster of Excellence (EXC2180) “Image Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany
- Departments of Clinical Pharmacology, and of Pharmacy and Biochemistry, University of Tuebingen, 72076 Tuebingen, Germany
- Correspondence: ; Tel.: +49-711-8101-3700
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
- iFIT Cluster of Excellence (EXC2180) “Image Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany
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163
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Karginov TA, Ménoret A, Vella AT. Optimal CD8 + T cell effector function requires costimulation-induced RNA-binding proteins that reprogram the transcript isoform landscape. Nat Commun 2022; 13:3540. [PMID: 35725727 PMCID: PMC9209503 DOI: 10.1038/s41467-022-31228-0] [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: 11/08/2021] [Accepted: 05/25/2022] [Indexed: 11/11/2022] Open
Abstract
Boosting T cell activation through costimulation directs defense against cancer and viral infections. Despite multiple studies targeting costimulation in clinical trials, the increased potency and reprogramming of T cells endowed by costimulation is poorly understood. Canonical dogma states that transcription mediates T cell activation. Here, we show that the spliceosome, controlling post-transcriptional alternative splicing and alternative polyadenylation, is the most enriched pathway in T cells after CD134/CD137 costimulation. Costimulation of CD8+ T cells significantly increases expression of 29 RNA-binding proteins while RNA-seq uncovers over 1000 differential alternative splicing and polyadenylation events. Using in vivo mouse and in vitro human models, we demonstrate that RNA-binding protein Tardbp is required for effector cytokine production, CD8+ T cell clonal expansion, and isoform regulation after costimulation. The prospect of immune response optimization through reprogramming of mRNA isoform production offered herein opens new avenues for experimentally and therapeutically tuning the activities of T cells.
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Affiliation(s)
- Timofey A Karginov
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Antoine Ménoret
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Anthony T Vella
- Department of Immunology, School of Medicine, University of Connecticut, UConn Health, 263 Farmington Avenue, Farmington, CT, 06030, USA.
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164
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Padam KSR, Morgan R, Hunter K, Chakrabarty S, Kumar NAN, Radhakrishnan R. Identification of HOX signatures contributing to oral cancer phenotype. Sci Rep 2022; 12:10123. [PMID: 35710803 PMCID: PMC9203786 DOI: 10.1038/s41598-022-14412-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
The role of evolutionarily conserved homeobox-containing HOX genes as transcriptional regulators in the developmental specification of organisms is well known. The contribution of HOX genes involvement in oral cancer phenotype has yet to be fully ascertained. TCGA-HNSC HTSeq-counts and clinical data were retrieved from the GDC portal for oral cavity neoplasms. GEO datasets (GSE72627, GSE30784, GSE37991) were accessed and analyzed using GEO2R. Differential HOX gene expression was profiled using the DESeq2 R package with a log2 fold change cut-off (- 1 and + 1) and Benjamini-Hochberg p-adjusted value at ≤ 0.01. Gene set over-representation analysis and semantic analysis associated with the disease ontology was performed using the ClusterProfiler R package, and pathway over-representation analysis was performed using IMPaLa. HOX protein interaction network was constructed using the Pathfind R package. HOX phenotype associations were performed using Mammalian Phenotype Ontology, Human Phenotype Ontology, PhenGenI associations, Jensen tissues, and OMIM entries. Drug connectivity mapping was carried out with Dr. Insight R package. HOXA2 was upregulated in oral dysplasia but silenced during tumor progression. Loss of HOXB2 expression was consistent in the potentially malignant oral lesions as well as in the primary tumor. HOXA7, HOXA10, HOXB7, HOXC6, HOXC10, HOXD10, and HOXD11 were consistently upregulated from premalignancy to malignancy and were notably associated with risk factors. Overrepresentation analysis suggested HOXA10 was involved in the transcriptional misregulation contributing to the oral cancer phenotype. HOX genes subnetwork analysis showed crucial interactions with cell cycle regulators, growth responsive elements, and proto-oncogenes. Phenotype associations specific to the oral region involving HOX genes provide intrinsic cues to tumor development. The 5' HOX genes were aberrantly upregulated during oral carcinogenesis reflecting their posterior prevalence.
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Affiliation(s)
- Kanaka Sai Ram Padam
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Richard Morgan
- School of Biomedical Sciences, University of West London, London, W5 5RF, UK
| | - Keith Hunter
- Academic Unit of Oral and Maxillofacial Medicine and Pathology, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Naveena A N Kumar
- Department of Surgical Oncology, Kasturba Medical College and Hospital, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India.
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165
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Liu Y, Senatore A, Sorce S, Nuvolone M, Guo J, Gümüş ZH, Aguzzi A. Brain aging is faithfully modelled in organotypic brain slices and accelerated by prions. Commun Biol 2022; 5:557. [PMID: 35676449 PMCID: PMC9177860 DOI: 10.1038/s42003-022-03496-5] [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: 06/12/2021] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
Mammalian models are essential for brain aging research. However, the long lifespan and poor amenability to genetic and pharmacological perturbations have hindered the use of mammals for dissecting aging-regulatory molecular networks and discovering new anti-aging interventions. To circumvent these limitations, we developed an ex vivo model system that faithfully mimics the aging process of the mammalian brain using cultured mouse brain slices. Genome-wide gene expression analyses showed that cultured brain slices spontaneously upregulated senescence-associated genes over time and reproduced many of the transcriptional characteristics of aged brains. Treatment with rapamycin, a classical anti-aging compound, largely abolished the time-dependent transcriptional changes in naturally aged brain slice cultures. Using this model system, we discovered that prions drastically accelerated the development of age-related molecular signatures and the pace of brain aging. We confirmed this finding in mouse models and human victims of Creutzfeldt-Jakob disease. These data establish an innovative, eminently tractable mammalian model of brain aging, and uncover a surprising acceleration of brain aging in prion diseases.
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Affiliation(s)
- Yingjun Liu
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland.
| | - Assunta Senatore
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Silvia Sorce
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Mario Nuvolone
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
- Amyloidosis Research and Treatment Center, Foundation IRCCS Policlinico San Matteo, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Jingjing Guo
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Zeynep H Gümüş
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland.
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Dogan B, Gumusoglu E, Ulgen E, Sezerman OU, Gunel T. Integrated bioinformatics analysis of validated and circulating miRNAs in ovarian cancer. Genomics Inform 2022; 20:e20. [PMID: 35794700 PMCID: PMC9299562 DOI: 10.5808/gi.21067] [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: 11/04/2021] [Accepted: 01/03/2022] [Indexed: 11/20/2022] Open
Abstract
Recent studies have focused on the early detection of ovarian cancer (OC) using tumor materials by liquid biopsy. The mechanisms of microRNAs (miRNAs) to impact OC and signaling pathways are still unknown. This study aims to reliably perform functional analysis of previously validated circulating miRNAs' target genes by using pathfindR. Also, overall survival and pathological stage analyses were evaluated with miRNAs' target genes which are common in the The Cancer Genome Atlas and GTEx datasets. Our previous studies have validated three downregulated miRNAs (hsa-miR-885-5p, hsa-miR-1909-5p, and hsalet7d-3p) having a diagnostic value in OC patients' sera, with high-throughput techniques. The predicted target genes of these miRNAs were retrieved from the miRDB database (v6.0). Active-subnetwork-oriented Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted by pathfindR using the target genes. Enrichment of KEGG pathways assessed by the analysis of pathfindR indicated that 24 pathways were related to the target genes. Ubiquitin-mediated proteolysis, spliceosome and Notch signaling pathway were the top three pathways with the lowest p-values (p < 0.001). Ninety-three common genes were found to be differentially expressed (p < 0.05) in the datasets. No significant genes were found to be significant in the analysis of overall survival analyses, but 24 genes were found to be significant with pathological stages analysis (p < 0.05). The findings of our study provide in-silico evidence that validated circulating miRNAs' target genes and enriched pathways are related to OC and have potential roles in theranostics applications. Further experimental investigations are required to validate our results which will ultimately provide a new perspective for translational applications in OC management.
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Affiliation(s)
- Berkcan Dogan
- Department of Medical Genetics, Faculty of Medicine, Bursa Uludag University, Bursa 16059, Turkey.,Department of Translational Medicine, Institute of Health Sciences, Bursa Uludag University, Bursa 16059, Turkey
| | - Ece Gumusoglu
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Ege Ulgen
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34750, Turkey
| | - Osman Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34750, Turkey
| | - Tuba Gunel
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
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167
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Lattin CR, Kelly TR, Kelly MW, Johnson KM. Constitutive gene expression differs in three brain regions important for cognition in neophobic and non-neophobic house sparrows (Passer domesticus). PLoS One 2022; 17:e0267180. [PMID: 35536842 PMCID: PMC9089922 DOI: 10.1371/journal.pone.0267180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022] Open
Abstract
Neophobia (aversion to new objects, food, and environments) is a personality trait that affects the ability of wildlife to adapt to new challenges and opportunities. Despite the ubiquity and importance of this trait, the molecular mechanisms underlying repeatable individual differences in neophobia in wild animals are poorly understood. We evaluated wild-caught house sparrows (Passer domesticus) for neophobia in the lab using novel object tests. We then selected a subset of neophobic and non-neophobic individuals (n = 3 of each, all females) and extracted RNA from four brain regions involved in learning, memory, threat perception, and executive function: striatum, caudal dorsomedial hippocampus, medial ventral arcopallium, and caudolateral nidopallium (NCL). Our analysis of differentially expressed genes (DEGs) used 11,889 gene regions annotated in the house sparrow reference genome for which we had an average of 25.7 million mapped reads/sample. PERMANOVA identified significant effects of brain region, phenotype (neophobic vs. non-neophobic), and a brain region by phenotype interaction. Comparing neophobic and non-neophobic birds revealed constitutive differences in DEGs in three of the four brain regions examined: hippocampus (12% of the transcriptome significantly differentially expressed), striatum (4%) and NCL (3%). DEGs included important known neuroendocrine mediators of learning, memory, executive function, and anxiety behavior, including serotonin receptor 5A, dopamine receptors 1, 2 and 5 (downregulated in neophobic birds), and estrogen receptor beta (upregulated in neophobic birds). These results suggest that some of the behavioral differences between phenotypes may be due to underlying gene expression differences in the brain. The large number of DEGs in neophobic and non-neophobic birds also implies that there are major differences in neural function between the two phenotypes that could affect a wide variety of behavioral traits beyond neophobia.
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Affiliation(s)
- Christine R. Lattin
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
- * E-mail:
| | - Tosha R. Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
| | - Morgan W. Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
| | - Kevin M. Johnson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
- Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA, United States of America
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168
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Castresana-Aguirre M, Guala D, Sonnhammer ELL. Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis. Front Genet 2022; 13:855766. [PMID: 35620466 PMCID: PMC9127507 DOI: 10.3389/fgene.2022.855766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
Functional analysis of gene sets derived from experiments is typically done by pathway annotation. Although many algorithms exist for analyzing the association between a gene set and a pathway, an issue which is generally ignored is that gene sets often represent multiple pathways. In such cases an association to a pathway is weakened by the presence of genes associated with other pathways. A way to counteract this is to cluster the gene set into more homogenous parts before performing pathway analysis on each module. We explored whether network-based pre-clustering of a query gene set can improve pathway analysis. The methods MCL, Infomap, and MGclus were used to cluster the gene set projected onto the FunCoup network. We characterized how well these methods are able to detect individual pathways in multi-pathway gene sets, and applied each of the clustering methods in combination with four pathway analysis methods: Gene Enrichment Analysis, BinoX, NEAT, and ANUBIX. Using benchmarks constructed from the KEGG pathway database we found that clustering can be beneficial by increasing the sensitivity of pathway analysis methods and by providing deeper insights of biological mechanisms related to the phenotype under study. However, keeping a high specificity is a challenge. For ANUBIX, clustering caused a minor loss of specificity, while for BinoX and NEAT it caused an unacceptable loss of specificity. GEA had very low sensitivity both before and after clustering. The choice of clustering method only had a minor effect on the results. We show examples of this approach and conclude that clustering can improve overall pathway annotation performance, but should only be used if the used enrichment method has a low false positive rate.
