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Cerdeira CD, Brigagão MRPL. Targeting Macrophage Polarization in Infectious Diseases: M1/M2 Functional Profiles, Immune Signaling and Microbial Virulence Factors. Immunol Invest 2024:1-62. [PMID: 38913937 DOI: 10.1080/08820139.2024.2367682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
INTRODUCTION An event of increasing interest during host-pathogen interactions is the polarization of patrolling/naive monocytes (MOs) into macrophage subsets (MФs). Therapeutic strategies aimed at modulating this event are under investigation. METHODS This review focuses on the mechanisms of induction/development and profile of MФs polarized toward classically proinflammatory (M1) or alternatively anti-inflammatory (M2) phenotypes in response to bacteria, fungi, parasites, and viruses. RESULTS AND DISCUSSION It highlights nuclear, cytoplasmic, and cell surface receptors (pattern recognition receptors/PPRs), microenvironmental mediators, and immune signaling. MФs polarize into phenotypes: M1 MФs, activated by IFN-γ, pathogen-associated molecular patterns (PAMPs, e.g. lipopolysaccharide) and membrane-bound PPRs ligands (TLRs/CLRs ligands); or M2 MФs, induced by interleukins (ILs-4, -10 and -13), antigen-antibody complexes, and helminth PAMPs. Polarization toward M1 and M2 profiles evolve in a pathogen-specific manner, with or without canonicity, and can vary widely. Ultimately, this can result in varying degrees of host protection or more severe disease outcome. On the one hand, the host is driving effective MФs polarization (M1 or M2); but on the other hand, microorganisms may skew the polarization through virulence factors to increase pathogenicity. Cellular/genomic reprogramming also ensures plasticity of M1/M2 phenotypes. Because modulation of polarization can occur at multiple points, new insights and emerging perspectives may have clinical implications during the inflammation-to-resolution transition; translated into practical applications as for therapeutic/vaccine design target to boost microbicidal response (M1, e.g. triggering oxidative burst) with specifics PAMPs/IFN-γ or promote tissue repair (M2, increasing arginase activity) via immunotherapy.
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Wang LL, Wang H, Lin SJ, Xu XY, Hu WJ, Liu J, Zhang HY. ABBV-744 alleviates LPS-induced neuroinflammation via regulation of BATF2-IRF4-STAT1/3/5 axis. Acta Pharmacol Sin 2024:10.1038/s41401-024-01318-4. [PMID: 38862817 DOI: 10.1038/s41401-024-01318-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/17/2024] [Indexed: 06/13/2024] Open
Abstract
Suppression of neuroinflammation using small molecule compounds targeting the key pathways in microglial inflammation has attracted great interest. Recently, increasing attention has been gained to the role of the second bromodomain (BD2) of the bromodomain and extra-terminal (BET) proteins, while its effect and molecular mechanism on microglial inflammation has not yet been explored. In this study, we evaluated the therapeutic effects of ABBV-744, a BD2 high selective BET inhibitor, on lipopolysaccharide (LPS)-induced microglial inflammation in vitro and in vivo, and explored the key pathways by which ABBV-744 regulated microglia-mediated neuroinflammation. We found that pretreatment of ABBV-744 concentration-dependently inhibited the expression of LPS-induced inflammatory mediators/enzymes including NO, TNF-α, IL-1β, IL-6, iNOS, and COX-2 in BV-2 microglial cells. These effects were validated in LPS-treated primary microglial cells. Furthermore, we observed that administration of ABBV-744 significantly alleviated LPS-induced activation of microglia and transcriptional levels of pro-inflammatory factors TNF-α and IL-1β in mouse hippocampus and cortex. RNA-Sequencing (RNA-seq) analysis revealed that ABBV-744 induced 508 differentially expressed genes (DEGs) in LPS-stimulated BV-2 cells, and gene enrichment and gene expression network analysis verified its regulation on activated microglial genes and inflammatory pathways. We demonstrated that pretreatment of ABBV-744 significantly reduced the expression levels of basic leucine zipper ATF-like transcription factor 2 (BATF2) and interferon regulatory factor 4 (IRF4), and suppressed JAK-STAT signaling pathway in LPS-stimulated BV-2 cells and mice, suggesting that the anti-neuroinflammatory effect of ABBV-744 might be associated with regulation of BATF2-IRF4-STAT1/3/5 pathway, which was confirmed by gene knockdown experiments. This study demonstrates the effect of a BD2 high selective BET inhibitor, ABBV-744, against microglial inflammation, and reveals a BATF2-IRF4-STAT1/3/5 pathway in regulation of microglial inflammation, which might provide new clues for discovery of effective therapeutic strategy against neuroinflammation.
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Affiliation(s)
- Le-le Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Huan Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Si-Jin Lin
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xing-Yu Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Wen-Juan Hu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jia Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hai-Yan Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
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Tiniakou I, Hsu PF, Lopez-Zepeda LS, Garipler G, Esteva E, Adams NM, Jang G, Soni C, Lau CM, Liu F, Khodadadi-Jamayran A, Rodrick TC, Jones D, Tsirigos A, Ohler U, Bedford MT, Nimer SD, Kaartinen V, Mazzoni EO, Reizis B. Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation. Sci Immunol 2024; 9:eadi1023. [PMID: 38608038 PMCID: PMC11182672 DOI: 10.1126/sciimmunol.adi1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 03/21/2024] [Indexed: 04/14/2024]
Abstract
The development of dendritic cells (DCs), including antigen-presenting conventional DCs (cDCs) and cytokine-producing plasmacytoid DCs (pDCs), is controlled by the growth factor Flt3 ligand (Flt3L) and its receptor Flt3. We genetically dissected Flt3L-driven DC differentiation using CRISPR-Cas9-based screening. Genome-wide screening identified multiple regulators of DC differentiation including subunits of TSC and GATOR1 complexes, which restricted progenitor growth but enabled DC differentiation by inhibiting mTOR signaling. An orthogonal screen identified the transcriptional repressor Trim33 (TIF-1γ) as a regulator of DC differentiation. Conditional targeting in vivo revealed an essential role of Trim33 in the development of all DCs, but not of monocytes or granulocytes. In particular, deletion of Trim33 caused rapid loss of DC progenitors, pDCs, and the cross-presenting cDC1 subset. Trim33-deficient Flt3+ progenitors up-regulated pro-inflammatory and macrophage-specific genes but failed to induce the DC differentiation program. Collectively, these data elucidate mechanisms that control Flt3L-driven differentiation of the entire DC lineage and identify Trim33 as its essential regulator.
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Affiliation(s)
- Ioanna Tiniakou
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Pei-Feng Hsu
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Lorena S. Lopez-Zepeda
- Department of Biology, Humboldt Universität zu Berlin; Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine; Berlin, Germany
| | - Görkem Garipler
- Department of Biology, New York University; New York, NY, USA
| | - Eduardo Esteva
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Nicholas M. Adams
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Geunhyo Jang
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Colleen M. Lau
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine; Ithaca, NY, USA
| | - Fan Liu
- Department of Biochemistry and Molecular Biology, Department of Medicine and Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine; Miami, FL, USA
| | - Alireza Khodadadi-Jamayran
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine; New York, NY, USA
| | - Tori C. Rodrick
- Metabolomics Laboratory, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine; New York, NY, USA
| | - Drew Jones
- Metabolomics Laboratory, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine; New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine; New York, NY, USA
| | - Uwe Ohler
- Department of Biology, Humboldt Universität zu Berlin; Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine; Berlin, Germany
| | - Mark T. Bedford
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center; Houston, TX, USA
| | - Stephen D. Nimer
- Department of Biochemistry and Molecular Biology, Department of Medicine and Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine; Miami, FL, USA
| | - Vesa Kaartinen
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry; Ann Arbor, MI, USA
| | | | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
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Gour N, Yong HM, Magesh A, Atakkatan A, Andrade F, Lajoie S, Dong X. A GPCR-neuropeptide axis dampens hyperactive neutrophils by promoting an alternative-like polarization during bacterial infection. Immunity 2024; 57:333-348.e6. [PMID: 38295799 PMCID: PMC10940224 DOI: 10.1016/j.immuni.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/10/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
The notion that neutrophils exist as a homogeneous population is being replaced with the knowledge that neutrophils adopt different functional states. Neutrophils can have a pro-inflammatory phenotype or an anti-inflammatory state, but how these states are regulated remains unclear. Here, we demonstrated that the neutrophil-expressed G-protein-coupled receptor (GPCR) Mrgpra1 is a negative regulator of neutrophil bactericidal functions. Mrgpra1-mediated signaling was driven by its ligand, neuropeptide FF (NPFF), which dictated the balance between pro- and anti-inflammatory programming. Specifically, the Mrgpra1-NPFF axis counter-regulated interferon (IFN) γ-mediated neutrophil polarization during acute lung infection by favoring an alternative-like polarization, suggesting that it may act to balance overzealous neutrophilic responses. Distinct, cross-regulated populations of neutrophils were the primary source of NPFF and IFNγ during infection. As a subset of neutrophils at steady state expressed NPFF, these findings could have broad implications in various infectious and inflammatory diseases. Therefore, a neutrophil-intrinsic pathway determines their cellular fate, function, and magnitude of infection.
