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Gcanga L, Tamgue O, Ozturk M, Pillay S, Jacobs R, Chia JE, Mbandi SK, Davids M, Dheda K, Schmeier S, Alam T, Roy S, Suzuki H, Brombacher F, Guler R. Host-Directed Targeting of LincRNA-MIR99AHG Suppresses Intracellular Growth of Mycobacterium tuberculosis. Nucleic Acid Ther 2022; 32:421-437. [PMID: 35895506 PMCID: PMC7613730 DOI: 10.1089/nat.2022.0009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) kills 1.6 million people worldwide every year, and there is an urgent need for targeting host-pathogen interactions as a strategy to reduce mycobacterial resistance to current antimicrobials. Noncoding RNAs are emerging as important regulators of numerous biological processes and avenues for exploitation in host-directed therapeutics. Although long noncoding RNAs (lncRNAs) are abundantly expressed in immune cells, their functional role in gene regulation and bacterial infections remains understudied. In this study, we identify an immunoregulatory long intergenic noncoding RNA, lincRNA-MIR99AHG, which is upregulated in mouse and human macrophages upon IL-4/IL-13 stimulation and downregulated after clinical Mtb HN878 strain infection and in peripheral blood mononuclear cells from active TB patients. To evaluate the functional role of lincRNA-MIR99AHG, we used antisense locked nucleic acid (LNA) GapmeR-mediated antisense oligonucleotide (ASO) lncRNA knockdown experiments. Knockdown of lincRNA-MIR99AHG with ASOs significantly reduced intracellular Mtb growth in mouse and human macrophages and reduced pro-inflammatory cytokine production. In addition, in vivo treatment of mice with MIR99AHG ASOs reduced the mycobacterial burden in the lung and spleen. Furthermore, in macrophages, lincRNA-MIR99AHG is translocated to the nucleus and interacts with high affinity to hnRNPA2/B1 following IL-4/IL-13 stimulation and Mtb HN878 infection. Together, these findings identify lincRNA-MIR99AHG as a positive regulator of inflammation and macrophage polarization to promote Mtb growth and a possible target for adjunctive host-directed therapy against TB.
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Affiliation(s)
- Lorna Gcanga
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa
| | - Ousman Tamgue
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa.,Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Mumin Ozturk
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa
| | - Shandre Pillay
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa
| | - Raygaana Jacobs
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa
| | - Julius Ebua Chia
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa
| | - Stanley Kimbung Mbandi
- Division of Immunology, Department of Pathology, South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Malika Davids
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunology, UCT Lung Institute, University of Cape Town, Cape Town, South Africa.,South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Keertan Dheda
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunology, UCT Lung Institute, University of Cape Town, Cape Town, South Africa.,South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa.,Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical medicine, London, United Kingdom
| | - Sebastian Schmeier
- College of Science, School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Tanvir Alam
- Information and Computing Technology Division, College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Sugata Roy
- RIKEN Center for Integrative Medical Sciences, Cellular Function Conversion Technology Team, Yokohama, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Cellular Function Conversion Technology Team, Yokohama, Japan
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Address correspondence to: Frank Brombacher, PhD, International Centre for Genetic Engineering and Biotechnology (ICGEB) Department of Pathology, Cape Town Component, Cape Town 7925, South Africa
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Reto Guler, PhD, Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town 7925, South Africa
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2
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Matsumoto H, Scicluna BP, Jim KK, Falahi F, Qin W, Gürkan B, Malmström E, Meijer MT, Butler JM, Khan HN, Takagi T, Ishii S, Schultz MJ, van de Beek D, de Vos AF, van 't Veer C, van der Poll T. HIVEP1 Is a Negative Regulator of NF-κB That Inhibits Systemic Inflammation in Sepsis. Front Immunol 2021; 12:744358. [PMID: 34804025 PMCID: PMC8602905 DOI: 10.3389/fimmu.2021.744358] [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: 07/20/2021] [Accepted: 10/12/2021] [Indexed: 11/23/2022] Open
Abstract
Our previous work identified human immunodeficiency virus type I enhancer binding protein 1 (HIVEP1) as a putative driver of LPS-induced NF-κB signaling in humans in vivo. While HIVEP1 is known to interact with NF-ĸB binding DNA motifs, its function in mammalian cells is unknown. We report increased HIVEP1 mRNA expression in monocytes from patients with sepsis and monocytes stimulated by Toll-like receptor agonists and bacteria. In complementary overexpression and gene deletion experiments HIVEP1 was shown to inhibit NF-ĸB activity and induction of NF-ĸB responsive genes. RNA sequencing demonstrated profound transcriptomic changes in HIVEP1 deficient monocytic cells and transcription factor binding site analysis showed enrichment for κB site regions. HIVEP1 bound to the promoter regions of NF-ĸB responsive genes. Inhibition of cytokine production by HIVEP1 was confirmed in LPS-stimulated murine Hivep1-/- macrophages and HIVEP1 knockdown zebrafish exposed to the common sepsis pathogen Streptococcus pneumoniae. These results identify HIVEP1 as a negative regulator of NF-κB in monocytes/macrophages that inhibits proinflammatory reactions in response to bacterial agonists in vitro and in vivo.