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Affiliation(s)
| | | | - Erik L. L. Sonnhammer
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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169
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Yang W, Denger A, Diener C, Küppers F, Soriano-Baguet L, Schäfer G, Yanamandra AK, Zhao R, Knörck A, Schwarz EC, Hart M, Lammert F, Roma LP, Brenner D, Christidis G, Helms V, Meese E, Hoth M, Qu B. Unspecific CTL Killing Is Enhanced by High Glucose via TNF-Related Apoptosis-Inducing Ligand. Front Immunol 2022; 13:831680. [PMID: 35265081 PMCID: PMC8899024 DOI: 10.3389/fimmu.2022.831680] [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: 12/08/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
TNF-related apoptosis inducing ligand (TRAIL) is expressed on cytotoxic T lymphocytes (CTLs) and TRAIL is linked to progression of diabetes. However, the impact of high glucose on TRAIL expression and its related killing function in CTLs still remains largely elusive. Here, we report that TRAIL is substantially up-regulated in CTLs in environments with high glucose (HG) both in vitro and in vivo. Non-mitochondrial reactive oxygen species, NFκB and PI3K/Akt are essential in HG-induced TRAIL upregulation in CTLs. TRAILhigh CTLs induce apoptosis of pancreatic beta cell line 1.4E7. Treatment with metformin and vitamin D reduces HG-enhanced expression of TRAIL in CTLs and coherently protects 1.4E7 cells from TRAIL-mediated apoptosis. Our work suggests that HG-induced TRAILhigh CTLs might contribute to the destruction of pancreatic beta cells in a hyperglycemia condition.
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Affiliation(s)
- Wenjuan Yang
- Biophysics, Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine, Saarland University, Homburg, Germany
| | - Andreas Denger
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Caroline Diener
- Institute of Human Genetics, School of Medicine, Saarland University, Homburg, Germany
| | - Frederic Küppers
- Internal Medicine II, University Hospital Saarland, Homburg, Germany
| | - Leticia Soriano-Baguet
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.,Immunology and Genetics, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.,Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Gertrud Schäfer
- Biophysics, Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine, Saarland University, Homburg, Germany
| | - Archana K Yanamandra
- Biophysics, Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine, Saarland University, Homburg, Germany.,INM-Leibniz Institute for New Materials, Saarbrücken, Germany
| | - Renping Zhao
- Biophysics, Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine, Saarland University, Homburg, Germany
| | - Arne Knörck
- Biophysics, Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine, Saarland University, Homburg, Germany
| | - Eva C Schwarz
- Biophysics, Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine, Saarland University, Homburg, Germany
| | - Martin Hart
- Institute of Human Genetics, School of Medicine, Saarland University, Homburg, Germany
| | - Frank Lammert
- Internal Medicine II, University Hospital Saarland, Homburg, Germany.,Hannover Medical School (MHH), Hannover, Germany
| | - Leticia Prates Roma
- Biophysics, Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine, Saarland University, Homburg, Germany
| | - Dirk Brenner
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.,Immunology and Genetics, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.,Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital University of Southern Denmark, Odense, Denmark
| | | | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, School of Medicine, Saarland University, Homburg, Germany
| | - Markus Hoth
- Biophysics, Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine, Saarland University, Homburg, Germany
| | - Bin Qu
- Biophysics, Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine, Saarland University, Homburg, Germany.,INM-Leibniz Institute for New Materials, Saarbrücken, Germany
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170
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Wight AE, Sido JM, Degryse S, Ao L, Nakagawa H, Qiu(Vivian) Y, Shen X, Oseghali O, Kim HJ, Cantor H. Antibody-mediated blockade of the IL23 receptor destabilizes intratumoral regulatory T cells and enhances immunotherapy. Proc Natl Acad Sci U S A 2022; 119:e2200757119. [PMID: 35482921 PMCID: PMC9170135 DOI: 10.1073/pnas.2200757119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/31/2022] [Indexed: 11/18/2022] Open
Abstract
Regulatory T cells (Treg) can impede antitumor immunity and currently represent a major obstacle to effective cancer immunotherapy. Targeting tumor-infiltrating regulatory Treg while sparing systemic Treg represents an optimal approach to this problem. Here, we provide evidence that the interleukin 23 receptor (IL23R) expressed by tumor-infiltrating Treg promotes suppressive activity. Disruption of the IL23R results in increased responsiveness of destabilized Treg to the IL12 cytokine, the production of γ-interferon, and the recruitment of CD8 T cells that inhibit tumor growth. Since the Treg destabilization pathway that is initiated by IL23R blockade is distinct and independent from the destabilization pathway coupled to glucocorticoid-induced TNFR-related protein (GITR) activation, we examined the impact of the coordinate induction of the two destabilization pathways on antitumor immune responses. Combined GITR and IL23R antibody treatment of mice inoculated with MC38 tumors resulted in robust and synergistic antitumor responses. These findings indicate that the delineation of independent Treg destabilization pathways may allow improved approaches to the development of combination immunotherapy for cancers.
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Affiliation(s)
- Andrew E. Wight
- Department of Cancer Immunology and Virology, Dana–Farber Cancer Institute, Boston, MA 02115
- Department of Immunology, Harvard Medical School, Boston, MA 02115
| | - Jessica M. Sido
- Department of Cancer Immunology and Virology, Dana–Farber Cancer Institute, Boston, MA 02115
- Department of Immunology, Harvard Medical School, Boston, MA 02115
| | - Sandrine Degryse
- Department of Cancer Immunology and Virology, Dana–Farber Cancer Institute, Boston, MA 02115
- Department of Immunology, Harvard Medical School, Boston, MA 02115
| | - Lin Ao
- Department of Cancer Immunology and Virology, Dana–Farber Cancer Institute, Boston, MA 02115
- Department of Immunology, Harvard Medical School, Boston, MA 02115
| | - Hidetoshi Nakagawa
- Department of Cancer Immunology and Virology, Dana–Farber Cancer Institute, Boston, MA 02115
- Department of Immunology, Harvard Medical School, Boston, MA 02115
| | - Yiguo Qiu(Vivian)
- Department of Cancer Immunology and Virology, Dana–Farber Cancer Institute, Boston, MA 02115
- Department of Immunology, Harvard Medical School, Boston, MA 02115
| | - Xianli Shen
- Department of Cancer Immunology and Virology, Dana–Farber Cancer Institute, Boston, MA 02115
- Department of Immunology, Harvard Medical School, Boston, MA 02115
| | - Oba Oseghali
- Department of Cancer Immunology and Virology, Dana–Farber Cancer Institute, Boston, MA 02115
| | - Hye-Jung Kim
- Department of Cancer Immunology and Virology, Dana–Farber Cancer Institute, Boston, MA 02115
- Department of Immunology, Harvard Medical School, Boston, MA 02115
| | - Harvey Cantor
- Department of Cancer Immunology and Virology, Dana–Farber Cancer Institute, Boston, MA 02115
- Department of Immunology, Harvard Medical School, Boston, MA 02115
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171
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Leifsdottir K, Thelin EP, Lassarén P, Siljehav V, Nilsson P, Eksborg S, Herlenius E. Proteomic profiles in cerebrospinal fluid predicted death and disability in term infants with perinatal asphyxia: A pilot study. Acta Paediatr 2022; 111:961-970. [PMID: 35106835 PMCID: PMC9305740 DOI: 10.1111/apa.16277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/23/2021] [Accepted: 01/31/2022] [Indexed: 11/29/2022]
Abstract
Aim Perinatal asphyxia, resulting in hypoxic‐ischaemic encephalopathy (HIE), has been associated with high mortality rates and severe lifelong neurodevelopmental disabilities. Our aim was to study the association between the proteomic profile in cerebrospinal fluid (CSF) and the degree of HIE and long‐term outcomes. Methods We prospectively enrolled 18‐term born infants with HIE and 10‐term born controls between 2000 and 2004 from the Karolinska University Hospital. An antibody suspension bead array and FlexMap3D analysis was used to characterise 178 unique brain‐derived and inflammation associated proteins in their CSF. Results Increased CSF concentrations of several brain‐specific proteins were observed in the proteome of HIE patients compared with the controls. An upregulation of neuroinflammatory pathways was also noted and this was confirmed by pathway analysis. Principal component analysis revealed a gradient from favourable to unfavourable HIE grades and outcomes. The proteins that provided strong predictors were structural proteins, including myelin basic protein and alpha‐II spectrin. The functional proteins included energy‐related proteins like neuron‐specific enolase and synaptic regulatory proteins. Increased CSF levels of 51 proteins correlated with adverse outcomes in infants with HIE. Conclusion Brain‐specific proteins and neuroinflammatory mediators in CSF may predict HIE degrees and outcomes after perinatal asphyxia.
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Affiliation(s)
- Kristin Leifsdottir
- Department of Women´s and Children´s Health Karolinska Institutet Stockholm Sweden
- Astrid Lindgren Children’s Hospital Karolinska University Hospital Stockholm Sweden
| | - Eric P Thelin
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
- Department of Neurology Karolinska University Hospital Stockholm Sweden
| | - Philipp Lassarén
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
| | - Veronica Siljehav
- Department of Women´s and Children´s Health Karolinska Institutet Stockholm Sweden
- Astrid Lindgren Children’s Hospital Karolinska University Hospital Stockholm Sweden
| | - Peter Nilsson
- Department of Protein Science KTH Royal Institute of Technology SciLifeLab Stockholm Sweden
| | - Staffan Eksborg
- Department of Women´s and Children´s Health Karolinska Institutet Stockholm Sweden
- Astrid Lindgren Children’s Hospital Karolinska University Hospital Stockholm Sweden
| | - Eric Herlenius
- Department of Women´s and Children´s Health Karolinska Institutet Stockholm Sweden
- Astrid Lindgren Children’s Hospital Karolinska University Hospital Stockholm Sweden
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172
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An RNA-sequencing transcriptome of the rodent Schwann cell response to peripheral nerve injury. J Neuroinflammation 2022; 19:105. [PMID: 35501870 PMCID: PMC9063194 DOI: 10.1186/s12974-022-02462-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/13/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The important contribution of glia to mechanisms of injury and repair of the nervous system is increasingly recognized. In stark contrast to the central nervous system (CNS), the peripheral nervous system (PNS) has a remarkable capacity for regeneration after injury. Schwann cells are recognized as key contributors to PNS regeneration, but the molecular underpinnings of the Schwann cell response to injury and how they interact with the inflammatory response remain incompletely understood. METHODS We completed bulk RNA-sequencing of Schwann cells purified acutely using immunopanning from the naïve and injured rodent sciatic nerve at 3, 5, and 7 days post-injury. We used qRT-PCR and in situ hybridization to assess cell purity and probe dataset integrity. Finally, we used bioinformatic analysis to probe Schwann cell-specific injury-induced modulation of cellular pathways. RESULTS Our data confirm Schwann cell purity and validate RNAseq dataset integrity. Bioinformatic analysis identifies discrete modules of genes that follow distinct patterns of regulation in the 1st days after injury and their corresponding molecular pathways. These findings enable improved differentiation of myeloid and glial components of neuroinflammation after peripheral nerve injury and highlight novel molecular aspects of the Schwann cell injury response such as acute downregulation of the AGE/RAGE pathway and of secreted molecules Sparcl1 and Sema5a. CONCLUSIONS We provide a helpful resource for further deciphering the Schwann cell injury response and a depth of transcriptional data that can complement the findings of recent single cell sequencing approaches. As more data become available on the response of CNS glia to injury, we anticipate that this dataset will provide a valuable platform for understanding key differences in the PNS and CNS glial responses to injury and for designing approaches to ameliorate CNS regeneration.