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Affiliation(s)
- Naina Gour
- Solomon H. Snyder Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Hwan Mee Yong
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Aishwarya Magesh
- Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD, USA; Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Aishwarya Atakkatan
- Solomon H. Snyder Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Felipe Andrade
- Division of Rheumatology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Stephane Lajoie
- Department of Otolaryngology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Xinzhong Dong
- Solomon H. Snyder Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Xu J, Liu LY, Zhi FJ, Song YJ, Zhang ZH, Li B, Zheng FY, Gao PC, Zhang SZ, Zhang YY, Zhang Y, Qiu Y, Jiang B, Li YQ, Peng C, Chu YF. DDX5 inhibits inflammation by modulating m6A levels of TLR2/4 transcripts during bacterial infection. EMBO Rep 2024; 25:770-795. [PMID: 38182816 PMCID: PMC10897170 DOI: 10.1038/s44319-023-00047-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/07/2024] Open
Abstract
DExD/H-box helicases are crucial regulators of RNA metabolism and antiviral innate immune responses; however, their role in bacteria-induced inflammation remains unclear. Here, we report that DDX5 interacts with METTL3 and METTL14 to form an m6A writing complex, which adds N6-methyladenosine to transcripts of toll-like receptor (TLR) 2 and TLR4, promoting their decay via YTHDF2-mediated RNA degradation, resulting in reduced expression of TLR2/4. Upon bacterial infection, DDX5 is recruited to Hrd1 at the endoplasmic reticulum in an MyD88-dependent manner and is degraded by the ubiquitin-proteasome pathway. This process disrupts the DDX5 m6A writing complex and halts m6A modification as well as degradation of TLR2/4 mRNAs, thereby promoting the expression of TLR2 and TLR4 and downstream NF-κB activation. The role of DDX5 in regulating inflammation is also validated in vivo, as DDX5- and METTL3-KO mice exhibit enhanced expression of inflammatory cytokines. Our findings show that DDX5 acts as a molecular switch to regulate inflammation during bacterial infection and shed light on mechanisms of quiescent inflammation during homeostasis.
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Affiliation(s)
- Jian Xu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Li-Yuan Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Fei-Jie Zhi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yin-Juan Song
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zi-Hui Zhang
- National Key Laboratory of Veterinary Public Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Bin Li
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Fu-Ying Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Peng-Cheng Gao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Su-Zi Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yu-Yu Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Ying Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ying Qiu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Bo Jiang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yong-Qing Li
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chen Peng
- National Key Laboratory of Veterinary Public Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Yue-Feng Chu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
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6
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Long H, Steimle JD, Grisanti Canozo FJ, Kim JH, Li X, Morikawa Y, Park M, Turaga D, Adachi I, Wythe JD, Samee MAH, Martin JF. Endothelial cells adopt a pro-reparative immune responsive signature during cardiac injury. Life Sci Alliance 2024; 7:e202201870. [PMID: 38012001 PMCID: PMC10681909 DOI: 10.26508/lsa.202201870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
Modulation of the heart's immune microenvironment is crucial for recovery after ischemic events such as myocardial infarction (MI). Endothelial cells (ECs) can have immune regulatory functions; however, interactions between ECs and the immune environment in the heart after MI remain poorly understood. We identified an EC-specific IFN responsive and immune regulatory gene signature in adult and pediatric heart failure (HF) tissues. Single-cell transcriptomic analysis of murine hearts subjected to MI uncovered an EC population (IFN-ECs) with immunologic gene signatures similar to those in human HF. IFN-ECs were enriched in regenerative-stage mouse hearts and expressed genes encoding immune responsive transcription factors (Irf7, Batf2, and Stat1). Single-cell chromatin accessibility studies revealed an enrichment of these TF motifs at IFN-EC signature genes. Expression of immune regulatory ligand genes by IFN-ECs suggests bidirectional signaling between IFN-ECs and macrophages in regenerative-stage hearts. Our data suggest that ECs may adopt immune regulatory signatures after cardiac injury to accompany the reparative response. The presence of these signatures in human HF and murine MI models suggests a potential role for EC-mediated immune regulation in responding to stress induced by acute injury in MI and chronic adverse remodeling in HF.
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Affiliation(s)
- Hali Long
- https://ror.org/02pttbw34 Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey D Steimle
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | | | - Jong Hwan Kim
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/00r4vsg44 Cardiomyocyte Renewal Laboratory, The Texas Heart Institute, Houston, TX, USA
| | - Xiao Li
- https://ror.org/00r4vsg44 Cardiomyocyte Renewal Laboratory, The Texas Heart Institute, Houston, TX, USA
| | - Yuka Morikawa
- https://ror.org/00r4vsg44 Cardiomyocyte Renewal Laboratory, The Texas Heart Institute, Houston, TX, USA
| | - Minjun Park
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Diwakar Turaga
- https://ror.org/02pttbw34 Section of Critical Care Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Iki Adachi
- https://ror.org/02pttbw34 Section of Cardiothoracic Surgery, Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Joshua D Wythe
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
| | - Md Abul Hassan Samee
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - James F Martin
- https://ror.org/02pttbw34 Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/00r4vsg44 Cardiomyocyte Renewal Laboratory, The Texas Heart Institute, Houston, TX, USA
- https://ror.org/02pttbw34 Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Center for Organ Repair and Renewal, Baylor College of Medicine, Houston, TX, USA
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Shim J, Park S, Venkateswaran S, Kumar D, Prince C, Parihar V, Maples L, Waller EK, Kugathasan S, Briones M, Lee M, Henry CJ, Prahalad S, Chandrakasan S. Early B-cell development and B-cell maturation are impaired in patients with active hemophagocytic lymphohistiocytosis. Blood 2023; 142:1972-1984. [PMID: 37624902 PMCID: PMC10731577 DOI: 10.1182/blood.2023020426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Hemophagocytic lymphohistiocytosis (HLH) is characterized by hyperinflammation and multiorgan dysfunction. Infections, including the reactivation of viruses, contribute to significant disease mortality in HLH. Although T-cell and natural killer cell-driven immune activation and dysregulation are well described, limited data exist on the status of B-cell compartment and humoral immune function in HLH. We noted marked suppression of early B-cell development in patients with active HLH. In vitro B-cell differentiation studies after exposure to HLH-defining cytokines, such as interferon gamma (IFN-γ) and tumor necrosis factor, recapitulated B-cell development arrest. Messenger RNA sequencing of human CD34+ cells exposed to IFN-γ demonstrated changes in genes and pathways affecting B-cell development and maturation. In addition, patients with active HLH exhibited a marked decrease in class-switched memory B (CSMB) cells and a decrease in bone marrow plasmablast/plasma cell compartments. The decrease in CSMB cells was associated with a decrease in circulating T follicular helper (cTfh) cells. Finally, lymph node and spleen evaluation in a patient with HLH revealed absent germinal center formation and hemophagocytosis with associated lymphopenia. Reassuringly, the frequency of CSMB and cTfh improved with the control of T-cell activation. Taken together, in patients with active HLH, these changes in B cells may affect the humoral immune response; however, further immune studies are needed to determine its clinical significance.
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Affiliation(s)
- Jenny Shim
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA
| | - Sunita Park
- Department of Pathology, Children’s Healthcare of Atlanta, Atlanta, GA
| | - Suresh Venkateswaran
- Division of Pediatric Gastroenterology, Department of Pediatrics, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA
| | - Deepak Kumar
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA
| | - Chengyu Prince
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA
| | - Vaunita Parihar
- Cancer Tissue and Pathology Shared Resource Core, Emory University School of Medicine, Atlanta, GA
| | - Larkin Maples
- Department of Pathology, Children’s Healthcare of Atlanta, Atlanta, GA
| | - Edmund K. Waller
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Department of Pediatrics, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA
| | - Michael Briones
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA
| | - Miyoung Lee
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA
| | - Curtis J. Henry
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA
| | - Sampath Prahalad
- Division of Pediatric Rheumatology, Department of Pediatrics, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA
| | - Shanmuganathan Chandrakasan
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA
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van der Geest R, Peñaloza HF, Xiong Z, Gonzalez-Ferrer S, An X, Li H, Fan H, Tabary M, Nouraie SM, Zhao Y, Zhang Y, Chen K, Alder JK, Bain WG, Lee JS. BATF2 enhances proinflammatory cytokine responses in macrophages and improves early host defense against pulmonary Klebsiella pneumoniae infection. Am J Physiol Lung Cell Mol Physiol 2023; 325:L604-L616. [PMID: 37724373 PMCID: PMC11068429 DOI: 10.1152/ajplung.00441.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 07/12/2023] [Accepted: 08/31/2023] [Indexed: 09/20/2023] Open
Abstract
Basic leucine zipper transcription factor ATF-like 2 (BATF2) is a transcription factor that is emerging as an important regulator of the innate immune system. BATF2 is among the top upregulated genes in human alveolar macrophages treated with LPS, but the signaling pathways that induce BATF2 expression in response to Gram-negative stimuli are incompletely understood. In addition, the role of BATF2 in the host response to pulmonary infection with a Gram-negative pathogen like Klebsiella pneumoniae (Kp) is not known. We show that induction of Batf2 gene expression in macrophages in response to Kp in vitro requires TRIF and type I interferon (IFN) signaling, but not MyD88 signaling. Analysis of the impact of BATF2 deficiency on macrophage effector functions in vitro showed that BATF2 does not directly impact macrophage phagocytic uptake and intracellular killing of Kp. However, BATF2 markedly enhanced macrophage proinflammatory gene expression and Kp-induced cytokine responses. In vivo, Batf2 gene expression was elevated in lung tissue of wild-type (WT) mice 24 h after pulmonary Kp infection, and Kp-infected BATF2-deficient (Batf2-/-) mice displayed an increase in bacterial burden in the lung, spleen, and liver compared with WT mice. WT and Batf2-/- mice showed similar recruitment of leukocytes following infection, but in line with in vitro observations, proinflammatory cytokine levels in the alveolar space were reduced in Batf2-/- mice. Altogether, these results suggest that BATF2 enhances proinflammatory cytokine responses in macrophages in response to Kp and contributes to the early host defense against pulmonary Kp infection.NEW & NOTEWORTHY This study investigates the signaling pathways that mediate induction of BATF2 expression downstream of TLR4 and also the impact of BATF2 on the host defense against pulmonary Kp infection. We demonstrate that Kp-induced upregulation of BATF2 in macrophages requires TRIF and type I IFN signaling. We also show that BATF2 enhances Kp-induced macrophage cytokine responses and that BATF2 contributes to the early host defense against pulmonary Kp infection.