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Affiliation(s)
- Hisatake Matsumoto
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Brendon P Scicluna
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Kin Ki Jim
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Neurology, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Fahimeh Falahi
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Wanhai Qin
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Berke Gürkan
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Erik Malmström
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Mariska T Meijer
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Joe M Butler
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Hina N Khan
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Tsuyoshi Takagi
- Department of Disease Model, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, Japan
| | | | - Marcus J Schultz
- Department of Intensive Care Medicine, Laboratory of Experimental Intensive Care and Anesthesiology (L·E·I·C·A), Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Mahidol-Oxford Tropical Medicine Research Unit (MORU), Mahidol University, Bangkok, Thailand.,Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Diederik van de Beek
- Department of Neurology, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Alex F de Vos
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Cornelis van 't Veer
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Division of Infectious Diseases, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
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3
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Hlaka L, Ozturk M, Chia JE, Jones SS, Pillay S, Poswayo SKL, Mpotje T, Nono JK, Simelane S, Parihar SP, Roy S, Suzuki H, Brombacher F, Guler R. IL-4i1 regulates immune protection during Mycobacterium tuberculosis infection. J Infect Dis 2021; 224:2170-2180. [PMID: 34739044 PMCID: PMC8672763 DOI: 10.1093/infdis/jiab558] [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: 02/23/2021] [Accepted: 11/01/2021] [Indexed: 11/24/2022] Open
Abstract
Background Interleukin 4 (IL-4i1)–induced gene 1 encodes L-phenylalanine oxidase that catabolizes phenylalanine into phenylpyruvate. IL-4i1 is mainly expressed by antigen-presenting cells (APCs), inhibits T-cell proliferation, regulates B-cell activation, modulates T cell responses, and drives macrophage polarization, but its role in bacterial infections is understudied. Methods We evaluated IL-4i1 deletion in macrophages and mice on infection with virulent H37Rv and W-Beijing lineage hypervirulent HN878 Mycobacterium tuberculosis (Mtb) strains. The bacterial growth and proinflammatory responses were measured in vitro and in vivo. Histopathological analysis, lung immune cell recruitment, and macrophage activation were assessed at the early and chronic stages of Mtb infection. Results IL-4i1–deficient (IL-4i1−/−) mice displayed increased protection against acute H37Rv, HN878 and chronic HN878 Mt infections, with reduced lung bacterial burdens and altered APC responses compared with wild-type mice. Moreover, “M1-like” interstitial macrophage numbers, and nitrite and Interferon-γ production were significantly increased in IL-4i1−/− mice compared with wild-type mice during acute Mtb HN878 infection. Conclusions Together, these data suggest that IL-4i1 regulates APC-mediated inflammatory responses during acute and chronic Mtb infection. Hence, IL-4i1 targeting has potential as an immunomodulatory target for host-directed therapy.