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173
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Isik Z, Leblebici A, Demir Karaman E, Karaca C, Ellidokuz H, Koc A, Ellidokuz EB, Basbinar Y. In silico identification of novel biomarkers for key players in transition from normal colon tissue to adenomatous polyps. PLoS One 2022; 17:e0267973. [PMID: 35486660 PMCID: PMC9053805 DOI: 10.1371/journal.pone.0267973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Adenomatous polyps of the colon are the most common neoplastic polyps. Although most of adenomatous polyps do not show malign transformation, majority of colorectal carcinomas originate from neoplastic polyps. Therefore, understanding of this transformation process would help in both preventive therapies and evaluation of malignancy risks. This study uncovers alterations in gene expressions as potential biomarkers that are revealed by integration of several network-based approaches. In silico analysis performed on a unified microarray cohort, which is covering 150 normal colon and adenomatous polyp samples. Significant gene modules were obtained by a weighted gene co-expression network analysis. Gene modules with similar profiles were mapped to a colon tissue specific functional interaction network. Several clustering algorithms run on the colon-specific network and the most significant sub-modules between the clusters were identified. The biomarkers were selected by filtering differentially expressed genes which also involve in significant biological processes and pathways. Biomarkers were also validated on two independent datasets based on their differential gene expressions. To the best of our knowledge, such a cascaded network analysis pipeline was implemented for the first time on a large collection of normal colon and polyp samples. We identified significant increases in TLR4 and MSX1 expressions as well as decrease in chemokine profiles with mostly pro-tumoral activities. These biomarkers might appear as both preventive targets and biomarkers for risk evaluation. As a result, this research proposes novel molecular markers that might be alternative to endoscopic approaches for diagnosis of adenomatous polyps.
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Affiliation(s)
- Zerrin Isik
- Faculty of Engineering, Department of Computer Engineering, Dokuz Eylul University, Izmir, Turkey
| | - Asım Leblebici
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Ezgi Demir Karaman
- Department of Computer Engineering, Institute of Natural and Applied Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Caner Karaca
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Hulya Ellidokuz
- Department of Preventive Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Turkey
| | - Altug Koc
- Gentan Genetic Medical Genetics Diagnosis Center, Izmir, Turkey
| | - Ender Berat Ellidokuz
- Faculty of Medicine, Department of Gastroenterology, Dokuz Eylul University, Izmir, Turkey
| | - Yasemin Basbinar
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Turkey
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174
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Vrooman LA, Rhon-Calderon EA, Suri KV, Dahiya AK, Lan Y, Schultz RM, Bartolomei MS. Placental Abnormalities are Associated With Specific Windows of Embryo Culture in a Mouse Model. Front Cell Dev Biol 2022; 10:884088. [PMID: 35547813 PMCID: PMC9081528 DOI: 10.3389/fcell.2022.884088] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/07/2022] [Indexed: 11/20/2022] Open
Abstract
Assisted Reproductive Technologies (ART) employ gamete/embryo handling and culture in vitro to produce offspring. ART pregnancies have an increased risk of low birth weight, abnormal placentation, pregnancy complications, and imprinting disorders. Embryo culture induces low birth weight, abnormal placental morphology, and lower levels of DNA methylation in placentas in a mouse model of ART. Whether preimplantation embryos at specific stages of development are more susceptible to these perturbations remains unresolved. Accordingly, we performed embryo culture for several discrete periods of preimplantation development and following embryo transfer, assessed fetal and placental outcomes at term. We observed a reduction in fetal:placental ratio associated with two distinct windows of preimplantation embryo development, one prior to the morula stage and the other from the morula to blastocyst stage, whereas placental morphological abnormalities and reduced imprinting control region methylation were only associated with culture prior to the morula stage. Extended culture to the blastocyst stage also induces additional placental DNA methylation changes compared to embryos transferred at the morula stage, and female concepti exhibited a higher loss of DNA methylation than males. By identifying specific developmental windows of susceptibility, this study provides a framework to optimize further culture conditions to minimize risks associated with ART pregnancies.
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Affiliation(s)
- Lisa A. Vrooman
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, United States
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Eric A. Rhon-Calderon
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Kashviya V. Suri
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Asha K. Dahiya
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Yemin Lan
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Richard M. Schultz
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, United States
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, United States
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175
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Janesick AS, Scheibinger M, Benkafadar N, Kirti S, Heller S. Avian auditory hair cell regeneration is accompanied by JAK/STAT-dependent expression of immune-related genes in supporting cells. Development 2022; 149:dev200113. [PMID: 35420675 PMCID: PMC10656459 DOI: 10.1242/dev.200113] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/31/2022] [Indexed: 11/20/2023]
Abstract
The avian hearing organ is the basilar papilla that, in sharp contrast to the mammalian cochlea, can regenerate sensory hair cells and thereby recover from deafness within weeks. The mechanisms that trigger, sustain and terminate the regenerative response in vivo are largely unknown. Here, we profile the changes in gene expression in the chicken basilar papilla after aminoglycoside antibiotic-induced hair cell loss using RNA-sequencing. We identified changes in gene expression of a group of immune-related genes and confirmed with single-cell RNA-sequencing that these changes occur in supporting cells. In situ hybridization was used to further validate these findings. We determined that the JAK/STAT signaling pathway is essential for upregulation of the damage-response genes in supporting cells during the second day after induction of hair cell loss. Four days after ototoxic damage, we identified newly regenerated, nascent auditory hair cells that express genes linked to termination of the JAK/STAT signaling response. The robust, transient expression of immune-related genes in supporting cells suggests a potential functional involvement of JAK/STAT signaling in sensory hair cell regeneration.
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Affiliation(s)
- Amanda S. Janesick
- Department of Otolaryngology – Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Mirko Scheibinger
- Department of Otolaryngology – Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Nesrine Benkafadar
- Department of Otolaryngology – Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Sakin Kirti
- Department of Otolaryngology – Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Stefan Heller
- Department of Otolaryngology – Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
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176
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Lampinen R, Górová V, Avesani S, Liddell JR, Penttilä E, Závodná T, Krejčík Z, Lehtola JM, Saari T, Kalapudas J, Hannonen S, Löppönen H, Topinka J, Koivisto AM, White AR, Giugno R, Kanninen KM. Biometal Dyshomeostasis in Olfactory Mucosa of Alzheimer's Disease Patients. Int J Mol Sci 2022; 23:ijms23084123. [PMID: 35456941 PMCID: PMC9032618 DOI: 10.3390/ijms23084123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/12/2022] Open
Abstract
Olfactory function, orchestrated by the cells of the olfactory mucosa at the rooftop of the nasal cavity, is disturbed early in the pathogenesis of Alzheimer's disease (AD). Biometals including zinc and calcium are known to be important for sense of smell and to be altered in the brains of AD patients. Little is known about elemental homeostasis in the AD patient olfactory mucosa. Here we aimed to assess whether the disease-related alterations to biometal homeostasis observed in the brain are also reflected in the olfactory mucosa. We applied RNA sequencing to discover gene expression changes related to metals in olfactory mucosal cells of cognitively healthy controls, individuals with mild cognitive impairment and AD patients, and performed analysis of the elemental content to determine metal levels. Results demonstrate that the levels of zinc, calcium and sodium are increased in the AD olfactory mucosa concomitantly with alterations to 17 genes related to metal-ion binding or metal-related function of the protein product. A significant elevation in alpha-2-macroglobulin, a known metal-binding biomarker correlated with brain disease burden, was observed on the gene and protein levels in the olfactory mucosa cells of AD patients. These data demonstrate that the olfactory mucosa cells derived from AD patients recapitulate certain impairments of biometal homeostasis observed in the brains of patients.
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Affiliation(s)
- Riikka Lampinen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland; (R.L.); (V.G.)
| | - Veronika Górová
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland; (R.L.); (V.G.)
| | - Simone Avesani
- Department of Computer Science, University of Verona, 37134 Verona, Italy; (S.A.); (R.G.)
| | - Jeffrey R. Liddell
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia;
| | - Elina Penttilä
- Department of Otorhinolaryngology, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland; (E.P.); (H.L.)
| | - Táňa Závodná
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.Z.); (Z.K.); (J.T.)
| | - Zdeněk Krejčík
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.Z.); (Z.K.); (J.T.)
| | - Juha-Matti Lehtola
- Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland; (J.-M.L.); (T.S.); (J.K.); (S.H.); (A.M.K.)
- Department of Neurology, NeuroCentre, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Toni Saari
- Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland; (J.-M.L.); (T.S.); (J.K.); (S.H.); (A.M.K.)
| | - Juho Kalapudas
- Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland; (J.-M.L.); (T.S.); (J.K.); (S.H.); (A.M.K.)
| | - Sanna Hannonen
- Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland; (J.-M.L.); (T.S.); (J.K.); (S.H.); (A.M.K.)
- Department of Neurology, NeuroCentre, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Heikki Löppönen
- Department of Otorhinolaryngology, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland; (E.P.); (H.L.)
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.Z.); (Z.K.); (J.T.)
| | - Anne M. Koivisto
- Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland; (J.-M.L.); (T.S.); (J.K.); (S.H.); (A.M.K.)
- Department of Neurology, NeuroCentre, Kuopio University Hospital, 70210 Kuopio, Finland
- Department of Neurology and Geriatrics, Helsinki University Hospital and Neurosciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Anthony R. White
- Department of Cell and Molecular Biology, Mental Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia;
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, 37134 Verona, Italy; (S.A.); (R.G.)
| | - Katja M. Kanninen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland; (R.L.); (V.G.)