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Affiliation(s)
- Rick van der Geest
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Hernán F Peñaloza
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Zeyu Xiong
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Shekina Gonzalez-Ferrer
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Xiaojing An
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Huihua Li
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Hongye Fan
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Mohammadreza Tabary
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - S Mehdi Nouraie
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Yanwu Zhao
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Kong Chen
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Jonathan K Alder
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - William G Bain
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Veterans Affairs Pittsburgh Health Care System, Pittsburgh, Pennsylvania, United States
| | - Janet S Lee
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Acute Lung Injury Center of Excellence, Department of Medicine, Pittsburgh, Pennsylvania, United States
- Division of Pulmonary and Critical Care Medicine, John T. Milliken Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
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9
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Amgalan B, Day CP, Przytycka TM. Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression. PLoS Comput Biol 2023; 19:e1011472. [PMID: 37721939 PMCID: PMC10538798 DOI: 10.1371/journal.pcbi.1011472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/28/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023] Open
Abstract
There is a growing awareness that tumor-adjacent normal tissues used as control samples in cancer studies do not represent fully healthy tissues. Instead, they are intermediates between healthy tissues and tumors. The factors that contribute to the deviation of such control samples from healthy state include exposure to the tumor-promoting factors, tumor-related immune response, and other aspects of tumor microenvironment. Characterizing the relation between gene expression of tumor-adjacent control samples and tumors is fundamental for understanding roles of microenvironment in tumor initiation and progression, as well as for identification of diagnostic and prognostic biomarkers for cancers. To address the demand, we developed and validated TranNet, a computational approach that utilizes gene expression in matched control and tumor samples to study the relation between their gene expression profiles. TranNet infers a sparse weighted bipartite graph from gene expression profiles of matched control samples to tumors. The results allow us to identify predictors (potential regulators) of this transition. To our knowledge, TranNet is the first computational method to infer such dependencies. We applied TranNet to the data of several cancer types and their matched control samples from The Cancer Genome Atlas (TCGA). Many predictors identified by TranNet are genes associated with regulation by the tumor microenvironment as they are enriched in G-protein coupled receptor signaling, cell-to-cell communication, immune processes, and cell adhesion. Correspondingly, targets of inferred predictors are enriched in pathways related to tissue remodelling (including the epithelial-mesenchymal Transition (EMT)), immune response, and cell proliferation. This implies that the predictors are markers and potential stromal facilitators of tumor progression. Our results provide new insights into the relationships between tumor adjacent control sample, tumor and the tumor environment. Moreover, the set of predictors identified by TranNet will provide a valuable resource for future investigations.
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Affiliation(s)
- Bayarbaatar Amgalan
- National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics/Center for Cancer Research/National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Teresa M. Przytycka
- National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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10
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Feilstrecker Balani G, dos Santos Cortez M, Picasky da Silveira Freitas JE, Freire de Melo F, Zarpelon-Schutz AC, Teixeira KN. Immune response modulation in inflammatory bowel diseases by Helicobacter pylori infection. World J Gastroenterol 2023; 29:4604-4615. [PMID: 37662864 PMCID: PMC10472898 DOI: 10.3748/wjg.v29.i30.4604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/01/2023] [Accepted: 07/24/2023] [Indexed: 08/10/2023] Open
Abstract
Many studies point to an association between Helicobacter pylori (H. pylori) infection and inflammatory bowel diseases (IBD). Although controversial, this association indicates that the presence of the bacterium somehow affects the course of IBD. It appears that H. pylori infection influences IBD through changes in the diversity of the gut microbiota, and hence in local chemical characteristics, and alteration in the pattern of gut immune response. The gut immune response appears to be modulated by H. pylori infection towards a less aggressive inflammatory response and the establishment of a targeted response to tissue repair. Therefore, a T helper 2 (Th2)/macrophage M2 response is stimulated, while the Th1/macrophage M1 response is suppressed. The immunomodulation appears to be associated with intrinsic factors of the bacteria, such as virulence factors - such oncogenic protein cytotoxin-associated antigen A, proteins such H. pylori neutrophil-activating protein, but also with microenvironmental changes that favor permanence of H. pylori in the stomach. These changes include the increase of gastric mucosal pH by urease activity, and suppression of the stomach immune response promoted by evasion mechanisms of the bacterium. Furthermore, there is a causal relationship between H. pylori infection and components of the innate immunity such as the NLR family pyrin domain containing 3 inflammasome that directs IBD toward a better prognosis.
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Affiliation(s)
| | | | | | - Fabrício Freire de Melo
- Campus Anísio Teixeira, Universidade Federal da Bahia, Instituto Multidisciplinar em Saúde, Vitória da Conquista 45.029-094, Bahia, Brazil
| | - Ana Carla Zarpelon-Schutz
- Campus Toledo, Universidade Federal do Paraná, Toledo 85.919-899, Paraná, Brazil
- Programa de Pós-graduação em Biotecnologia - Setor Palotina, Universidade Federal do Paraná, Palotina 85.950-000, Paraná, Brazil
| | - Kádima Nayara Teixeira
- Campus Toledo, Universidade Federal do Paraná, Toledo 85.919-899, Paraná, Brazil
- Programa Multicêntrico de Pós-graduação em Bioquímica e Biologia Molecular - Setor Palotina, Universidade Federal do Paraná, Palotina 85.950-000, Paraná, Brazil
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11
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Yang Y, Wang Z, He M, Diao L, Yu B, Li D. NAD+ biosynthesis metabolism predicts prognosis and indicates immune microenvironment for breast cancer. Pathol Oncol Res 2023; 29:1610956. [PMID: 37006438 PMCID: PMC10063816 DOI: 10.3389/pore.2023.1610956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023]
Abstract
The growing evidence implies that tumor cells need to increase NAD+ levels by upregulating NAD+ biosynthesis to satisfy their growth demand. NAD+ biosynthesis metabolism is implicated in tumor progression. Breast cancer (BC) is the most common malignant malignancy in the world. Nevertheless, the prognostic significance of NAD+ biosynthesis and its relationship with the tumor immune microenvironment in breast cancer still need further investigation. In this study, we obtained the mRNA expression data and clinical information of BC samples from public databases and calculated the level of NAD+ biosynthesis activity by single-sample gene set enrichment analysis (ssGSEA). We then explored the relationship between the NAD+ biosynthesis score, infiltrating immune cells, prognosis significance, immunogenicity and immune checkpoint molecules. The results demonstrated that patients with high NAD+ biosynthetic score displayed poor prognosis, high immune infiltration, high immunogenicity, elevated PD-L1 expression, and might more benefit from immunotherapy. Taken together, our studies not only deepened the understanding of NAD+ biosynthesis metabolism of breast cancer but also provided new insights into personalized treatment strategies and immunological therapies to improve the outcomes of breast cancer patients.
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Affiliation(s)
- Yuting Yang
- Department of Immunology, Medical College of Qingdao University, Qingdao, Shandong, China
| | - Ze Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Mengqi He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Lihong Diao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Biyue Yu
- School of Life Sciences, Hebei University, Baoding, Hebei, China
| | - Dong Li
- Department of Immunology, Medical College of Qingdao University, Qingdao, Shandong, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
- *Correspondence: Dong Li,
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12
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Amgalan B, Day CP, Przytycka TM. Exploring tumor-normal cross-talk with TranNet: role of the environment in tumor progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529899. [PMID: 36945455 PMCID: PMC10028821 DOI: 10.1101/2023.02.24.529899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
There is a growing awareness that tumor-adjacent normal tissues used as control samples in cancer studies do not represent fully healthy tissues. Instead, they are intermediates between healthy tissues and tumors. The factors that contribute to the deviation of such control samples from healthy state include exposure to the tumor-promoting factors, tumor-related immune response, and other aspects of tumor microenvironment. Characterizing the relation between gene expression of tumor-adjacent control samples and tumors is fundamental for understanding roles of microenvironment in tumor initiation and progression, as well as for identification of diagnostic and prognostic biomarkers for cancers. To address the demand, we developed and validated TranNet, a computational approach that utilizes gene expression in matched control and tumor samples to study the relation between their gene expression profiles. TranNet infers a sparse weighted bipartite graph from gene expression profiles of matched control samples to tumors. The results allow us to identify predictors (potential regulators) of this transition. To our knowledge, TranNet is the first computational method to infer such regulation. We applied TranNet to the data of several cancer types and their matched control samples from The Cancer Genome Atlas (TCGA). Many predictors identified by TranNet are genes associated with regulation by the tumor microenvironment as they are enriched in G-protein coupled receptor signaling, cell-to-cell communication, immune processes, and cell adhesion. Correspondingly, targets of inferred predictors are enriched in pathways related to tissue remodelling (including the epithelial-mesenchymal Transition (EMT)), immune response, and cell proliferation. This implies that the predictors are markers and potential stromal facilitators of tumor progression. Our results provide new insights for the relationships between tumor adjacent control sample, tumor and the tumor environment. Moreover, the set of predictors identified by TranNet will provide a valuable resource for future investigations. The TranNet method was implemented in python, source codes and the data sets used for and generated during this study are available at the Github site https://github.com/ncbi/TranNet .