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Affiliation(s)
- Lerato Hlaka
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa.,The Jackson Laboratory for Genomic Medicine, Connecticut, 06032, United States
| | - Mumin Ozturk
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Julius E Chia
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Shelby-Sara Jones
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Shandre Pillay
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Sibongiseni K L Poswayo
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Thabo Mpotje
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Justin K Nono
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa.,Laboratory of ImmunoBiology and Helminth Infections (IBHI), Institute of Medical Research and Medicinal Plant Studies, Ministry of Scientific Research and Innovation, Yaoundé, 13033, Cameroon
| | - Simphiwe Simelane
- Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Suraj P Parihar
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Sugata Roy
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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4
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Elizarova A, Ozturk M, Guler R, Medvedeva YA. MIREyA: a computational approach to detect miRNA-directed gene activation. F1000Res 2021; 10:249. [PMID: 34527215 PMCID: PMC8411277 DOI: 10.12688/f1000research.28142.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 11/20/2022] Open
Abstract
Emerging studies demonstrate the ability of microRNAs (miRNAs) to activate genes via different mechanisms. Specifically, miRNAs may trigger an enhancer promoting chromatin remodelling in the enhancer region, thus activating the enhancer and its target genes. Here we present MIREyA, a pipeline developed to predict such miRNA-gene-enhancer trios based on an expression dataset which obviates the need to write custom scripts. We applied our pipeline to primary murine macrophages infected by Mycobacterium tuberculosis (HN878 strain) and detected Mir22, Mir221, Mir222, Mir155 and Mir1956, which could up-regulate genes related to immune responses. We believe that MIREyA is a useful tool for detecting putative miRNA-directed gene activation cases. MIREyA is available from: https://github.com/veania/MIREyA.
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Affiliation(s)
- Anna Elizarova
- Group of Regulatory Transcriptomics and Epigenomics, Research Center of Biotechnology, Institute of Bioengineering, Russian Academy of Sciences, Moscow, 117312, Russian Federation.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, 141701, Russian Federation
| | - Mumin Ozturk
- International Centre for Genetic Engineering and Biotechnology, Cape Town, Cape Town, 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, Cape Town, 7925, South Africa
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology, Cape Town, Cape Town, 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, Cape Town, 7925, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Yulia A Medvedeva
- Group of Regulatory Transcriptomics and Epigenomics, Research Center of Biotechnology, Institute of Bioengineering, Russian Academy of Sciences, Moscow, 117312, Russian Federation.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, 141701, Russian Federation
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5
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Roy D, Ehtesham NZ, Hasnain SE. Is Mycobacterium tuberculosis carcinogenic to humans? FASEB J 2021; 35:e21853. [PMID: 34416038 DOI: 10.1096/fj.202001581rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 05/20/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022]
Abstract
We highlight the ability of the tuberculosis (TB) causing bacterial pathogen, Mycobacterium tuberculosis (Mtb), to induce key characteristics that are associated with established IARC classified Group 1 and Group 2A carcinogenic agents. There is sufficient evidence from epidemiological case-control, cohort and meta-analysis studies of increased lung cancer (LC) risk in pre-existing/active/old TB cases. Similar to carcinogens and other pathogenic infectious agents, exposure to aerosol-containing Mtb sprays in mice produce malignant transformation of cells that result in squamous cell carcinoma. Convincing, mechanistic data show several characteristics shared between TB and LC which include chronic inflammation, genomic instability and replicative immortality, just to name a few cancer hallmarks. These hallmarks of cancer may serve as precursors to malignant transformation. Together, these findings form the basis of our postulate that Mtb is a complete human pulmonary carcinogen. We also discuss how Mtb may act as both an initiating agent and promoter of tumor growth. Forthcoming experimental studies will not only serve as proof-of-concept but will also pivot our understanding of how to manage/treat TB cases as well as offer solutions to clinical conundrums of TB lesions masquerading as tumors. Clinical validation of our concept may also help pave the way for next generation personalized medicine for the management of pulmonary TB/cancer particularly for cases that are not responding well to conventional chemotherapy or TB drugs.
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Affiliation(s)
- Deodutta Roy
- Department of Environmental Health Sciences, Florida International University, Miami, FL, USA
| | - Nasreen Z Ehtesham
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Seyed Ehtesham Hasnain
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, India.,Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), New Delhi, India
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6
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Ruan QL, Yang QL, Gao YX, Wu J, Lin SR, Zhou JY, Shao LY, Wang S, Liu QQ, Gao Y, Jiang N, Zhang WH. Transcriptional signatures of human peripheral blood mononuclear cells can identify the risk of tuberculosis progression from latent infection among individuals with silicosis. Emerg Microbes Infect 2021; 10:1536-1544. [PMID: 34042560 PMCID: PMC8354161 DOI: 10.1080/22221751.2021.1915184] [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] [Indexed: 11/23/2022]
Abstract
Host immune factor plays an important role in the progression of latent tuberculosis infection (LTBI) to active tuberculosis (TB) disease. However, whether global gene expression measured in blood biomarkers allows the identification of prospective signatures for TB risk remains unknown. Hence, we aimed to assess the ability of the transcriptome signatures in the human peripheral blood mononuclear cells (PBMCs) of LTBI subjects to differentiate future TB progressors from non-progressors. In a randomized clinical trial of TB preventive treatment of 513 participants with silicosis, we randomly collected PBMC samples from 50 LTBI subjects in the observational group, which was monitored for TB disease progression for 37 months. The prospective signatures of TB risk between the two participants who developed active TB (progressors) and four matched individuals who remained healthy (non-progressors) were compared using differential expression analysis, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, and Weighted Gene Co-expression Network Analysis. The 20 TB-specific differentially expressed genes, which were significantly downregulated in TB progressors, were revealed to be associated with interferon-gamma response-related genes. Therefore, the PBMC transcriptome profiles analyzed in this study may help identify LTBI individuals who are at risk of progressing to active TB among silicosis patients and may provide new insights for targeted intervention to prevent disease progression.