- Correspondence:
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177
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Wang Y, Pan P, Khan A, Çil Ç, Pineda MA. Synovial Fibroblast Sialylation Regulates Cell Migration and Activation of Inflammatory Pathways in Arthritogenesis. Front Immunol 2022; 13:847581. [PMID: 35371069 PMCID: PMC8971784 DOI: 10.3389/fimmu.2022.847581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/28/2022] [Indexed: 12/30/2022] Open
Abstract
Synovial fibroblasts have emerged as critical underlying factors to perpetuate chronic joint inflammation in Rheumatoid Arthritis. Like any other cell, synovial fibroblasts are covered with a complex layer of glycans that can change in response to extracellular signals, such as inflammation. We have previously shown that inflammatory synovial fibroblasts show decreased levels of sialic acid, but our understanding of sialic acid-dependent pathophysiological pathways in these stromal cells is still very limited. In this report, we used in vivo and in vitro studies with exogenous sialidases and RNA sequencing to investigate the responses of murine synovial fibroblasts upon desialylation. Our results show that hyposialylated fibroblasts present a dysregulated migratory ability and an activated phenotype characterized by the expression of inflammatory mediators, such as cytokines and chemokines, and anti-viral related mechanisms. Removal of surface sialic acid also affected the expression of sialyltransferases, revealing the existence of a positive feedback to sustain reduced sialylation. Moreover, we demonstrate that synovial fibroblasts subsets have distinct sialyltransferase expression profiles, both in healthy and arthritic mice. These findings underline the ability of sialic acid to modulate homeostatic and inflammatory responses in non-immune synovial fibroblasts, suggesting that sialylation plays a key role in perpetuating local inflammation in the arthritic joint.
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Affiliation(s)
- Yilin Wang
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Piaopiao Pan
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Aneesah Khan
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Çağlar Çil
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Miguel A. Pineda
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom,Research Into Inflammatory Arthritis Centre Versus Arthritis (RACE), Glasgow, United Kingdom,*Correspondence: Miguel A. Pineda,
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178
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Floudas A, Gorman A, Neto N, Monaghan MG, Elliott Z, Fearon U, Marzaioli V. Inside the Joint of Inflammatory Arthritis Patients: Handling and Processing of Synovial Tissue Biopsies for High Throughput Analysis. Front Med (Lausanne) 2022; 9:830998. [PMID: 35372383 PMCID: PMC8967180 DOI: 10.3389/fmed.2022.830998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Inflammatory arthritis is a chronic systemic autoimmune disease of unknown etiology, which affects the joints. If untreated, these diseases can have a detrimental effect on the patient's quality of life, leading to disabilities, and therefore, exhibit a significant socioeconomic impact and burden. While studies of immune cell populations in arthritis patient's peripheral blood have been informative regarding potential immune cell dysfunction and possible patient stratification, there are considerable limitations in identifying the early events that lead to synovial inflammation. The joint, as the site of inflammation and the local microenvironment, exhibit unique characteristics that contribute to disease pathogenesis. Understanding the contribution of immune and stromal cell interactions within the inflamed joint has been met with several technical challenges. Additionally, the limited availability of synovial tissue biopsies is a key incentive for the utilization of high-throughput techniques in order to maximize information gain. This review aims to provide an overview of key methods and novel techniques that are used in the handling, processing and analysis of synovial tissue biopsies and the potential synergy between these techniques. Herein, we describe the utilization of high dimensionality flow cytometric analysis, single cell RNA sequencing, ex vivo functional assays and non-intrusive metabolic characterization of synovial cells on a single cell level based on fluorescent lifetime imaging microscopy. Additionally, we recommend important points of consideration regarding the effect of different storage and handling techniques on downstream analysis of synovial tissue samples. The introduction of new powerful techniques in the study of synovial tissue inflammation, brings new challenges but importantly, significant opportunities. Implementation of novel approaches will accelerate our path toward understanding of the mechanisms involved in the pathogenesis of inflammatory arthritis and lead to the identification of new avenues of therapeutic intervention.
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Affiliation(s)
- Achilleas Floudas
- Molecular Rheumatology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- European League Against Rheumatism (EULAR) Centre of Excellence, Centre for Arthritis and Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin (UCD), Dublin, Ireland
- *Correspondence: Achilleas Floudas
| | - Aine Gorman
- European League Against Rheumatism (EULAR) Centre of Excellence, Centre for Arthritis and Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin (UCD), Dublin, Ireland
| | - Nuno Neto
- Trinity Centre for Biomedical Engineering, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Michael G. Monaghan
- Trinity Centre for Biomedical Engineering, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Zoe Elliott
- European League Against Rheumatism (EULAR) Centre of Excellence, Centre for Arthritis and Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin (UCD), Dublin, Ireland
| | - Ursula Fearon
- Molecular Rheumatology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- European League Against Rheumatism (EULAR) Centre of Excellence, Centre for Arthritis and Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin (UCD), Dublin, Ireland
| | - Viviana Marzaioli
- Molecular Rheumatology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- European League Against Rheumatism (EULAR) Centre of Excellence, Centre for Arthritis and Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin (UCD), Dublin, Ireland
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179
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Computing microRNA-gene interaction networks in pan-cancer using miRDriver. Sci Rep 2022; 12:3717. [PMID: 35260634 PMCID: PMC8904490 DOI: 10.1038/s41598-022-07628-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
DNA copy number aberrated regions in cancer are known to harbor cancer driver genes and the short non-coding RNA molecules, i.e., microRNAs. In this study, we integrated the multi-omics datasets such as copy number aberration, DNA methylation, gene and microRNA expression to identify the signature microRNA-gene associations from frequently aberrated DNA regions across pan-cancer utilizing a LASSO-based regression approach. We studied 7294 patient samples associated with eighteen different cancer types from The Cancer Genome Atlas (TCGA) database and identified several cancer-specific and common microRNA-gene interactions enriched in experimentally validated microRNA-target interactions. We highlighted several oncogenic and tumor suppressor microRNAs that were cancer-specific and common in several cancer types. Our method substantially outperformed the five state-of-art methods in selecting significantly known microRNA-gene interactions in multiple cancer types. Several microRNAs and genes were found to be associated with tumor survival and progression. Selected target genes were found to be significantly enriched in cancer-related pathways, cancer hallmark and Gene Ontology (GO) terms. Furthermore, subtype-specific potential gene signatures were discovered in multiple cancer types.
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180
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EGCG Prevents the Onset of an Inflammatory and Cancer-Associated Adipocyte-like Phenotype in Adipose-Derived Mesenchymal Stem/Stromal Cells in Response to the Triple-Negative Breast Cancer Secretome. Nutrients 2022; 14:nu14051099. [PMID: 35268073 PMCID: PMC8912398 DOI: 10.3390/nu14051099] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/23/2022] Open
Abstract
Background: Triple-negative breast cancer (TNBC) cells secretome induces a pro-inflammatory microenvironment within the adipose tissue, which hosts both mature adipocytes and adipose-derived mesenchymal stem/stromal cells (ADMSC). The subsequent acquisition of a cancer-associated adipocyte (CAA)-like phenotype is, however, unknown in ADMSC. While epidemiological studies suggest that consuming a polyphenol-rich diet reduces the incidence of some obesity-related cancers, the chemopreventive impact of green tea-derived epigallocatechin-3-gallate (EGCG) against the cues that trigger the CAA phenotype remain undocumented in ADMSC. Methods: Human ADMSC were exposed to human TNBC-derived MDA-MB-231 conditioned media (TNBC cells secretome) supplemented or not with EGCG. Differential gene expression was assessed through RNA-Seq analysis and confirmed by RT-qPCR. Protein expression levels and the activation status of signal transduction pathways mediators were determined by Western blotting. ADMSC chemotaxis was assessed by a real-time cell migration assay. Results: The TNBC cells secretome induced in ADMSC the expression of the CAA cytokines CCL2, CCL5, IL-1β, and IL-6, and of immunomodulators COX2, HIF-1α, VEGFα, and PD-L1. The epithelial-to-mesenchymal biomarker Snail was found to control the CAA phenotype. EGCG inhibited the induction of CAA genes and the activation status of Smad2 and NF-κB. The induced chemotactic response was also inhibited by EGCG. Conclusion: The induction of an inflammatory and CAA-like phenotype in ADMSC can be triggered by the TNBC cells secretome, while still efficiently prevented by diet-derived polyphenols.
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181
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Wilson RJ, Lyons SP, Koves TR, Bryson VG, Zhang H, Li T, Crown SB, Ding JD, Grimsrud PA, Rosenberg PB, Muoio DM. Disruption of STIM1-mediated Ca 2+ sensing and energy metabolism in adult skeletal muscle compromises exercise tolerance, proteostasis, and lean mass. Mol Metab 2022; 57:101429. [PMID: 34979330 PMCID: PMC8814391 DOI: 10.1016/j.molmet.2021.101429] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Stromal interaction molecule 1 (STIM1) is a single-pass transmembrane endoplasmic/sarcoplasmic reticulum (E/SR) protein recognized for its role in a store operated Ca2+ entry (SOCE), an ancient and ubiquitous signaling pathway. Whereas STIM1 is known to be indispensable during development, its biological and metabolic functions in mature muscles remain unclear. METHODS Conditional and tamoxifen inducible muscle STIM1 knock-out mouse models were coupled with multi-omics tools and comprehensive physiology to understand the role of STIM1 in regulating SOCE, mitochondrial quality and bioenergetics, and whole-body energy homeostasis. RESULTS This study shows that STIM1 is abundant in adult skeletal muscle, upregulated by exercise, and is present at SR-mitochondria interfaces. Inducible tissue-specific deletion of STIM1 (iSTIM1 KO) in adult muscle led to diminished lean mass, reduced exercise capacity, and perturbed fuel selection in the settings of energetic stress, without affecting whole-body glucose tolerance. Proteomics and phospho-proteomics analyses of iSTIM1 KO muscles revealed molecular signatures of low-grade E/SR stress and broad activation of processes and signaling networks involved in proteostasis. CONCLUSION These results show that STIM1 regulates cellular and mitochondrial Ca2+ dynamics, energy metabolism and proteostasis in adult skeletal muscles. Furthermore, these findings provide insight into the pathophysiology of muscle diseases linked to disturbances in STIM1-dependent Ca2+ handling.
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Affiliation(s)
- Rebecca J Wilson
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA
| | - Scott P Lyons
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA
| | - Timothy R Koves
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA; Department of Medicine, Division of Geriatrics, Duke University School of Medicine, Durham, NC 27705, USA
| | - Victoria G Bryson
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA; Department of Medicine, Division of Cardiology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Hengtao Zhang
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA; Department of Medicine, Division of Cardiology, Duke University School of Medicine, Durham, NC 27705, USA
| | - TianYu Li
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA; Department of Medicine, Division of Cardiology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Scott B Crown
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA
| | - Jin-Dong Ding
- Department of Medicine, Division of Ophthalmology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Paul A Grimsrud
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University School of Medicine, Durham, NC 27705, USA
| | - Paul B Rosenberg
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA; Department of Medicine, Division of Cardiology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Deborah M Muoio
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University School of Medicine, Durham, NC 27705, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27705, USA.