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Affiliation(s)
- Bayarbaatar Amgalan
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA
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13
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Le DT, Florez MA, Kus P, Tran BT, Kain B, Zhu Y, Christensen K, Jain A, Malovannaya A, King KY. BATF2 promotes HSC myeloid differentiation by amplifying IFN response mediators during chronic infection. iScience 2023; 26:106059. [PMID: 36824275 PMCID: PMC9942003 DOI: 10.1016/j.isci.2023.106059] [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: 07/08/2022] [Revised: 10/11/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Basic leucine zipper ATF-like transcription factor 2 (BATF2), an interferon-activated immune response regulator, is a key factor responsible for myeloid differentiation and depletion of HSC during chronic infection. To delineate the mechanism of BATF2 function in HSCs, we assessed Batf2 KO mice during chronic infection and found that they produced less pro-inflammatory cytokines, less immune cell recruitment to the spleen, and impaired myeloid differentiation with better preservation of HSC capacity compared to WT. Co-IP analysis revealed that BATF2 forms a complex with JUN to amplify pro-inflammatory signaling pathways including CCL5 during infection. Blockade of CCL5 receptors phenocopied Batf2 KO differentiation defects, whereas treatment with recombinant CCL5 was sufficient to rescue IFNγ-induced myeloid differentiation and recruit more immune cells to the spleen in Batf2 KO mice. By revealing the mechanism of BATF2-induced myeloid differentiation of HSCs, these studies elucidate potential therapeutic strategies to boost immunity while preserving HSC function during chronic infection.
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Affiliation(s)
- Duy T. Le
- Graduate Program in Immunology, Graduate School of Biomedical Sciences (GSBS), Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
- Department of Pediatrics, Division of Infectious Diseases, Baylor College of Medicine, 1102 Bates Street Suite 1150, Houston, TX, USA
| | - Marcus A. Florez
- Department of Pediatrics, Division of Infectious Diseases, Baylor College of Medicine, 1102 Bates Street Suite 1150, Houston, TX, USA
- Graduate Program in Translational Biology and Molecular Medicine, GSBS, Baylor College of Medicine, Houston, TX, USA
| | - Pawel Kus
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Brandon T. Tran
- Department of Pediatrics, Division of Infectious Diseases, Baylor College of Medicine, 1102 Bates Street Suite 1150, Houston, TX, USA
- Graduate Program in Cancer and Cell Biology, GSBS, Baylor College of Medicine, Houston, TX, USA
| | - Bailee Kain
- Department of Pediatrics, Division of Infectious Diseases, Baylor College of Medicine, 1102 Bates Street Suite 1150, Houston, TX, USA
- Graduate Program in Translational Biology and Molecular Medicine, GSBS, Baylor College of Medicine, Houston, TX, USA
| | - Yingmin Zhu
- Protein and Antibody Production Core, Baylor College of Medicine, Houston, TX, USA
| | - Kurt Christensen
- Protein and Antibody Production Core, Baylor College of Medicine, Houston, TX, USA
| | - Antrix Jain
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX, USA
| | - Anna Malovannaya
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Katherine Y. King
- Graduate Program in Immunology, Graduate School of Biomedical Sciences (GSBS), Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
- Department of Pediatrics, Division of Infectious Diseases, Baylor College of Medicine, 1102 Bates Street Suite 1150, Houston, TX, USA
- Corresponding author
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14
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Yang L, Shen WW, Shao W, Zhao Q, Pang GZ, Yang Y, Tao XF, Zhang WP, Mei Q, Shen YX. MANF ameliorates DSS-induced mouse colitis via restricting Ly6C hiCX3CR1 int macrophage transformation and suppressing CHOP-BATF2 signaling pathway. Acta Pharmacol Sin 2023; 44:1175-1190. [PMID: 36635421 DOI: 10.1038/s41401-022-01045-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 12/19/2022] [Indexed: 01/14/2023] Open
Abstract
Mesencephalic astrocyte-derived neurotrophic factor (MANF), an endoplasmic reticulum stress-inducible secreting protein, has evolutionarily conserved immune-regulatory function that contributes to the negative regulation of inflammation in macrophages. In this study, we investigated the profiles of MANF in the macrophages of the patients with active inflammatory bowel disease (IBD) and the mice with experimental colitis, which was induced in both myeloid cell-specific MANF knockout mice and wild-type mice by 3% dextran sodium sulfate (DSS) for 7 days. We found that MANF expression was significantly increased in intestinal macrophages from both the mice with experimental colitis and patients with active IBD. DSS-induced colitis was exacerbated in myeloid cell-specific MANF knockout mice. Injection of recombinant human MANF (rhMANF, 10 mg·kg-1·d-1, i.v.) from D4 to D6 significantly ameliorated experimental colitis in DSS-treated mice. More importantly, MANF deficiency in myeloid cells resulted in a dramatic increase in the number of Ly6ChiCX3CRint proinflammatory macrophages in colon lamina propria of DSS-treated mice, and the proinflammatory cytokines and chemokines were upregulated as well. Meanwhile, we demonstrated that MANF attenuated Th17-mediated immunopathology by inhibiting BATF2-mediated innate immune response and downregulating CXCL9, CXCL10, CXCL11 and IL-12p40; MANF functioned as a negative regulator in inflammatory macrophages via inhibiting CHOP-BATF2 signaling pathway, thereby protecting against DSS-induced mouse colitis. These results suggest that MANF ameliorates colon injury by negatively regulating inflammatory macrophage transformation, which shed light on a potential therapeutic target for IBD.
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Affiliation(s)
- Lin Yang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.,Biopharmaceutical Institute, Anhui Medical University, Hefei, 230032, China
| | - Wen-Wen Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.,Biopharmaceutical Institute, Anhui Medical University, Hefei, 230032, China
| | - Wei Shao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.,Biopharmaceutical Institute, Anhui Medical University, Hefei, 230032, China
| | - Qing Zhao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.,Biopharmaceutical Institute, Anhui Medical University, Hefei, 230032, China
| | - Gao-Zong Pang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.,Biopharmaceutical Institute, Anhui Medical University, Hefei, 230032, China
| | - Yi Yang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.,Biopharmaceutical Institute, Anhui Medical University, Hefei, 230032, China.,First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Xiao-Fang Tao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.,Biopharmaceutical Institute, Anhui Medical University, Hefei, 230032, China
| | - Wei-Ping Zhang
- First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Qiong Mei
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.,Biopharmaceutical Institute, Anhui Medical University, Hefei, 230032, China
| | - Yu-Xian Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China. .,Biopharmaceutical Institute, Anhui Medical University, Hefei, 230032, China.
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15
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Loss of the Immunomodulatory Transcription Factor BATF2 in Humans Is Associated with a Neurological Phenotype. Cells 2023; 12:cells12020227. [PMID: 36672163 PMCID: PMC9856319 DOI: 10.3390/cells12020227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/21/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Epilepsy and mental retardation are known to be associated with pathogenic mutations in a broad range of genes that are expressed in the brain and have a role in neurodevelopment. Here, we report on a family with three affected individuals whose clinical symptoms closely resemble a neurodevelopmental disorder. Whole-exome sequencing identified a homozygous stop-gain mutation, p.Gln19*, in the BATF2 gene in the patients. The BATF2 transcription factor is predominantly expressed in macrophages and monocytes and has been reported to modulate AP-1 transcription factor-mediated pro-inflammatory responses. Transcriptome analysis showed altered base-level expression of interferon-stimulated genes in the patients' blood, typical for type I interferonopathies. Peripheral blood mononuclear cells from all three patients demonstrated elevated responses to innate immune stimuli, which could be reproduced in CRISPR-Cas9-generated BATF2-/- human monocytic cell lines. BATF2 is, therefore, a novel disease-associated gene candidate for severe epilepsy and mental retardation related to dysregulation of immune responses, which underscores the relevance of neuroinflammation for epilepsy.