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Affiliation(s)
- Qiao-Ling Ruan
- Department of Infectious Diseases, Huashan Hospital, School of Life Science, Fudan University, Shanghai, People's Republic of China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Qing-Luan Yang
- Department of Infectious Diseases, Huashan Hospital, School of Life Science, Fudan University, Shanghai, People's Republic of China
| | - Yi-Xin Gao
- Department of Infectious Diseases, Huashan Hospital, School of Life Science, Fudan University, Shanghai, People's Republic of China
| | - Jing Wu
- Department of Infectious Diseases, Huashan Hospital, School of Life Science, Fudan University, Shanghai, People's Republic of China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Si-Ran Lin
- Department of Infectious Diseases, Huashan Hospital, School of Life Science, Fudan University, Shanghai, People's Republic of China
| | - Jing-Yu Zhou
- Department of Infectious Diseases, Huashan Hospital, School of Life Science, Fudan University, Shanghai, People's Republic of China
| | - Ling-Yun Shao
- Department of Infectious Diseases, Huashan Hospital, School of Life Science, Fudan University, Shanghai, People's Republic of China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Sen Wang
- Department of Infectious Diseases, Huashan Hospital, School of Life Science, Fudan University, Shanghai, People's Republic of China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Qian-Qian Liu
- Department of Infectious Diseases, Huashan Hospital, School of Life Science, Fudan University, Shanghai, People's Republic of China
| | - Yan Gao
- Department of Infectious Diseases, Huashan Hospital, School of Life Science, Fudan University, Shanghai, People's Republic of China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Ning Jiang
- Department of Infectious Diseases, Huashan Hospital, School of Life Science, Fudan University, Shanghai, People's Republic of China
| | - Wen-Hong Zhang
- Department of Infectious Diseases, Huashan Hospital, School of Life Science, Fudan University, Shanghai, People's Republic of China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
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7
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Whole-Transcriptome RNA Sequencing Reveals Significant Differentially Expressed mRNAs, miRNAs, and lncRNAs and Related Regulating Biological Pathways in the Peripheral Blood of COVID-19 Patients. Mediators Inflamm 2021; 2021:6635925. [PMID: 33833618 PMCID: PMC8018221 DOI: 10.1155/2021/6635925] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/20/2021] [Accepted: 02/27/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was initially identified in China and currently worldwide dispersed, resulting in the coronavirus disease 2019 (COVID-19) pandemic. Notably, COVID-19 is characterized by systemic inflammation. However, the potential mechanisms of the “cytokine storm” of COVID-19 are still limited. In this study, fourteen peripheral blood samples from COVID-19 patients (n = 10) and healthy donors (n = 4) were collected to perform the whole-transcriptome sequencing. Lung tissues of COVID-19 patients (70%) presenting with ground-glass opacity. Also, the leukocytes and lymphocytes were significantly decreased in COVID-19 compared with the control group (p < 0.05). In total, 25,482 differentially expressed messenger RNAs (DE mRNA), 23 differentially expressed microRNAs (DE miRNA), and 410 differentially expressed long noncoding RNAs (DE lncRNAs) were identified in the COVID-19 samples compared to the healthy controls. Gene Ontology (GO) analysis showed that the upregulated DE mRNAs were mainly involved in antigen processing and presentation of endogenous antigen, positive regulation of T cell mediated cytotoxicity, and positive regulation of gamma-delta T cell activation. The downregulated DE mRNAs were mainly concentrated in the glycogen biosynthetic process. We also established the protein-protein interaction (PPI) networks of up/downregulated DE mRNAs and identified 4 modules. Functional enrichment analyses indicated that these module targets were associated with positive regulation of cytokine production, cytokine-mediated signaling pathway, leukocyte differentiation, and migration. A total of 6 hub genes were selected in the PPI module networks including AKT1, TNFRSF1B, FCGR2A, CXCL8, STAT3, and TLR2. Moreover, a competing endogenous RNA network showed the interactions between lncRNAs, mRNAs, and miRNAs. Our results highlight the potential pathogenesis of excessive cytokine production such as MSTRG.119845.30/hsa-miR-20a-5p/TNFRSF1B, MSTRG.119845.30/hsa-miR-29b-2-5p/FCGR2A, and MSTRG.106112.2/hsa-miR-6501-5p/STAT3 axis, which may also play an important role in the development of ground-glass opacity in COVID-19 patients. This study gives new insights into inflammation regulatory mechanisms of coding and noncoding RNAs in COVID-19, which may provide novel diagnostic biomarkers and therapeutic avenues for COVID-19 patients.