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182
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Li Y, Ritzel RM, Lei Z, Cao T, He J, Faden AI, Wu J. Sexual dimorphism in neurological function after SCI is associated with disrupted neuroinflammation in both injured spinal cord and brain. Brain Behav Immun 2022; 101:1-22. [PMID: 34954073 PMCID: PMC8885910 DOI: 10.1016/j.bbi.2021.12.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/29/2021] [Accepted: 12/18/2021] [Indexed: 10/19/2022] Open
Abstract
Whereas human spinal cord injury (SCI) is more common in men, the prevalence is growing in women. However, little is known about the effect of biological sex on brain dysfunction and injury mechanisms. To model the highest per capita rate of injury (ages between 16 and 30 years old) in humans, in the present study, young adult or a young/middle-aged male and female C57BL/6 mice were subjected to moderate contusion SCI. When mice were injured at 10-12-week-old, transcriptomic analysis of inflammation-related genes and flow cytometry revealed a more aggressive neuroinflammatory profile in male than females following 3 d SCI, ostensibly driven by sex-specific changes myeloid cell function rather than cell number. Female mice were generally more active at baseline, as evidenced by greater distance traveled in the open field. After SCI, female mice had more favorable locomotor function than male animals. At 13 weeks post-injury, male mice showed poor performance in cognitive and depressive-like behavioral tests, while injured female mice showed fewer deficits in these tasks. However, when injured at 6 months old followed by 8 months post-injury, male mice had considerably less inflammatory activation compared with female animals despite having similar or worse outcomes in affective, cognitive, and motor tasks. Collectively, these findings indicate that sex differences in functional outcome after SCI are associated with the age at onset of injury, as well as disrupted neuroinflammation not only at the site of injury but also in remote brain regions. Thus, biological sex should be considered when designing new therapeutic agents.
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Affiliation(s)
- Yun Li
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, Baltimore, MD, 21201 USA
| | - Rodney M. Ritzel
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, Baltimore, MD, 21201 USA
| | - Zhuofan Lei
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, Baltimore, MD, 21201 USA
| | - Tuoxin Cao
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, Baltimore, MD, 21201 USA
| | - Junyun He
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, Baltimore, MD, 21201 USA
| | - Alan I Faden
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, Baltimore, MD, 21201 USA,University of Maryland Center to Advance Chronic Pain Research, University of Maryland, Baltimore, MD, 21201 USA
| | - Junfang Wu
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, Baltimore, MD 21201, USA; University of Maryland Center to Advance Chronic Pain Research, University of Maryland, Baltimore, MD 21201, USA.
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183
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Adrover JM, Carrau L, Daßler-Plenker J, Bram Y, Chandar V, Houghton S, Redmond D, Merrill JR, Shevik M, tenOever BR, Lyons SK, Schwartz RE, Egeblad M. Disulfiram inhibits neutrophil extracellular trap formation protecting rodents from acute lung injury and SARS-CoV-2 infection. JCI Insight 2022; 7:157342. [PMID: 35133984 PMCID: PMC8983145 DOI: 10.1172/jci.insight.157342] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/26/2022] [Indexed: 12/15/2022] Open
Abstract
Severe acute lung injury has few treatment options and a high mortality rate. Upon injury, neutrophils infiltrate the lungs and form neutrophil extracellular traps (NETs), damaging the lungs and driving an exacerbated immune response. Unfortunately, no drug preventing NET formation has completed clinical development. Here, we report that disulfiram — an FDA-approved drug for alcohol use disorder — dramatically reduced NETs, increased survival, improved blood oxygenation, and reduced lung edema in a transfusion-related acute lung injury (TRALI) mouse model. We then tested whether disulfiram could confer protection in the context of SARS-CoV-2 infection, as NETs are elevated in patients with severe COVID-19. In SARS-CoV-2–infected golden hamsters, disulfiram reduced NETs and perivascular fibrosis in the lungs, and it downregulated innate immune and complement/coagulation pathways, suggesting that it could be beneficial for patients with COVID-19. In conclusion, an existing FDA-approved drug can block NET formation and improve disease course in 2 rodent models of lung injury for which treatment options are limited.
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Affiliation(s)
- Jose M Adrover
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States of America
| | - Lucia Carrau
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Juliane Daßler-Plenker
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States of America
| | - Yaron Bram
- Department of Medicine, Weill Cornell Medicine, New York, United States of America
| | - Vasuretha Chandar
- Department of Medicine, Weill Cornell Medicine, New York, United States of America
| | - Sean Houghton
- Division of Regenerative Medicine, Weill Cornell Medicine, New York, United States of America
| | - David Redmond
- Division of Regenerative Medicine, Weill Cornell Medicine, New York, United States of America
| | - Joseph R Merrill
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States of America
| | - Margaret Shevik
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States of America
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Scott K Lyons
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States of America
| | - Robert E Schwartz
- Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Mikala Egeblad
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States of America
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184
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Ikenaga C, Date H, Kanagawa M, Mitsui J, Ishiura H, Yoshimura J, Pinal‐Fernandez I, Mammen AL, Lloyd TE, Tsuji S, Shimizu J, Toda T, Goto J. Muscle transcriptomics shows overexpression of
cadherin 1
in inclusion body myositis. Ann Neurol 2022; 91:317-328. [PMID: 35064929 PMCID: PMC9092834 DOI: 10.1002/ana.26304] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/18/2022]
Abstract
Objective This study aimed to elucidate the molecular features of inclusion body myositis (IBM). Methods We performed RNA sequencing analysis of muscle biopsy samples from 67 participants, consisting of 58 myositis patients with the pathological finding of CD8‐positive T cells invading non‐necrotic muscle fibers expressing major histocompatibility complex class I (43 IBM, 6 polymyositis, and 9 unclassifiable myositis), and 9 controls. Results Cluster analysis, principal component analysis, and pathway analysis showed that differentially expressed genes and pathways identified in IBM and polymyositis were mostly comparable. However, pathways related to cell adhesion molecules were upregulated in IBM as compared with polymyositis and controls (p < 0.01). Notably, CDH1, which encodes the epidermal cell junction protein cadherin 1, was overexpressed in the muscles of IBM, which was validated by another RNA sequencing dataset from previous publications. Western blotting confirmed the presence of mature cadherin 1 protein in the muscles of IBM. Immunohistochemical staining confirmed the positivity for anti‐cadherin 1 antibody in the muscles of IBM, whereas there was no muscle fiber positive for anti‐cadherin 1 antibody in immune‐mediated necrotizing myopathy, antisynthetase syndrome, and controls. The fibers stained with anti‐cadherin 1 antibody did not have rimmed vacuoles or abnormal protein accumulation. Experimental skeletal muscle regeneration and differentiation systems showed that CDH1 is expressed during skeletal muscle regeneration and differentiation. Interpretation CDH1 was detected as a differentially expressed gene, and immunohistochemistry showed that cadherin 1 exists in the muscles of IBM, whereas it was rarely seen in those of other idiopathic inflammatory myopathies. Cadherin 1 upregulation in muscle could provide a valuable clue to the pathological mechanisms of IBM. ANN NEUROL 2022;91:317–328
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Affiliation(s)
- Chiseko Ikenaga
- Department of Neurology, Graduate School of Medicine the University of Tokyo Tokyo Japan
- Department of Neurology Johns Hopkins University School of Medicine Baltimore MD US
| | - Hidetoshi Date
- Department of Neurology, National Center Hospital National Center of Neurology and Psychiatry Tokyo Japan
| | - Motoi Kanagawa
- Division of Molecular Brain Science Kobe University Graduate School of Medicine Kobe Japan
- Department of Cell Biology and Molecular Medicine Ehime University Graduate School of Medicine Ehime Japan
| | - Jun Mitsui
- Department of Molecular Neurology, Graduate School of Medicine The University of Tokyo Tokyo Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine the University of Tokyo Tokyo Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences The University of Tokyo Chiba Japan
| | - Iago Pinal‐Fernandez
- Department of Neurology Johns Hopkins University School of Medicine Baltimore MD US
- Muscle Disease Unit National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health Bethesda MD US
- Faculty of Health Sciences and Faculty of Computer Science, Multimedia and Telecommunications Universitat Oberta de Catalunya Barcelona Spain
| | - Andrew L. Mammen
- Department of Neurology Johns Hopkins University School of Medicine Baltimore MD US
- Muscle Disease Unit National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health Bethesda MD US
| | - Thomas E. Lloyd
- Department of Neurology Johns Hopkins University School of Medicine Baltimore MD US
- Solomon H. Synder Department of Neuroscience Johns Hopkins University School of Medicine Baltimore MD US
| | - Shoji Tsuji
- Department of Molecular Neurology, Graduate School of Medicine The University of Tokyo Tokyo Japan
- Institute of Medical Genomics International University of Health and Welfare Chiba Japan
| | - Jun Shimizu
- Department of Neurology, Graduate School of Medicine the University of Tokyo Tokyo Japan
- Department of Physical Therapy Tokyo University of Technology Tokyo Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine the University of Tokyo Tokyo Japan
- Division of Molecular Brain Science Kobe University Graduate School of Medicine Kobe Japan
| | - Jun Goto
- Department of Neurology International University of Health and Welfare, Mita Hospital Tokyo Japan
- Department of Neurology International University of Health and Welfare, Ichikawa Hospital Chiba Japan
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185
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Li BB, Scott EY, Olafsen NE, Matthews J, Wheeler AR. Analysis of the effects of aryl hydrocarbon receptor expression on cancer cell invasion via three-dimensional microfluidic invasion assays. LAB ON A CHIP 2022; 22:313-325. [PMID: 34904612 DOI: 10.1039/d1lc00854d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that binds to xenobiotics and activates expression of response elements to metabolize these compounds. The AHR pathway has been associated with a long list of diseases including cancer; however, it is debated whether AHR is tumorigenic or tumour-inhibiting. In particular, there are contradictory reports in the literature regarding the effects of AHR expression level on metastatic breast cancer. Here we used a 3D invasion assay called cell invasion in digital microfluidic microgel systems (CIMMS) to study the effect of AHR expression on invasion. In this study, MDA-MB-231 cells with stable knockout of AHR (AHRko) showed enhanced invasive characteristics and reduced proliferation, and cells with transient overexpression of AHR showed reduced invasiveness. Overexpression of AHR with a mutation in the DNA binding domain showed no difference in invasiveness compared to control, which suggests that the changes in invasiveness are related to the expression of AHR. CIMMS also allowed for extraction of sub-populations of invaded cells for RNA sequencing experiments. A comparison of the transcriptomes of invaded subpopulations of wild-type and AHRko cells identified 1809 genes that were differentially expressed, with enriched pathways including cell cycle, proliferation, survival, immunoproteasome activation, and activation of matrix metalloproteases. In sum, the data reported here for MDA-MB-231 cells suggests some new interpretations of the discrepancy in the literature on the role of AHR in breast cancer. We propose that the unique combination of functional discrimination with transcriptome profiling provided by CIMMS will be valuable for a wide range of mechanistic invasion-biology studies in the future.