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16
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Asano S, Okada-Ogawa A, Kobayashi M, Yonemoto M, Hojo Y, Shibuta I, Noma N, Iwata K, Hitomi S, Shinoda M. Involvement of interferon gamma signaling in spinal trigeminal caudal subnucleus astrocyte in orofacial neuropathic pain in rats with infraorbital nerve injury. Mol Pain 2023; 19:17448069231222403. [PMID: 38073236 DOI: 10.1177/17448069231222403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023] Open
Abstract
Background: Trigeminal nerve injury causes orofacial pain that can interfere with activities of daily life. However, the underlying mechanism remains unknown, and the appropriate treatment has not been established yet. This study aimed to examine the involvement of interferon gamma (IFN-γ) signaling in the spinal trigeminal caudal subnucleus (Vc) in orofacial neuropathic pain. Methods: Infraorbital nerve (ION) injury (IONI) was performed in rats by partial ION ligation. The head-withdrawal reflex threshold (HWT) to mechanical stimulation of the whisker pad skin was measured in IONI or sham rats, as well as following a continuous intracisterna magna administration of IFN-γ and a mixture of IFN-γ and fluorocitrate (inhibitor of astrocytes activation) in naïve rats, or an IFN-γ antagonist in IONI rats. The IFN-γ receptor immunohistochemistry and IFN-γ Western blotting were analyzed in the Vc after IONI or sham treatment. The glial fibrillary acid protein (GFAP) immunohistochemistry and Western blotting were also analyzed after administration of IFN-γ and the mixture of IFN-γ and fluorocitrate. Moreover, the change in single neuronal activity in the Vc was examined in the IONI, sham, and IONI group administered IFN-γ antagonist. Results: The HWT decreased after IONI. The IFN-γ and IFN-γ receptor were upregulated after IONI, and the IFN-γ receptor was expressed in Vc astrocytes. IFN-γ administration decreased the HWT, whereas the mixture of IFN-γ and fluorocitrate recovered the decrement of HWT. IFN-γ administration upregulated GFAP expression, while the mixture of IFN-γ and fluorocitrate recovered the upregulation of GFAP expression. IONI significantly enhanced the neuronal activity of the mechanical-evoked responses, and administration of an IFN-γ antagonist significantly inhibited these enhancements. Conclusions: IFN-γ signaling through the receptor in astrocytes is a key mechanism underlying orofacial neuropathic pain associated with trigeminal nerve injury. These findings will aid in the development of therapeutics for orofacial neuropathic pain.
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Affiliation(s)
- Sayaka Asano
- Department of Anesthesiology, Tokyo Metropolitan Tama Medical Center, Tokyo, Japan
- Department of Physiology, Nihon University School of Dentistry, Tokyo, Japan
| | - Akiko Okada-Ogawa
- Department of Oral Medicine, Nihon University School of Dentistry, Tokyo, Japan
- Division of Orofacial Pain Clinic, Nihon University Dental Hospital, Tokyo, Japan
| | - Momoyo Kobayashi
- Department of Oral Medicine, Nihon University School of Dentistry, Tokyo, Japan
| | - Mamiko Yonemoto
- Department of Physiology, Nihon University School of Dentistry, Tokyo, Japan
| | - Yasushi Hojo
- Department of Physiology, Nihon University School of Dentistry, Tokyo, Japan
| | - Ikuko Shibuta
- Department of Physiology, Nihon University School of Dentistry, Tokyo, Japan
| | - Noboru Noma
- Department of Oral Medicine, Nihon University School of Dentistry, Tokyo, Japan
- Division of Orofacial Pain Clinic, Nihon University Dental Hospital, Tokyo, Japan
| | - Koichi Iwata
- Department of Physiology, Nihon University School of Dentistry, Tokyo, Japan
| | - Suzuro Hitomi
- Department of Physiology, Nihon University School of Dentistry, Tokyo, Japan
| | - Masamichi Shinoda
- Department of Physiology, Nihon University School of Dentistry, Tokyo, Japan
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17
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Bosch-Camós L, Alonso U, Esteve-Codina A, Chang CY, Martín-Mur B, Accensi F, Muñoz M, Navas MJ, Dabad M, Vidal E, Pina-Pedrero S, Pleguezuelos P, Caratù G, Salas ML, Liu L, Bataklieva S, Gavrilov B, Rodríguez F, Argilaguet J. Cross-protection against African swine fever virus upon intranasal vaccination is associated with an adaptive-innate immune crosstalk. PLoS Pathog 2022; 18:e1010931. [PMID: 36350837 PMCID: PMC9645615 DOI: 10.1371/journal.ppat.1010931] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022] Open
Abstract
African swine fever virus (ASFV) is causing a worldwide pandemic affecting the porcine industry and leading to important global economic consequences. The virus causes a highly lethal hemorrhagic disease in wild boars and domestic pigs. Lack of effective vaccines hampers the control of virus spread, thus increasing the pressure on the scientific community for urgent solutions. However, knowledge on the immune components associated with protection is very limited. Here we characterized the in vitro recall response induced by immune cells from pigs intranasally vaccinated with the BA71ΔCD2 deletion mutant virus. Vaccination conferred dose-dependent cross-protection associated with both ASFV-specific antibodies and IFNγ-secreting cells. Importantly, bulk and single-cell transcriptomics of blood and lymph node cells from vaccinated pigs revealed a positive feedback from adaptive to innate immunity. Indeed, activation of Th1 and cytotoxic T cells was concomitant with a rapid IFNγ-dependent triggering of an inflammatory response characterized by TNF-producing macrophages, as well as CXCL10-expressing lymphocytes and cross-presenting dendritic cells. Altogether, this study provides a detailed phenotypic characterization of the immune cell subsets involved in cross-protection against ASFV, and highlights key functional immune mechanisms to be considered for the development of an effective ASF vaccine. African swine fever (ASF) pandemic is currently the number one threat for the porcine industry worldwide. Lack of treatments hampers its control, and the insufficient knowledge regarding the immune effector mechanisms required for protection hinders rational vaccine design. Here we present the first comprehensive study characterizing the complex cellular immune response involved in cross-protection against ASF. We show that, upon in vitro reactivation, cells from immune pigs induce a Th1-biased recall response that in turn enhances the antiviral innate response. Our results suggest that this positive feedback regulation of innate immunity plays a key role in the early control of ASF virus infection. Altogether, this work represents a step forward in the understanding of ASF immunology and provide critical immune components that should be considered to more rationally design future ASF vaccines.
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Affiliation(s)
- Laia Bosch-Camós
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Uxía Alonso
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Chia-Yu Chang
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Beatriz Martín-Mur
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Francesc Accensi
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Departament de Sanitat i Anatomia animals. Facultat de Veterinària, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Marta Muñoz
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - María J. Navas
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Enric Vidal
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Sonia Pina-Pedrero
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Patricia Pleguezuelos
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Ginevra Caratù
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - María L. Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autònoma de Madrid, Madrid, Spain
| | - Lihong Liu
- National Veterinary Institute (SVA), Uppsala, Sweden
| | | | - Boris Gavrilov
- Biologics Development, Huvepharma, 3A Nikolay Haytov Street, Sofia, Bulgaria
| | - Fernando Rodríguez
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- * E-mail: (FR); (JA)
| | - Jordi Argilaguet
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- * E-mail: (FR); (JA)
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18
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Jones SS, Ozturk M, Kieswetter NS, Poswayo SKL, Hazra R, Tamgue O, Parihar SP, Suzuki H, Brombacher F, Guler R. Lyl1-deficiency promotes inflammatory responses and increases mycobacterial burden in response to Mycobacterium tuberculosis infection in mice. Front Immunol 2022; 13:948047. [PMID: 36119114 PMCID: PMC9481033 DOI: 10.3389/fimmu.2022.948047] [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: 05/19/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
Lymphoblastic leukemia 1 (Lyl1) is a well-studied transcription factor known to exhibit oncogenic potential in various forms of leukemia with pivotal roles in hematopoietic stem cell biology. While its role in early hematopoiesis is well established, its function in mature innate cells is less explored. Here, we identified Lyl1 as a drastically perturbed gene in the Mycobacterium tuberculosis (Mtb) infected mouse macrophage transcriptome. We report that Lyl1 downregulation upon immune stimulation is a host-driven process regulated by NFκB and MAP kinase pathways. Interestingly, Lyl1-deficient macrophages have decreased bacterial killing potential with reduced nitric oxide (NO) levels while expressing increased levels of pro-inflammatory interleukin-1 and CXCL1. Lyl1-deficient mice show reduced survival to Mtb HN878 infection with increased bacterial burden and exacerbated inflammatory responses in chronic stages. We observed that increased susceptibility to infection was accompanied by increased neutrophil recruitment and IL-1, CXCL1, and CXCL5 levels in the lung homogenates. Collectively, these results suggest that Lyl1 controls Mtb growth, reduces neutrophilic inflammation and reveals an underappreciated role for Lyl1 in innate immune responses.