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Yang C, Lan W, Ye S, Zhu B, Fu Z. Transcriptomic Analyses Reveal the Protective Immune Regulation of Conjugated Linoleic Acids in Sheep Ruminal Epithelial Cells. Front Physiol 2020; 11:588082. [PMID: 33192603 PMCID: PMC7658390 DOI: 10.3389/fphys.2020.588082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022] Open
Abstract
The ruminal epithelium is continuously challenged by antigens released by the lysis of dead microbial cells within the rumen. However, the innate immune system of the ruminal epithelium can almost always actively respond to these challenges. The cross talk between the ruminal microbiota and innate immune cells in the ruminal epithelium has been suggested to play an important role in sustaining the balance of immune tolerance and inflammatory response in the rumen. We hypothesized that conjugated linoleic acid (CLA), a functional microbial metabolite in the rumen, may contribute to the immune regulation in rumen epithelial cells (RECs); therefore, we first established an immortal REC line and then investigated the regulatory effects of CLA on the immune responses in these RECs. The results showed that long-term REC cultures were successfully established via SV40T-induced immortalization. Transcriptome analysis showed that a 100 μM CLA mixture consisting of 50:50 cis-9, trans-11:trans-10, cis-12 CLA significantly downregulated the expression of the inflammatory response-related genes TNF-α, IL-6, CX3CL1, IRF1, ICAM1 and EDN1, and upregulated the expression of the cell proliferation-related genes FGF7, FGF21, EREG, AREG and HBEGF and the lipid metabolism-related genes PLIN2, CPT1A, ANGPTL4, ABHD5 and SREBF1 in the RECs upon LPS stimulation. Correspondingly, the GO terms regulation of cell adhesion, response to stimulus and cytokine production and KEGG pathways TNF and HIF-1 signaling, ECM-receptor interaction and cell adhesion molecules were identified for the significantly downregulated genes, while the GO terms epithelial cell proliferation and regulation of epithelial cell migration and the KEGG pathways PPAR, ErbB and adipocytokine signaling were identified for the RECs with significantly upregulated CLA-pretreated genes upon LPS stimulation. These findings revealed that CLA conferred protective immunity onto the RECs by inhibiting proinflammatory processes, promoting cell proliferation and regulating lipid metabolism related to the immune response.