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Affiliation(s)
- Bingyu B Li
- Institute of Biomedical Engineering, University of Toronto, 164 College St, Toronto, ON, M5S 3G9, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
| | - Erica Y Scott
- Institute of Biomedical Engineering, University of Toronto, 164 College St, Toronto, ON, M5S 3G9, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Department of Chemistry, University of Toronto, 80 St George St., Toronto, ON, M5S 3H6, Canada
| | - Ninni E Olafsen
- Institute of Basic Medical Sciences, University of Oslo, Oslo, 0317, Norway
| | - Jason Matthews
- Institute of Basic Medical Sciences, University of Oslo, Oslo, 0317, Norway
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - Aaron R Wheeler
- Institute of Biomedical Engineering, University of Toronto, 164 College St, Toronto, ON, M5S 3G9, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Department of Chemistry, University of Toronto, 80 St George St., Toronto, ON, M5S 3H6, Canada
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186
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Silva GCV, Grefenhagen AI, Borges P, Matte U. Hearing Impairment in Mucopolysaccharidosis: A Systems Biology Approach. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2022. [DOI: 10.1590/2326-4594-jiems-2021-0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | - Pamella Borges
- Hospital de Clínicas de Porto Alegre, Brazil; University of Houston, United States of America
| | - Ursula Matte
- Hospital de Clínicas de Porto Alegre, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
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Iwahashi N, Umakoshi H, Ogata M, Fukumoto T, Kaneko H, Terada E, Katsuhara S, Uchida N, Sasaki K, Yokomoto-Umakoshi M, Matsuda Y, Sakamoto R, Ogawa Y. Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples. Front Endocrinol (Lausanne) 2022; 13:808331. [PMID: 35185794 PMCID: PMC8850780 DOI: 10.3389/fendo.2022.808331] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/11/2022] [Indexed: 11/24/2022] Open
Abstract
Whole transcriptome profiling is a promising technique in adrenal studies; however, whole transcriptome profiling of adrenal disease using formalin-fixed paraffin-embedded (FFPE) samples has to be further explored. The aim of this study was to evaluate the utility of transcriptome data from FFPE samples of adrenocortical tumors. We performed whole transcriptome profiling of FFPE and fresh frozen samples of adrenocortical carcinoma (ACC, n = 3), aldosterone-producing adenoma (APA, n = 3), and cortisol-producing adenoma (CPA, n = 3), and examined the similarity between the transcriptome data. We further examined whether the transcriptome data of FFPE samples could be used to distinguish tumor types and detect marker genes. The number of read counts was smaller in FFPE samples than in fresh frozen samples (P < 0.01), while the number of genes detected was similar (P = 0.39). The gene expression profiles of FFPE and fresh frozen samples were highly correlated (r = 0.93, P < 0.01). Tumor types could be distinguished by consensus clustering and principal component analysis using transcriptome data from FFPE samples. In the differential expression analysis between ACC and APA-CPA, known marker genes of ACC (e.g., CCNB2, TOP2A, and MAD2L1) were detected in FFPE samples of ACC. In the differential expression analysis between APA and CPA, known marker genes of APA (e.g., CYP11B2, VSNL1, and KCNJ5) were detected in the APA of FFPE samples. The results suggest that FFPE samples may be a reliable alternative to fresh frozen samples for whole transcriptome profiling of adrenocortical tumors.
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Affiliation(s)
- Norifusa Iwahashi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hironobu Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- *Correspondence: Hironobu Umakoshi, ; Yoshihiro Ogawa,
| | - Masatoshi Ogata
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tazuru Fukumoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroki Kaneko
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Eriko Terada
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shunsuke Katsuhara
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naohiro Uchida
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsuhiko Sasaki
- Clinical Laboratory Department, Kyushu Pro Search Limited Liability Partnership, Fukuoka, Japan
| | - Maki Yokomoto-Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yayoi Matsuda
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryuichi Sakamoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- *Correspondence: Hironobu Umakoshi, ; Yoshihiro Ogawa,
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Ruiz E, Kandil E, Alhassan S, Toraih E, Errami Y, Elmageed ZYA, Zerfaoui M. An Integrative Multi-Omics Analysis of The Molecular Links between Aging and Aggressiveness in Thyroid Cancers. Aging Dis 2022; 14:992-1012. [PMID: 37191407 DOI: 10.14336/ad.2022.1021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/21/2022] [Indexed: 11/19/2022] Open
Abstract
Aging modifies risk in all cancers, but age is used as a clinical staging criterion uniquely in thyroid cancer (TC). The molecular drivers of age-dependent TC onset and aggressiveness remain poorly understood. We applied an integrative, multi-omics data analysis approach to characterize these signatures. Our analysis reveals that aging, independent of BRAFV600E mutational status, drives a significant accumulation of aggressiveness-related markers and poorer survival outcomes, most noticeably at age 55 and over. We identified that chromosomal alterations in loci 1p/1q as aging-associated drivers of aggressiveness, and that depleted infiltration with tumor surveillant CD8+T and follicular helper T cells, dysregulation of proteostasis- and senescence-related processes, and ERK1/2 signaling cascade are key features of the aging thyroid and TC onset/progression and aggressiveness in aging patients but not in young individuals. A panel of 23 genes, including those related to cell division such as CENPF, ERCC6L, and the kinases MELK and NEK2, were identified and rigorously characterized as aging-dependent and aggressiveness-specific markers. These genes effectively stratified patients into aggressive clusters with distinct phenotypic enrichment and genomic/transcriptomic profiles. This panel also showed excellent performance in predicting metastasis stage, BRAFV600E, TERT promoter mutation, and survival outcomes and was superior to the American Thyroid Association (ATA) methodology in predicting aggressiveness risk. Our analysis established clinically relevant biomarkers for TC aggressiveness factoring in aging as an important component.
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Marini F, Ludt A, Linke J, Strauch K. GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data. BMC Bioinformatics 2021; 22:610. [PMID: 34949163 PMCID: PMC8697502 DOI: 10.1186/s12859-021-04461-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/26/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The interpretation of results from transcriptome profiling experiments via RNA sequencing (RNA-seq) can be a complex task, where the essential information is distributed among different tabular and list formats-normalized expression values, results from differential expression analysis, and results from functional enrichment analyses. A number of tools and databases are widely used for the purpose of identification of relevant functional patterns, yet often their contextualization within the data and results at hand is not straightforward, especially if these analytic components are not combined together efficiently. RESULTS We developed the GeneTonic software package, which serves as a comprehensive toolkit for streamlining the interpretation of functional enrichment analyses, by fully leveraging the information of expression values in a differential expression context. GeneTonic is implemented in R and Shiny, leveraging packages that enable HTML-based interactive visualizations for executing drilldown tasks seamlessly, viewing the data at a level of increased detail. GeneTonic is integrated with the core classes of existing Bioconductor workflows, and can accept the output of many widely used tools for pathway analysis, making this approach applicable to a wide range of use cases. Users can effectively navigate interlinked components (otherwise available as flat text or spreadsheet tables), bookmark features of interest during the exploration sessions, and obtain at the end a tailored HTML report, thus combining the benefits of both interactivity and reproducibility. CONCLUSION GeneTonic is distributed as an R package in the Bioconductor project ( https://bioconductor.org/packages/GeneTonic/ ) under the MIT license. Offering both bird's-eye views of the components of transcriptome data analysis and the detailed inspection of single genes, individual signatures, and their relationships, GeneTonic aims at simplifying the process of interpretation of complex and compelling RNA-seq datasets for many researchers with different expertise profiles.
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Affiliation(s)
- Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Str. 69, 55131 Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Annekathrin Ludt
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Str. 69, 55131 Mainz, Germany
| | - Jan Linke
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Str. 69, 55131 Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Konstantin Strauch
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Str. 69, 55131 Mainz, Germany
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190
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Wang Q, Karvelsson ST, Kotronoulas A, Gudjonsson T, Halldorsson S, Rolfsson O. Glutamine-fructose-6-phosphate transaminase 2 (GFPT2) is upregulated in breast epithelial-mesenchymal transition and responds to oxidative stress. Mol Cell Proteomics 2021; 21:100185. [PMID: 34923141 PMCID: PMC8803663 DOI: 10.1016/j.mcpro.2021.100185] [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: 05/26/2021] [Revised: 10/20/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022] Open
Abstract
Breast cancer cells that have undergone partial epithelial–mesenchymal transition (EMT) are believed to be more invasive than cells that have completed EMT. To study metabolic reprogramming in different mesenchymal states, we analyzed protein expression following EMT in the breast epithelial cell model D492 with single-shot LFQ supported by a SILAC proteomics approach. The D492 EMT cell model contains three cell lines: the epithelial D492 cells, the mesenchymal D492M cells, and a partial mesenchymal, tumorigenic variant of D492 that overexpresses the oncogene HER2. The analysis classified the D492 and D492M cells as basal-like and D492HER2 as claudin-low. Comparative analysis of D492 and D492M to tumorigenic D492HER2 differentiated metabolic markers of migration from those of invasion. Glutamine-fructose-6-phosphate transaminase 2 (GFPT2) was one of the top dysregulated enzymes in D492HER2. Gene expression analysis of the cancer genome atlas showed that GFPT2 expression was a characteristic of claudin-low breast cancer. siRNA-mediated knockdown of GFPT2 influenced the EMT marker vimentin and both cell growth and invasion in vitro and was accompanied by lowered metabolic flux through the hexosamine biosynthesis pathway (HBP). Knockdown of GFPT2 decreased cystathionine and sulfide:quinone oxidoreductase (SQOR) in the transsulfuration pathway that regulates H2S production and mitochondrial homeostasis. Moreover, GFPT2 was within the regulation network of insulin and EGF, and its expression was regulated by reduced glutathione (GSH) and suppressed by the oxidative stress regulator GSK3-β. Our results demonstrate that GFPT2 controls growth and invasion in the D492 EMT model, is a marker for oxidative stress, and associated with poor prognosis in claudin-low breast cancer. GFPT2 is upregulated following EMT. GFPT2 is a marker for claudin-low breast cancer. GFPT2 affects vimentin, cell proliferation, and cell invasion. GFPT2 responds to oxidative stress. GFPT2 is regulated by insulin and EGF.
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Affiliation(s)
- Qiong Wang
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Sigurdur Trausti Karvelsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Aristotelis Kotronoulas
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Thorarinn Gudjonsson
- Stem Cell Research Unit, Biomedical Center, Department of Anatomy, Faculty of Medicine, School of Health Sciences, University of Iceland, Vatnsmyrarvegi 16, 101 Reykjavík, Iceland
| | - Skarphedinn Halldorsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Ottar Rolfsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland.
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191
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Hathaway QA, Majumder N, Goldsmith WT, Kunovac A, Pinti MV, Harkema JR, Castranova V, Hollander JM, Hussain S. Transcriptomics of single dose and repeated carbon black and ozone inhalation co-exposure highlight progressive pulmonary mitochondrial dysfunction. Part Fibre Toxicol 2021; 18:44. [PMID: 34911549 PMCID: PMC8672524 DOI: 10.1186/s12989-021-00437-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 11/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Air pollution is a complex mixture of particles and gases, yet current regulations are based on single toxicant levels failing to consider potential interactive outcomes of co-exposures. We examined transcriptomic changes after inhalation co-exposure to a particulate and a gaseous component of air pollution and hypothesized that co-exposure would induce significantly greater impairments to mitochondrial bioenergetics. A whole-body inhalation exposure to ultrafine carbon black (CB), and ozone (O3) was performed, and the impact of single and multiple exposures was studied at relevant deposition levels. C57BL/6 mice were exposed to CB (10 mg/m3) and/or O3 (2 ppm) for 3 h (either a single exposure or four independent exposures). RNA was isolated from lungs and mRNA sequencing performed using the Illumina HiSeq. Lung pathology was evaluated by histology and immunohistochemistry. Electron transport chain (ETC) activities, electron flow, hydrogen peroxide production, and ATP content were assessed. RESULTS Compared to individual exposure groups, co-exposure induced significantly greater neutrophils and protein levels in broncho-alveolar lavage fluid as well as a significant increase in mRNA expression of oxidative stress and inflammation related genes. Similarly, a significant increase in hydrogen peroxide production was observed after co-exposure. After single and four exposures, co-exposure revealed a greater number of differentially expressed genes (2251 and 4072, respectively). Of these genes, 1188 (single exposure) and 2061 (four exposures) were uniquely differentially expressed, with 35 mitochondrial ETC mRNA transcripts significantly impacted after four exposures. Both O3 and co-exposure treatment significantly reduced ETC maximal activity for complexes I (- 39.3% and - 36.2%, respectively) and IV (- 55.1% and - 57.1%, respectively). Only co-exposure reduced ATP Synthase activity (- 35.7%) and total ATP content (30%). Further, the ability for ATP Synthase to function is limited by reduced electron flow (- 25%) and translation of subunits, such as ATP5F1, following co-exposure. CONCLUSIONS CB and O3 co-exposure cause unique transcriptomic changes in the lungs that are characterized by functional deficits to mitochondrial bioenergetics. Alterations to ATP Synthase function and mitochondrial electron flow underly a pathological adaptation to lung injury induced by co-exposure.