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Affiliation(s)
- Shelby-Sara Jones
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town, 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, 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, South Africa
| | - Mumin Ozturk
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town, 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, South Africa
- Epigenomics & Single Cell Biophysics Group, Department of Cell Biology Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Nathan Scott Kieswetter
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town, 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, South Africa
| | - Sibongiseni K. L. Poswayo
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town, 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, South Africa
| | - Rudranil Hazra
- 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, South Africa
| | - Ousman Tamgue
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town, 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, South Africa
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Suraj P. Parihar
- 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, South Africa
| | - Harukazu Suzuki
- Laboratory for. Cellular Function Conversion Technology RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town, 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, 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, South Africa
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town, 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, 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, South Africa
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19
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Voinsky I, Zoabi Y, Shomron N, Harel M, Cassuto H, Tam J, Rose S, Scheck AC, Karim MA, Frye RE, Aran A, Gurwitz D. Blood RNA Sequencing Indicates Upregulated BATF2 and LY6E and Downregulated ISG15 and MT2A Expression in Children with Autism Spectrum Disorder. Int J Mol Sci 2022; 23:ijms23179843. [PMID: 36077244 PMCID: PMC9456089 DOI: 10.3390/ijms23179843] [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: 08/08/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 11/16/2022] Open
Abstract
Mutations in over 100 genes are implicated in autism spectrum disorder (ASD). DNA SNPs, CNVs, and epigenomic modifications also contribute to ASD. Transcriptomics analysis of blood samples may offer clues for pathways dysregulated in ASD. To expand and validate published findings of RNA-sequencing (RNA-seq) studies, we performed RNA-seq of whole blood samples from an Israeli discovery cohort of eight children with ASD compared with nine age- and sex-matched neurotypical children. This revealed 10 genes with differential expression. Using quantitative real-time PCR, we compared RNAs from whole blood samples of 73 Israeli and American children with ASD and 26 matched neurotypical children for the 10 dysregulated genes detected by RNA-seq. This revealed higher expression levels of the pro-inflammatory transcripts BATF2 and LY6E and lower expression levels of the anti-inflammatory transcripts ISG15 and MT2A in the ASD compared to neurotypical children. BATF2 was recently reported as upregulated in blood samples of Japanese adults with ASD. Our findings support an involvement of these genes in ASD phenotypes, independent of age and ethnicity. Upregulation of BATF2 and downregulation of ISG15 and MT2A were reported to reduce cancer risk. Implications of the dysregulated genes for pro-inflammatory phenotypes, immunity, and cancer risk in ASD are discussed.
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Affiliation(s)
- Irena Voinsky
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yazeed Zoabi
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Moria Harel
- Shaare Zedek Medical Center, Jerusalem 91031, Israel
| | | | - Joseph Tam
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Shannon Rose
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, AR 72205, USA
| | - Adrienne C. Scheck
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Mohammad A. Karim
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Richard E. Frye
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
- Rossignol Medical Center, Phoenix, AZ 85050, USA
| | - Adi Aran
- Shaare Zedek Medical Center, Jerusalem 91031, Israel
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
- Correspondence: (A.A.); (D.G.)
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence: (A.A.); (D.G.)
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20
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Li Z, Wang Z, Sun T, Liu S, Ding S, Sun L. Identifying key genes in CD4+ T cells of systemic lupus erythematosus by integrated bioinformatics analysis. Front Genet 2022; 13:941221. [PMID: 36046235 PMCID: PMC9420982 DOI: 10.3389/fgene.2022.941221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by excessive activation of T and B lymphocytes and breakdown of immune tolerance to autoantigens. Despite several mechanisms including the genetic alterations and inflammatory responses have been reported, the overall signature genes in CD4+ T cells and how they affect the pathological process of SLE remain to be elucidated. This study aimed to identify the crucial genes, potential biological processes and pathways underlying SLE pathogenesis by integrated bioinformatics. The gene expression profiles of isolated peripheral CD4+ T cells from SLE patients with different disease activity and healthy controls (GSE97263) were analyzed, and 14 co-expression modules were identified using weighted gene co-expression network analysis (WGCNA). Some of these modules showed significantly positive or negative correlations with SLE disease activity, and primarily enriched in the regulation of type I interferon and immune responses. Next, combining time course sequencing (TCseq) with differentially expressed gene (DEG) analysis, crucial genes in lupus CD4+ T cells were revealed, including some interferon signature genes (ISGs). Among these genes, we identified 4 upregulated genes (PLSCR1, IFI35, BATF2 and CLDN5) and 2 downregulated genes (GDF7 and DERL3) as newfound key genes. The elevated genes showed close relationship with the SLE disease activity. In general, our study identified 6 novel biomarkers in CD4+ T cells that might contribute to the diagnosis and treatment of SLE.
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Affiliation(s)
- Zutong Li
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Zhilong Wang
- Department of Reproductive Medicine Center, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Tian Sun
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Shanshan Liu
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Shuai Ding
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- *Correspondence: Lingyun Sun, ; Shuai Ding,
| | - Lingyun Sun
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- *Correspondence: Lingyun Sun, ; Shuai Ding,
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21
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Thakur C, Tripathi A, Ravichandran S, Shivananjaiah A, Chakraborty A, Varadappa S, Chikkavenkatappa N, Nagarajan D, Lakshminarasimhaiah S, Singh A, Chandra N. A new blood-based RNA signature (R 9), for monitoring effectiveness of tuberculosis treatment in a South Indian longitudinal cohort. iScience 2022; 25:103745. [PMID: 35118358 PMCID: PMC8800112 DOI: 10.1016/j.isci.2022.103745] [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: 05/17/2020] [Revised: 03/31/2021] [Accepted: 01/06/2022] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis (TB) treatment involves a multidrug regimen for six months, and until two months, it is unclear if treatment is effective. This delay can lead to the evolution of drug resistance, lung damage, disease spread, and transmission. We identify a blood-based 9-gene signature using a computational pipeline that constructs and interrogates a genome-wide transcriptome-integrated protein-interaction network. The identified signature is able to determine treatment response at week 1-2 in three independent public datasets. Signature-based R9-score correctly detected treatment response at individual timepoints (204 samples) from a newly developed South Indian longitudinal cohort involving 32 patients with pulmonary TB. These results are consistent with conventional clinical metrics and can discriminate good from poor treatment responders at week 2 (AUC 0.93(0.81-1.00)). In this work, we provide proof of concept that the R9-score can determine treatment effectiveness, making a case for designing a larger clinical study.
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Affiliation(s)
- Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Ashutosh Tripathi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | | | - Akshatha Shivananjaiah
- SDS Tuberculosis Research Centre and Rajiv Gandhi Institute of Chest Diseases, Bangalore, India
| | - Anushree Chakraborty
- SDS Tuberculosis Research Centre and Rajiv Gandhi Institute of Chest Diseases, Bangalore, India
| | - Sreekala Varadappa
- SDS Tuberculosis Research Centre and Rajiv Gandhi Institute of Chest Diseases, Bangalore, India
| | | | - Deepesh Nagarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
- National Mathematics Initiative, Indian Institute of Science, Bangalore, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
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22
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Kieswetter NS, Ozturk M, Hlaka L, Chia JE, Nichol RJO, Cross JM, McGee LMC, Tyson-Hirst I, Beveridge R, Brombacher F, Carter KC, Suckling CJ, Scott FJ, Guler R. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1061-1071. [PMID: 35084027 PMCID: PMC8969509 DOI: 10.1093/jac/dkac001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/20/2021] [Indexed: 11/14/2022] Open
Abstract
Background Objectives Methods Results Conclusions
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Affiliation(s)
- Nathan S. Kieswetter
- 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
| | - 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
| | - 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
| | - Julius Ebua 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
| | - Ryan J. O. Nichol
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - Jasmine M. Cross
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - Leah M. C. McGee
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - Izaak Tyson-Hirst
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - 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
| | - Katharine C. Carter
- Strathclyde Institute of Pharmacy of Biomedical Sciences, University of Strathclyde, Glasgow G4 0NR, Scotland
| | - Colin J. Suckling
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - Fraser J. Scott
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - 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
- Corresponding author. E-mail:
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23
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Identification of Unique Key miRNAs, TFs, and mRNAs in Virulent MTB Infection Macrophages by Network Analysis. Int J Mol Sci 2021; 23:ijms23010382. [PMID: 35008808 PMCID: PMC8745702 DOI: 10.3390/ijms23010382] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/25/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022] Open
Abstract
Although Mycobacterium tuberculosis (MTB) has existed for thousands of years, its immune escape mechanism remains obscure. Increasing evidence signifies that microRNAs (miRNAs) play pivotal roles in the progression of tuberculosis (TB). RNA sequencing was used to sequence miRNAs in human acute monocytic leukemia cells (THP-1) infected by the virulent MTB-1458 strain and the avirulent vaccine strain Mycobacterium bovis Bacillus Calmette-Guérin (BCG). Sets of differentially expressed miRNAs (DE-miRNAs) between MTB-1458/BCG-infected groups and uninfected groups were identified, among which 18 were differentially expressed only in the MTB-1458-infected THP-1 group. Then, 13 transcription factors (TFs) and 81 target genes of these 18 DE-miRNAs were matched. Gene Ontology classification as well as Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the candidate targets were predominantly involved in apoptotic-associated and interferon-γ-mediated signaling pathways. A TF-miRNA-mRNA interaction network was constructed to analyze the relationships among these 18 DE-miRNAs and their targets and TFs, as well as display the hub miRNAs, TFs, and target genes. Considering the degrees from network analysis and the reported functions, this study focused on the BHLHE40-miR-378d-BHLHE40 regulation axis and confirmed that BHLHE40 was a target of miR-378d. This cross-talk among DE-miRNAs, mRNAs, and TFs might be an important feature in TB, and the findings merited further study and provided new insights into immune defense and evasion underlying host-pathogen interactions.