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Affiliation(s)
- Chunlei Yang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Wei Lan
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Shijie Ye
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Binna Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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Youk H, Kim M, Lee CJ, Oh J, Park S, Kang SM, Kim JH, Ann SJ, Lee SH. Nlrp3, Csf3, and Edn1 in Macrophage Response to Saturated Fatty Acids and Modified Low-Density Lipoprotein. Korean Circ J 2020; 51:68-80. [PMID: 32975056 PMCID: PMC7779813 DOI: 10.4070/kcj.2020.0117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 07/09/2020] [Accepted: 07/28/2020] [Indexed: 12/17/2022] Open
Abstract
Background and Objectives The relationship between metabolic stress, inflammation, and cardiovascular disease is being studied steadily. The aim of this study was to evaluate the effect of palmitate (PA) and minimally modified low-density lipoprotein (mmLDL) on macrophages and to identify the associated pathways. Methods J774 macrophages were incubated with PA or mmLDL and lipopolysaccharide (LPS). Secretion of inflammatory chemokines and the expression of corresponding genes were determined. The phosphorylation of extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase was also assessed. RNA sequencing of macrophages was performed to identify the genes regulated by PA or mmLDL. Some of the genes regulated by the 2 agents were validated by knocking down the cells using small interfering RNA. Results PA or mmLDL promoted the secretion of interleukin (IL)-6 and IL-1β in LPS-stimulated macrophages, and this was accompanied by higher phosphorylation of ERK. RNA sequencing revealed dozens of genes that were regulated in this process, such as Csf3 and Edn1, which were affected by PA and mmLDL, respectively. These agents also increased Nlrp3 expression. The effect of Csf3 or Edn1 silencing on inflammation was modest, whereas toll-like receptor (TLR) 4 inhibition reduced a large proportion of macrophage activation. Conclusions We demonstrated that the proinflammatory milieu with high levels of PA or mmLDL promoted macrophage activation and the expression of associated genes such as Nlrp3, Csf3, and Edn1. Although the TLR4 pathway appeared to be most relevant, additional role of other genes in this process provided insights regarding the potential targets for intervention.
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Affiliation(s)
- Harin Youk
- Graduate Program of Science for Aging, Graduate School of Yonsei University, Seoul, Korea
| | - Miso Kim
- Graduate Program of Science for Aging, Graduate School of Yonsei University, Seoul, Korea
| | - Chan Joo Lee
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jaewon Oh
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sungha Park
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Seok Min Kang
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jeong Ho Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Soo Jin Ann
- Graduate Program of Science for Aging, Graduate School of Yonsei University, Seoul, Korea.
| | - Sang Hak Lee
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea.
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Imran S, Neeland MR, Shepherd R, Messina N, Perrett KP, Netea MG, Curtis N, Saffery R, Novakovic B. A Potential Role for Epigenetically Mediated Trained Immunity in Food Allergy. iScience 2020; 23:101171. [PMID: 32480123 PMCID: PMC7262566 DOI: 10.1016/j.isci.2020.101171] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/01/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
The prevalence of IgE-mediated food allergy is increasing at a rapid pace in many countries. The association of high food allergy rates with Westernized lifestyles suggests the role of gene-environment interactions, potentially underpinned by epigenetic variation, in mediating this process. Recent studies have implicated innate immune system dysfunction in the development and persistence of food allergy. These responses are characterized by increased circulating frequency of innate immune cells and heightened inflammatory responses to bacterial stimulation in food allergic patients. These signatures mirror those described in trained immunity, whereby innate immune cells retain a “memory” of earlier microbial encounters, thus influencing subsequent immune responses. Here, we propose that a robust multi-omics approach that integrates immunological, transcriptomic, and epigenomic datasets, combined with well-phenotyped and longitudinal food allergy cohorts, can inform the potential role of trained immunity in food allergy.
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Affiliation(s)
- Samira Imran
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia
| | - Melanie R Neeland
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia
| | - Rebecca Shepherd
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia
| | - Nicole Messina
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia
| | - Kirsten P Perrett
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia; Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Australia
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands; Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Nigel Curtis
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia
| | - Boris Novakovic
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia.
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Noll KE, Whitmore AC, West A, McCarthy MK, Morrison CR, Plante KS, Hampton BK, Kollmus H, Pilzner C, Leist SR, Gralinski LE, Menachery VD, Schäfer A, Miller D, Shaw G, Mooney M, McWeeney S, Pardo-Manuel de Villena F, Schughart K, Morrison TE, Baric RS, Ferris MT, Heise MT. Complex Genetic Architecture Underlies Regulation of Influenza-A-Virus-Specific Antibody Responses in the Collaborative Cross. Cell Rep 2020; 31:107587. [PMID: 32348764 PMCID: PMC7195006 DOI: 10.1016/j.celrep.2020.107587] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/20/2020] [Accepted: 04/08/2020] [Indexed: 02/07/2023] Open
Abstract
Host genetic factors play a fundamental role in regulating humoral immunity to viral infection, including influenza A virus (IAV). Here, we utilize the Collaborative Cross (CC), a mouse genetic reference population, to study genetic regulation of variation in antibody response following IAV infection. CC mice show significant heritable variation in the magnitude, kinetics, and composition of IAV-specific antibody response. We map 23 genetic loci associated with this variation. Analysis of a subset of these loci finds that they broadly affect the antibody response to IAV as well as other viruses. Candidate genes are identified based on predicted variant consequences and haplotype-specific expression patterns, and several show overlap with genes identified in human mapping studies. These findings demonstrate that the host antibody response to IAV infection is under complex genetic control and highlight the utility of the CC in modeling and identifying genetic factors with translational relevance to human health and disease.