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Affiliation(s)
- Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA
- Mitochondria, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
- Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA
| | - Nairrita Majumder
- Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, 64 Medical Center Drive, PO Box 9229, Morgantown, WV, 26506-9229, USA
| | - William T Goldsmith
- Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, 64 Medical Center Drive, PO Box 9229, Morgantown, WV, 26506-9229, USA
| | - Amina Kunovac
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA
- Mitochondria, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
- Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA
| | - Mark V Pinti
- Mitochondria, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
- West Virginia University School of Pharmacy, Morgantown, WV, USA
| | - Jack R Harkema
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Vince Castranova
- Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA
- Mitochondria, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
- Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA
| | - Salik Hussain
- Mitochondria, Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA.
- Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA.
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, 64 Medical Center Drive, PO Box 9229, Morgantown, WV, 26506-9229, USA.
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Gadepalli VS, Kim H, Liu Y, Han T, Cheng L. XDeathDB: a visualization platform for cell death molecular interactions. Cell Death Dis 2021; 12:1156. [PMID: 34907160 PMCID: PMC8669630 DOI: 10.1038/s41419-021-04397-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/07/2021] [Accepted: 11/09/2021] [Indexed: 12/23/2022]
Abstract
Lots of cell death initiator and effector molecules, signalling pathways and subcellular sites have been identified as key mediators in both cell death processes in cancer. The XDeathDB visualization platform provides a comprehensive cell death and their crosstalk resource for deciphering the signaling network organization of interactions among different cell death modes associated with 1461 cancer types and COVID-19, with an aim to understand the molecular mechanisms of physiological cell death in disease and facilitate systems-oriented novel drug discovery in inducing cell deaths properly. Apoptosis, autosis, efferocytosis, ferroptosis, immunogenic cell death, intrinsic apoptosis, lysosomal cell death, mitotic cell death, mitochondrial permeability transition, necroptosis, parthanatos, and pyroptosis related to 12 cell deaths and their crosstalk can be observed systematically by the platform. Big data for cell death gene-disease associations, gene-cell death pathway associations, pathway-cell death mode associations, and cell death-cell death associations is collected by literature review articles and public database from iRefIndex, STRING, BioGRID, Reactom, Pathway's commons, DisGeNET, DrugBank, and Therapeutic Target Database (TTD). An interactive webtool, XDeathDB, is built by web applications with R-Shiny, JavaScript (JS) and Shiny Server Iso. With this platform, users can search specific interactions from vast interdependent networks that occur in the realm of cell death. A multilayer spectral graph clustering method that performs convex layer aggregation to identify crosstalk function among cell death modes for a specific cancer. 147 hallmark genes of cell death could be observed in detail in these networks. These potential druggable targets are displayed systematically and tailoring networks to visualize specified relations is available to fulfil user-specific needs. Users can access XDeathDB for free at https://pcm2019.shinyapps.io/XDeathDB/ .
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Affiliation(s)
- Venkat Sundar Gadepalli
- Research Information Technology, College of Medicine, Ohio State University, 1585 Neil Ave, Columbus, OH, 43210, USA
| | - Hangil Kim
- 1Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Yueze Liu
- The Grainger College of Engineering, The University of Illinois-Urbana-Champaign, Urbana and Champaign, Champaign, IL, 61801, USA
| | - Tao Han
- 1Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Lijun Cheng
- 1Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA.
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193
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Proteomic profiling of MIS-C patients indicates heterogeneity relating to interferon gamma dysregulation and vascular endothelial dysfunction. Nat Commun 2021; 12:7222. [PMID: 34893640 PMCID: PMC8664884 DOI: 10.1038/s41467-021-27544-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/25/2021] [Indexed: 01/19/2023] Open
Abstract
Multi-system Inflammatory Syndrome in Children (MIS-C) is a major complication of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in pediatric patients. Weeks after an often mild or asymptomatic initial infection with SARS-CoV-2 children may present with a severe shock-like picture and marked inflammation. Children with MIS-C present with varying degrees of cardiovascular and hyperinflammatory symptoms. Here we perform a comprehensive analysis of the plasma proteome of more than 1400 proteins in children with SARS-CoV-2. We hypothesize that the proteome would reflect heterogeneity in hyperinflammation and vascular injury, and further identify pathogenic mediators of disease. We show that protein signatures demonstrate overlap between MIS-C, and the inflammatory syndromes macrophage activation syndrome (MAS) and thrombotic microangiopathy (TMA). We demonstrate that PLA2G2A is an important marker of MIS-C that associates with TMA. We find that IFNγ responses are dysregulated in MIS-C patients, and that IFNγ levels delineate clinical heterogeneity.
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194
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Tejeda-Mora H, Leon LG, Demmers J, Baan CC, Reinders MEJ, Bleck B, Lombardo E, Merino A, Hoogduijn MJ. Proteomic Analysis of Mesenchymal Stromal Cell-Derived Extracellular Vesicles and Reconstructed Membrane Particles. Int J Mol Sci 2021; 22:ijms222312935. [PMID: 34884740 PMCID: PMC8657583 DOI: 10.3390/ijms222312935] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EV) derived from mesenchymal stromal cells (MSC) are a potential therapy for immunological and degenerative diseases. However, large-scale production of EV free from contamination by soluble proteins is a major challenge. The generation of particles from isolated membranes of MSC, membrane particles (MP), may be an alternative to EV. In the present study we generated MP from the membranes of lysed MSC after removal of the nuclei. The yield of MP per MSC was 1 × 105 times higher than EV derived from the same number of MSC. To compare the proteome of MP and EV, proteomic analysis of MP and EV was performed. MP contained over 20 times more proteins than EV. The proteins present in MP evidenced a multi-organelle origin of MP. The projected function of the proteins in EV and MP was very different. Whilst proteins in EV mainly play a role in extracellular matrix organization, proteins in MP were interconnected in diverse molecular pathways, including protein synthesis and degradation pathways and demonstrated enzymatic activity. Treatment of MSC with IFNγ led to a profound effect on the protein make up of EV and MP, demonstrating the possibility to modify the phenotype of EV and MP through modification of parent MSC. These results demonstrate that MP are an attractive alternative to EV for the development of potential therapies. Functional studies will have to demonstrate therapeutic efficacy of MP in preclinical disease models.
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Affiliation(s)
- Hector Tejeda-Mora
- Erasmus MC Transplant Institute, Department of Internal Medicine, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (H.T.-M.); (C.C.B.); (M.E.J.R.); (A.M.)
| | - Leticia G. Leon
- The Netherlands Cancer Institute, Department of Pathology, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands;
| | - Jeroen Demmers
- Proteomics Center, Erasmus MC, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands;
| | - Carla C. Baan
- Erasmus MC Transplant Institute, Department of Internal Medicine, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (H.T.-M.); (C.C.B.); (M.E.J.R.); (A.M.)
| | - Marlies E. J. Reinders
- Erasmus MC Transplant Institute, Department of Internal Medicine, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (H.T.-M.); (C.C.B.); (M.E.J.R.); (A.M.)
| | - Bertram Bleck
- Takeda, Gastrointestinal Drug Discovery Unit, Cambridge, MA 02139, USA;
| | - Eleuterio Lombardo
- Takeda Madrid, Cell Therapy Technology Center-Cell Therapies, 28046 Madrid, Spain;
| | - Ana Merino
- Erasmus MC Transplant Institute, Department of Internal Medicine, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (H.T.-M.); (C.C.B.); (M.E.J.R.); (A.M.)
| | - Martin J. Hoogduijn
- Erasmus MC Transplant Institute, Department of Internal Medicine, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (H.T.-M.); (C.C.B.); (M.E.J.R.); (A.M.)
- Correspondence:
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195
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Wu Y, Yu XL, Xiao X, Li M, Li Y. Joint-Tissue Integrative Analysis Identified Hundreds of Schizophrenia Risk Genes. Mol Neurobiol 2021; 59:107-116. [PMID: 34628600 DOI: 10.1007/s12035-021-02572-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/16/2021] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies (GWAS) have identified a large number of schizophrenia risk variants, and most of them are mapped to noncoding regions. By leveraging multiple joint-tissue gene expression data and GWAS data, we herein performed a transcriptome-wide association study (TWAS) and Mendelian randomization (MR) analysis and identified 144 genes whose mRNA levels were related to genetic risk of schizophrenia. Most of these genes exhibited diametrically opposite trends of expression in prenatal and postnatal brain tissues, despite that their expression levels in dorsolateral prefrontal cortex (DLPFC) tissues did not significantly differ between schizophrenics and healthy controls. We then found significant enrichment of these genes in dopamine-related pathways that were repeatedly implicated in schizophrenia pathogenesis and in the action of antipsychotic drugs. Gene expression analysis using single cell RNA-sequencing (scRNA-seq) data of mid-gestation fetal brains further revealed enrichment of these genes in glutamatergic excitatory neurons and cycling progenitors. These lines of evidence, in consistency with previous findings, confirmed the polygenic nature of schizophrenia and highlighted involvement of early neurodevelopment aberrations in this disorder. Further investigations using advanced algorithms in both bulk brain tissues and in single cells and at different developmental stages are necessary to characterize transcriptomic features of schizophrenia pathogenesis along brain development.
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Affiliation(s)
- Yong Wu
- Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xiao-Lin Yu
- Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yi Li
- Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China. .,Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, 430074, Hubei, China.