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24
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Pawlica P, Yario TA, White S, Wang J, Moss WN, Hui P, Vinetz JM, Steitz JA. SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes. Proc Natl Acad Sci U S A 2021; 118:e2116668118. [PMID: 34903581 PMCID: PMC8719879 DOI: 10.1073/pnas.2116668118] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19), continues to be a pressing health concern. In this study, we investigated the impact of SARS-CoV-2 infection on host microRNA (miRNA) populations in three human lung-derived cell lines, as well as in nasopharyngeal swabs from SARS-CoV-2-infected individuals. We did not detect any major and consistent differences in host miRNA levels after SARS-CoV-2 infection. However, we unexpectedly discovered a viral miRNA-like small RNA, named CoV2-miR-O7a (for SARS-CoV-2 miRNA-like ORF7a-derived small RNA). Its abundance ranges from low to moderate as compared to host miRNAs and it associates with Argonaute proteins-core components of the RNA interference pathway. We identify putative targets for CoV2-miR-O7a, including Basic Leucine Zipper ATF-Like Transcription Factor 2 (BATF2), which participates in interferon signaling. We demonstrate that CoV2-miR-O7a production relies on cellular machinery, yet is independent of Drosha protein, and is enhanced by the presence of a strong and evolutionarily conserved hairpin formed within the ORF7a sequence.
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Affiliation(s)
- Paulina Pawlica
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536;
| | - Therese A Yario
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536
- HHMI, Yale University School of Medicine, New Haven, CT 06536
| | - Sylvia White
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06536
| | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06536
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06536
| | - Joseph M Vinetz
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536;
- HHMI, Yale University School of Medicine, New Haven, CT 06536
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25
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Llewellyn HP, Arat S, Gao J, Wen J, Xia S, Kalabat D, Oziolor E, Virgen-Slane R, Affolter T, Ji C. T cells and monocyte-derived myeloid cells mediate immunotherapy-related hepatitis in a mouse model. J Hepatol 2021; 75:1083-1095. [PMID: 34242700 DOI: 10.1016/j.jhep.2021.06.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/14/2021] [Accepted: 06/20/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Immune checkpoint inhibitors (ICIs) are associated with immune-related adverse events (irAEs) which are more severe when ICIs are used in combination. We aimed to use a mouse model to elucidate the molecular mechanisms of immune-related hepatitis, one of the common irAEs associated with ICIs. METHODS Immune phenotyping and molecular profiling were performed on Pdcd1-/- mice treated with anti-CTLA4 and/or the IDO1 inhibitor epacadostat or a 4-1BB agonistic antibody. RESULTS ICI combination-induced hepatitis and 4-1BB agonist-mediated hepatitis share similar features yet maintain distinct immune signatures. Both were characterized by an expansion of periportal infiltrates and pan-zonal inflammation albeit with different morphologic characteristics. In both cases, infiltrates were predominantly CD4+ and CD8+ T cells with upregulated T-cell activation markers, ICOS and CD44. Depletion of CD8+ T cells abolished ICI-mediated hepatitis. Single-cell transcriptomics revealed that the hepatitis induced by combination ICIs is associated with a robust immune activation signature in all subtypes of T cells and T helper 1 skewing. Expression profiling revealed a central role for IFNγ and liver monocyte-derived macrophages in promoting a pro-inflammatory T-cell response to ICI combination and 4-1BB agonism. CONCLUSION We developed a novel mouse model which offers significant value in yielding deeper mechanistic insight into immune-mediated liver toxicity associated with various immunotherapies. LAY SUMMARY Hepatitis is one of the common immune-related adverse events in cancer patients receiving immune checkpoint inhibitor (ICI) therapy. The mechanisms of ICI-induced hepatitis are not well understood. In this paper, we identify key molecular mechanisms mediating immune intracellular crosstalk between liver T cells and macrophages in response to ICI in a mouse model.
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Affiliation(s)
- Heather P Llewellyn
- Global Biomarkers, Drug Safety Research and Development (DSRD), La Jolla, CA, USA
| | - Seda Arat
- Global Pathology and Investigative Toxicology, DSRD, Groton, CT, USA
| | - Jingjin Gao
- Oncology Research Unit, Pfizer, La Jolla, CA, USA
| | - Ji Wen
- Oncology Research Unit, Pfizer, La Jolla, CA, USA
| | - Shuhua Xia
- Global Pathology and Investigative Toxicology, DSRD, Groton, CT, USA
| | - Dalia Kalabat
- Global Pathology and Investigative Toxicology, DSRD, Groton, CT, USA
| | - Elias Oziolor
- Global Pathology and Investigative Toxicology, DSRD, Groton, CT, USA
| | - Richard Virgen-Slane
- Global Biomarkers, Drug Safety Research and Development (DSRD), La Jolla, CA, USA
| | | | - Changhua Ji
- Regulatory and Immunosafety Strategy, DSRD, Pfizer, La Jolla, CA, USA.
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26
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Mathison AJ, Kerketta R, de Assuncao TM, Leverence E, Zeighami A, Urrutia G, Stodola TJ, di Magliano MP, Iovanna JL, Zimmermann MT, Lomberk G, Urrutia R. Kras G12D induces changes in chromatin territories that differentially impact early nuclear reprogramming in pancreatic cells. Genome Biol 2021; 22:289. [PMID: 34649604 PMCID: PMC8518179 DOI: 10.1186/s13059-021-02498-6] [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: 11/10/2020] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma initiation is most frequently caused by Kras mutations. RESULTS Here, we apply biological, biochemical, and network biology methods to validate GEMM-derived cell models using inducible KrasG12D expression. We describe the time-dependent, chromatin remodeling program that impacts function during early oncogenic signaling. We find that the KrasG12D-induced transcriptional response is dominated by downregulated expression concordant with layers of epigenetic events. More open chromatin characterizes the ATAC-seq profile associated with a smaller group of upregulated genes and epigenetic marks. RRBS demonstrates that promoter hypermethylation does not account for the silencing of the extensive gene promoter network. Moreover, ChIP-Seq reveals that heterochromatin reorganization plays little role in this early transcriptional program. Notably, both gene activation and silencing primarily depend on the marking of genes with a combination of H3K27ac, H3K4me3, and H3K36me3. Indeed, integrated modeling of all these datasets shows that KrasG12D regulates its transcriptional program primarily through unique super-enhancers and enhancers, and marking specific gene promoters and bodies. We also report chromatin remodeling across genomic areas that, although not contributing directly to cis-gene transcription, are likely important for KrasG12D functions. CONCLUSIONS In summary, we report a comprehensive, time-dependent, and coordinated early epigenomic program for KrasG12D in pancreatic cells, which is mechanistically relevant to understanding chromatin remodeling events underlying transcriptional outcomes needed for the function of this oncogene.
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Affiliation(s)
- Angela J Mathison
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Romica Kerketta
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Elise Leverence
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Atefeh Zeighami
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Guillermo Urrutia
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Timothy J Stodola
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Juan L Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Michael T Zimmermann
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Gwen Lomberk
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA.
| | - Raul Urrutia
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
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27
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Gong Z, Gu Y, Xiong K, Niu J, Zheng R, Su B, Fan L, Xie J. The Evaluation and Validation of Blood-Derived Novel Biomarkers for Precise and Rapid Diagnosis of Tuberculosis in Areas With High-TB Burden. Front Microbiol 2021; 12:650567. [PMID: 34194403 PMCID: PMC8236956 DOI: 10.3389/fmicb.2021.650567] [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: 03/14/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) remains a highly contagious public health threat. Precise and prompt diagnosis and monitoring of treatment responses are urgently needed for clinics. To pursue novel and satisfied host blood-derived biomarkers, we streamlined a bioinformatic pipeline by integrating differentially expressed genes, a gene co-expression network, and short time-series analysis to mine the published transcriptomes derived from whole blood of TB patients in the GEO database, followed by validating the diagnostic performance of biomarkers in both independent datasets and blood samples of Chinese patients using quantitative real-time PCR (qRT-PCR). We found that four genes, namely UBE2L6 (Ubiquitin/ISG15-conjugating enzyme E2 L6), BATF2 (Basic leucine zipper transcriptional factor ATF-like), SERPING1 (Plasma protease C1 inhibitor), and VAMP5 (Vesicle-associated membrane protein 5), had high diagnostic value for active TB. The transcription levels of these four gene combinations can reach up to 88% sensitivity and 78% specificity (average) for the diagnosis of active TB; the highest sensitivity can achieve 100% by parallel of BATF2 and VAMP5, and the highest specificity can reach 89.5% through a combination of SERPIG1, UBE2L6, and VAMP5, which were significantly higher than 75.3% sensitivity and 69.1% specificity by T-SPOT.TB in the same patients. Quite unexpectedly, the gene set can assess the efficacy of anti-TB response and differentiate active TB from Latent TB infection. The data demonstrated these four biomarkers might have great potency and advantage over IGRAs in the diagnosis of TB.