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Affiliation(s)
- Kelsey E Noll
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alan C Whitmore
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mary K McCarthy
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heike Kollmus
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Carolin Pilzner
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vineet D Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Darla Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ginger Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael Mooney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA; OHSU Knight Cancer Center Institute, Oregon Health and Science University, Portland, OR, USA
| | - Shannon McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA; OHSU Knight Cancer Center Institute, Oregon Health and Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany; University of Veterinary Medicine Hannover, Hannover, Germany; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Thomas E Morrison
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ralph S Baric
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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Barth NKH, Li L, Taher L. Independent Transposon Exaptation Is a Widespread Mechanism of Redundant Enhancer Evolution in the Mammalian Genome. Genome Biol Evol 2020; 12:1-17. [PMID: 31950992 PMCID: PMC7093719 DOI: 10.1093/gbe/evaa004] [Citation(s) in RCA: 6] [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] [Accepted: 01/08/2020] [Indexed: 02/07/2023] Open
Abstract
Many regulatory networks appear to involve partially redundant enhancers. Traditionally, such enhancers have been hypothesized to originate mainly by sequence duplication. An alternative model postulates that they arise independently, through convergent evolution. This mechanism appears to be counterintuitive to natural selection: Redundant sequences are expected to either diverge and acquire new functions or accumulate mutations and become nonfunctional. Nevertheless, we show that at least 31% of the redundant enhancer pairs in the human genome (and 17% in the mouse genome) indeed originated in this manner. Specifically, for virtually all transposon-derived redundant enhancer pairs, both enhancer partners have evolved independently, from the exaptation of two different transposons. In addition to conferring robustness to the system, redundant enhancers could provide an evolutionary advantage by fine-tuning gene expression. Consistent with this hypothesis, we observed that the target genes of redundant enhancers exhibit higher expression levels and tissue specificity as compared with other genes. Finally, we found that although enhancer redundancy appears to be an intrinsic property of certain mammalian regulatory networks, the corresponding enhancers are largely species-specific. In other words, the redundancy in these networks is most likely a result of convergent evolution.
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Affiliation(s)
- Nicolai K H Barth
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Lifei Li
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Leila Taher
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
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A Comparative Analysis of Edwardsiella tarda-Induced Transcriptome Profiles in RAW264.7 Cells Reveals New Insights into the Strategy of Bacterial Immune Evasion. Int J Mol Sci 2019; 20:ijms20225724. [PMID: 31731575 PMCID: PMC6888325 DOI: 10.3390/ijms20225724] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/08/2019] [Accepted: 11/10/2019] [Indexed: 01/15/2023] Open
Abstract
Edwardsiella tarda is a Gram-negative bacterial pathogen with a broad host range, including fish, reptiles, and mammals. One prominent virulence feature of E. tarda is its ability to survive and replicate in host phagocytes, but the relevant molecular mechanism is largely unknown. In this study, we examined the transcriptome profiles of RAW264.7 cells, a murine macrophage cell line, infected with live E. tarda or stimulated with dead E. tarda for 4 h and 8 h. Eighteen libraries were constructed, and an average of 69 million clean reads per library were obtained, with ~81.63% of the reads being successfully mapped to the reference genome. In total, 208 and 232 differentially expressed genes (DEGs) were identified between live and dead E. tarda-treated cells at 4 h and 8 h post-infection, respectively. The DEGs were markedly enriched in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with immunity. Live E. tarda differed strikingly from dead E. tarda in the regulation of immune related genes. Compared with dead E. tarda-treated cells, live E. tarda-treated cells exhibited marked and significant suppression in the induction of a large amount of immune genes, including RIG-I-like receptors, cytokines, and interferon-related genes. Furthermore, some of the immune genes highly regulated by live E. tarda formed complicated interaction networks with each other. Together, the results of this study revealed a transcriptome profile specifically induced by the active virulence elements of live E. tarda during the infection process, thus adding new insights into the intracellular infection mechanism of E. tarda. This study also provided a valuable set of target genes for further study of the immune evasion strategy of E. tarda.
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