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Sarsenbayeva A, Jui BN, Fanni G, Barbosa P, Ahmed F, Kristófi R, Cen J, Chowdhury A, Skrtic S, Bergsten P, Fall T, Eriksson JW, Pereira MJ. Impaired HMG-CoA Reductase Activity Caused by Genetic Variants or Statin Exposure: Impact on Human Adipose Tissue, β-Cells and Metabolome. Metabolites 2021; 11:574. [PMID: 34564389 PMCID: PMC8468287 DOI: 10.3390/metabo11090574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 11/20/2022] Open
Abstract
Inhibition of 3-hydroxy-3-methyl-glutaryl-CoA (HMG-CoA) reductase is associated with an increased risk of new-onset type 2 diabetes. We studied the association of genetic or pharmacological HMG-CoA reductase inhibition with plasma and adipose tissue (AT) metabolome and AT metabolic pathways. We also investigated the effects of statin-mediated pharmacological inhibition of HMG-CoA reductase on systemic insulin sensitivity by measuring the HOMA-IR index in subjects with or without statin therapy. The direct effects of simvastatin (20-250 nM) or its active metabolite simvastatin hydroxy acid (SA) (8-30 nM) were investigated on human adipocyte glucose uptake, lipolysis, and differentiation and pancreatic insulin secretion. We observed that the LDL-lowering HMGCR rs12916-T allele was negatively associated with plasma phosphatidylcholines and sphingomyelins, and HMGCR expression in AT was correlated with various metabolic and mitochondrial pathways. Clinical data showed that statin treatment was associated with HOMA-IR index after adjustment for age, sex, BMI, HbA1c, LDL-c levels, and diabetes status in the subjects. Supra-therapeutic concentrations of simvastatin reduced glucose uptake in adipocytes and normalized fatty acid-induced insulin hypersecretion from β-cells. Our data suggest that inhibition of HMG-CoA reductase is associated with insulin resistance. However, statins have a very mild direct effect on AT and pancreas, hence, other tissues as the liver or muscle appear to be of greater importance.
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Affiliation(s)
- Assel Sarsenbayeva
- Department of Medical Sciences, Clinical Diabetology and Metabolism, Uppsala University, 751 85 Uppsala, Sweden; (A.S.); (B.N.J.); (G.F.); (F.A.); (R.K.); (T.F.); (J.W.E.)
| | - Bipasha Nandi Jui
- Department of Medical Sciences, Clinical Diabetology and Metabolism, Uppsala University, 751 85 Uppsala, Sweden; (A.S.); (B.N.J.); (G.F.); (F.A.); (R.K.); (T.F.); (J.W.E.)
| | - Giovanni Fanni
- Department of Medical Sciences, Clinical Diabetology and Metabolism, Uppsala University, 751 85 Uppsala, Sweden; (A.S.); (B.N.J.); (G.F.); (F.A.); (R.K.); (T.F.); (J.W.E.)
| | - Pedro Barbosa
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal;
- Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Fozia Ahmed
- Department of Medical Sciences, Clinical Diabetology and Metabolism, Uppsala University, 751 85 Uppsala, Sweden; (A.S.); (B.N.J.); (G.F.); (F.A.); (R.K.); (T.F.); (J.W.E.)
| | - Robin Kristófi
- Department of Medical Sciences, Clinical Diabetology and Metabolism, Uppsala University, 751 85 Uppsala, Sweden; (A.S.); (B.N.J.); (G.F.); (F.A.); (R.K.); (T.F.); (J.W.E.)
| | - Jing Cen
- Department of Medical Cell Biology, Uppsala University, 751 85 Uppsala, Sweden; (J.C.); (A.C.); (P.B.)
| | - Azazul Chowdhury
- Department of Medical Cell Biology, Uppsala University, 751 85 Uppsala, Sweden; (J.C.); (A.C.); (P.B.)
| | - Stanko Skrtic
- Innovation Strategies & External Liaison, Pharmaceutical Technologies & Development, AstraZeneca, 431 83 Gothenburg, Sweden;
- Institute of Medicine at Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Peter Bergsten
- Department of Medical Cell Biology, Uppsala University, 751 85 Uppsala, Sweden; (J.C.); (A.C.); (P.B.)
| | - Tove Fall
- Department of Medical Sciences, Clinical Diabetology and Metabolism, Uppsala University, 751 85 Uppsala, Sweden; (A.S.); (B.N.J.); (G.F.); (F.A.); (R.K.); (T.F.); (J.W.E.)
| | - Jan W. Eriksson
- Department of Medical Sciences, Clinical Diabetology and Metabolism, Uppsala University, 751 85 Uppsala, Sweden; (A.S.); (B.N.J.); (G.F.); (F.A.); (R.K.); (T.F.); (J.W.E.)
| | - Maria J. Pereira
- Department of Medical Sciences, Clinical Diabetology and Metabolism, Uppsala University, 751 85 Uppsala, Sweden; (A.S.); (B.N.J.); (G.F.); (F.A.); (R.K.); (T.F.); (J.W.E.)
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197
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Sodagari HR, Sahibzada S, Robertson I, Habib I, Wang P. Whole-Genome Comparative Analysis Reveals Association Between Salmonella Genomic Variation and Egg Production Systems. Front Vet Sci 2021; 8:666767. [PMID: 34322531 PMCID: PMC8311177 DOI: 10.3389/fvets.2021.666767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Non-typhoidal Salmonella, particularly Salmonella enterica serovar Typhimurium (S. Typhimurium), is the predominant endemic serovar in the Australian egg production industry and is one of the most frequently reported serovars in foodborne infections in Australia. This study was conducted to investigate the genomic characteristics of Salmonella isolated from retail table eggs in Western Australia and to identify the impact of production systems on genomic characteristics of Salmonella such as virulence and antimicrobial resistance. A total of 40 non-typhoidal Salmonella isolates [S. Typhimurium isolates (n = 28) and Salmonella Infantis isolates (n = 12)] sourced from retail eggs produced by different production systems (barn-laid, cage, and free-range) in Western Australia were sequenced by whole-genome sequencing. The isolates were de novo assembled, annotated, and analyzed. The results indicated an association between Salmonella genomic variation and the system used to raise poultry for egg production (p-value < 0.05). All but one of the S. Infantis isolates were recovered from eggs collected from poultry raised under barn and cage production systems. A higher proportion (83.3%) of S. Typhimurium isolates were recovered from the eggs produced by free-range production system as compared with those produced under barn (76.9%) and cage production systems (53.3%). Our analysis indicated that Salmonella isolated from the eggs produced by barn and cage production systems had more virulence genes than the isolates of the free-range produced eggs. A low carriage of antimicrobial-resistant gene was detected in the isolates of this study. We have built a Salmonella genomics database and characteristics-linked gene pools to facilitate future study, characterization, and tracing of Salmonella outbreaks.
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Affiliation(s)
- Hamid Reza Sodagari
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Shafi Sahibzada
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Ian Robertson
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Ihab Habib
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
- Department of Veterinary Medicine, College of Food and Agriculture, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Penghao Wang
- Medical, Molecular and Forensic Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
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198
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DNA Methylation Profiling for the Diagnosis and Prognosis of Patients with Nontuberculous Mycobacterium Lung Disease. Curr Issues Mol Biol 2021; 43:501-512. [PMID: 34203447 PMCID: PMC8929150 DOI: 10.3390/cimb43020038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
The incidence of nontuberculous Mycobacterium (NTM) lung disease is rapidly increasing; however, its diagnosis and prognosis remain unclear while selecting patients who will respond to appropriate treatment. Differences in DNA methylation patterns between NTM patients with good or poor prognosis could provide important therapeutic targets. We used the Illumina MethylationEPIC (850k) DNA methylation microarray to determine the pattern between differentially methylated regions (DMRs) in NTM patients with good or poor prognosis (n = 4/group). Moreover, we merged and compared 20 healthy controls from previous Illumina Methylation450k DNA methylation microarray data. We selected and visualized the DMRs in the form of heatmaps, and enriched terms associated with these DMRs were identified by functional annotation with the “pathfinder” package. In total, 461 and 293 DMRs (|Log2 fold change| > 0.1 and P < 0.03) were more methylated in patients with four poor and four good prognoses, respectively. Furthermore, 337 and 771 DMRs (|Log2 fold change| > 0.08 and P < 0.001) were more methylated in eight NTM patients and 20 healthy controls, respectively. TGFBr1 was significantly less methylated, whereas HLA-DR1 and HLA-DR5 were more methylated in patients with poor prognosis (compared to those with good prognosis). LRP5, E2F1, and ADCY3 were the top three less-methylated genes in NTM patients (compared with the controls). The mTOR and Wnt signaling pathway-related genes were less methylated in patients with NTM. Collectively, genes related to Th1- cell differentiation, such as TGFBr1 and HLA-DR, may be used as biomarkers for predicting the treatment response in patients with NTM lung disease.
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199
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Bioinformatic Analysis Reveals Central Role for Tumor-Infiltrating Immune Cells in Uveal Melanoma Progression. J Immunol Res 2021; 2021:9920234. [PMID: 34195299 PMCID: PMC8214507 DOI: 10.1155/2021/9920234] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/05/2021] [Accepted: 05/23/2021] [Indexed: 12/13/2022] Open
Abstract
Tumor-infiltrating immune cells are capable of effective cancer surveillance, and their abundance is linked to better prognosis in numerous tumor types. However, in uveal melanoma (UM), extensive immune infiltrate is associated with poor survival. This study aims to decipher the role of different tumor-infiltrating cell subsets in UM in order to identify potential targets for future immunotherapeutic treatment. We have chosen the TCGA-UVM cohort as a training dataset and GSE22138 as a testing dataset by mining publicly available databases. The abundance of 22 immune cell types was estimated using CIBERSORTx. Then, to determine the significance of tumor-infiltrating cell subsets in UM, we built a multicell type prognostic signature, which was validated in the testing cohort. The created signature was built upon the negative prognostic role of CD8+ T cells and M0 macrophages and the positive role of neutrophils. Based on the created signature score, we divided the patients into low- and high-risk groups. Kaplan-Meier, Cox, and ROC analyses demonstrated superior performance of our risk score compared to either clinical or pathologic characteristics of both cohorts. Further, we found the molecular pathways associated with cancer immunoevasion and metastasis to be enriched in the high-risk group, explaining both the lack of adequate immune surveillance despite increased infiltration of CD8+ T cells as well as the higher metastatic potential. Genes associated with tryptophan metabolism (IDO1 and KYNU) and metalloproteinases were among the most differentially expressed between the high- and low-risk groups. Our correlation analyses interpreted in context of published in vitro data strongly suggest the central role of CD8+ T cells in shifting the UM tumor microenvironment towards suppressive and metastasis-promoting. Therefore, we propose further investigations of IDO1 and metalloproteinases as novel targets for immunotherapy in lymphocyte-rich metastatic UM patients.
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200
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He L, Davila-Velderrain J, Sumida TS, Hafler DA, Kellis M, Kulminski AM. NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data. Commun Biol 2021; 4:629. [PMID: 34040149 PMCID: PMC8155058 DOI: 10.1038/s42003-021-02146-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/19/2021] [Indexed: 11/18/2022] Open
Abstract
The increasing availability of single-cell data revolutionizes the understanding of biological mechanisms at cellular resolution. For differential expression analysis in multi-subject single-cell data, negative binomial mixed models account for both subject-level and cell-level overdispersions, but are computationally demanding. Here, we propose an efficient NEgative Binomial mixed model Using a Large-sample Approximation (NEBULA). The speed gain is achieved by analytically solving high-dimensional integrals instead of using the Laplace approximation. We demonstrate that NEBULA is orders of magnitude faster than existing tools and controls false-positive errors in marker gene identification and co-expression analysis. Using NEBULA in Alzheimer's disease cohort data sets, we found that the cell-level expression of APOE correlated with that of other genetic risk factors (including CLU, CST3, TREM2, C1q, and ITM2B) in a cell-type-specific pattern and an isoform-dependent manner in microglia. NEBULA opens up a new avenue for the broad application of mixed models to large-scale multi-subject single-cell data.
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Affiliation(s)
- Liang He
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA.
| | - Jose Davila-Velderrain
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - Tomokazu S Sumida
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Cardiovascular Medicine, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA.
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