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Affiliation(s)
- Zhen Gong
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Yinzhong Gu
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Kunlong Xiong
- Shanghai Key Laboratory of Tuberculosis, Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinxia Niu
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Ruijuan Zheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bo Su
- Shanghai Key Laboratory of Tuberculosis, Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lin Fan
- Shanghai Key Laboratory of Tuberculosis, Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
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28
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Kieswetter NS, Ozturk M, Jones SS, Senzani S, Chengalroyen MD, Brombacher F, Kana B, Guler R. Deletion of N-acetylmuramyl-L-alanine amidases alters the host immune response to Mycobacterium tuberculosis infection. Virulence 2021; 12:1227-1238. [PMID: 33980132 PMCID: PMC8128173 DOI: 10.1080/21505594.2021.1914448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Peptidoglycan (PG), a heteropolysaccharide component of the mycobacterial cell wall can be shed during tuberculosis infection with immunomodulatory consequences. As such, changes in PG structure are expected to have important implications on disease progression and host responses during infection with Mycobacterium tuberculosis. Mycobacterial amidases have important roles in remodeling of PG during cell division and are implicated in susceptibility to antibiotics. However, their role in modulating host immunity remains unknown. We assessed the bacterial burden and host immune responses to M. tuberculosis mutants defective for either one of two PG N-acetylmuramyl-L-alanine amidases, Ami1 and Ami4, in bone marrow-derived macrophages (BMDM) and C57BL/6 mice. In infected BMDM, the single deletion of both genes resulted in increased proinflammatory cytokine responses. In mice, infection with the Δami1 mutant led to differential induction of pro-inflammatory cytokines and chemokines, decreased cellular recruitment and reduced lung pathology during the acute phase of the infection. While increased proinflammatory cytokines production was observed in BMDM infected with the Δami4 mutant, these effects did not prevail in mice. Infection using the Δami1 and Δami4 Mtb mutants showed that these genes are dispensable for intracellular mycobacterial growth in macrophages and mycobacterial burden in mice. These findings suggest that both Ami1 and Ami4 in M. tuberculosis are not essential for mycobacterial growth within the host. In summary, we show that amidases are important for modulating host immunity during Mtb infection in murine macrophages and mice.
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Affiliation(s)
- Nathan Scott Kieswetter
- Cape Town Component, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Department of Pathology, 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, South Africa
| | - Mumin Ozturk
- Cape Town Component, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Department of Pathology, 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, South Africa
| | - Shelby-Sara Jones
- Cape Town Component, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Department of Pathology, 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, South Africa
| | - Sibusiso Senzani
- DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Melissa Dalcina Chengalroyen
- DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Frank Brombacher
- Cape Town Component, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Department of Pathology, 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, 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, South Africa
| | - Bavesh Kana
- DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Reto Guler
- Cape Town Component, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Department of Pathology, 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, 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, South Africa
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29
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Ge L, Zhang Y, Zhao X, Wang J, Zhang Y, Wang Q, Yu H, Zhang Y, You Y. EIF2AK2 selectively regulates the gene transcription in immune response and histones associated with systemic lupus erythematosus. Mol Immunol 2021; 132:132-141. [PMID: 33588244 DOI: 10.1016/j.molimm.2021.01.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 01/21/2021] [Accepted: 01/28/2021] [Indexed: 12/13/2022]
Abstract
PKR, also known as EIF2AK2, is an IFN-stimulated gene (ISG) and shows a higher expression in probands with systemic lupus erythematosus (SLE), which is likely responsible for the impaired translational and proliferative responses to mitogens in T cells from SLE patients. In this study, we overexpressed EIF2AK2 in HeLa cells to study EIF2AK2-regulated genes using RNA-seq technology, followed by bioinformatic analysis of target genes of EIF2AK2-regulated transcriptional factors (TFs). Overexpression of EIF2AK2 promotes HeLa cell apoptosis. EIF2AK2 selectively represses the transcription of histone protein genes associated with SLE, immune response genes and TF genes, which was validated by RT-qPCR experiments. Analysis of motifs overrepresented in the promoter regions of EIF2AK2-regulated genes revealed eighteen EIF2AK2-regulated TFs involved in establishing the EIF2AK2 network. Eight out of these predicted EIF2AK2-regulated TFs were further verified by RT-qPCR selectively in both HeLa and Jurkat cells, and most such as HEY2, TFEC, BATF2, GATA3 and ATF3 and FOXO6 are known to regulate immune response. Our results suggest that the dsRNA-dependent kinase EIF2AK2 selectively regulates the transcription of immune response and SLE-associated histone protein genes, and such a selectivity is likely to be operated by EIF2AK2-targeted TFs. The EIF2AK2-TFs axis potentially offers new therapeutic targets for counteracting immunological disease in the future.
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Affiliation(s)
- Lan Ge
- Department of Dermatology, Southwest Hospital, Third Military Medical University(Army Medical University), Chongqing, 400038, China.
| | - Yuhong Zhang
- Laboratory of Human Health and Genome Regulation, ABLife Inc., Wuhan, Hubei 430075, China; Center for Genome Analysis, ABLife Inc., Wuhan, Hubei 430075, China.
| | - Xingwang Zhao
- Department of Dermatology, Southwest Hospital, Third Military Medical University(Army Medical University), Chongqing, 400038, China.
| | - Juan Wang
- Department of Dermatology, Southwest Hospital, Third Military Medical University(Army Medical University), Chongqing, 400038, China.
| | - Yu Zhang
- Center for Genome Analysis, ABLife Inc., Wuhan, Hubei 430075, China.
| | - Qi Wang
- Center for Genome Analysis, ABLife Inc., Wuhan, Hubei 430075, China.
| | - Han Yu
- Laboratory of Human Health and Genome Regulation, ABLife Inc., Wuhan, Hubei 430075, China.
| | - Yi Zhang
- Laboratory of Human Health and Genome Regulation, ABLife Inc., Wuhan, Hubei 430075, China; Center for Genome Analysis, ABLife Inc., Wuhan, Hubei 430075, China.
| | - Yi You
- Department of Dermatology, Southwest Hospital, Third Military Medical University(Army Medical University), Chongqing, 400038, China.
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30
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Bondar G, Silacheva I, Bao TM, Deshmukh S, Kulkarni NS, Nakade T, Grogan T, Elashoff D, Deng MC. Initial independent validation of a genomic heart failure survival prediction algorithm. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2021. [DOI: 10.1080/23808993.2021.1882847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Galyna Bondar
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, UCLA Medical Center, Los Angeles, California, United States
- LeukoLifeDx, Inc.,Rumson, New Jersey, United States
| | - Irina Silacheva
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, UCLA Medical Center, Los Angeles, California, United States
| | - Tra-Mi Bao
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, UCLA Medical Center, Los Angeles, California, United States
- LeukoLifeDx, Inc.,Rumson, New Jersey, United States
| | - Sumeet Deshmukh
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Neha S. Kulkarni
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK
| | - Taisuke Nakade
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, UCLA Medical Center, Los Angeles, California, United States
| | - Tristan Grogan
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, UCLA Medical Center, Los Angeles, California, United States
| | - David Elashoff
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, UCLA Medical Center, Los Angeles, California, United States
| | - Mario C. Deng
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, UCLA Medical Center, Los Angeles, California, United States
- LeukoLifeDx, Inc.,Rumson, New Jersey, United States
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31
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Johnson WE, Odom A, Cintron C, Muthaiah M, Knudsen S, Joseph N, Babu S, Lakshminarayanan S, Jenkins DF, Zhao Y, Nankya E, Horsburgh CR, Roy G, Ellner J, Sarkar S, Salgame P, Hochberg NS. Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler. BMC Infect Dis 2021; 21:106. [PMID: 33482742 PMCID: PMC7821401 DOI: 10.1186/s12879-020-05598-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Background Gene expression signatures have been used as biomarkers of tuberculosis (TB) risk and outcomes. Platforms are needed to simplify access to these signatures and determine their validity in the setting of comorbidities. We developed a computational profiling platform of TB signature gene sets and characterized the diagnostic ability of existing signature gene sets to differentiate active TB from LTBI in the setting of malnutrition. Methods We curated 45 existing TB-related signature gene sets and developed our TBSignatureProfiler software toolkit that estimates gene set activity using multiple enrichment methods and allows visualization of single- and multi-pathway results. The TBSignatureProfiler software is available through Bioconductor and on GitHub. For evaluation in malnutrition, we used whole blood gene expression profiling from 23 severely malnourished Indian individuals with TB and 15 severely malnourished household contacts with latent TB infection (LTBI). Severe malnutrition was defined as body mass index (BMI) < 16 kg/m2 in adults and based on weight-for-height Z scores in children < 18 years. Gene expression was measured using RNA-sequencing. Results The comparison and visualization functions from the TBSignatureProfiler showed that TB gene sets performed well in malnourished individuals; 40 gene sets had statistically significant discriminative power for differentiating TB from LTBI, with area under the curve ranging from 0.662–0.989. Three gene sets were not significantly predictive. Conclusion Our TBSignatureProfiler is a highly effective and user-friendly platform for applying and comparing published TB signature gene sets. Using this platform, we found that existing gene sets for TB function effectively in the setting of malnutrition, although differences in gene set applicability exist. RNA-sequencing gene sets should consider comorbidities and potential effects on diagnostic performance. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-020-05598-z.
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Affiliation(s)
- W Evan Johnson
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA. .,Bioinformatics Program, Boston University, Boston, MA, USA. .,Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA.
| | - Aubrey Odom
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA.,Bioinformatics Program, Boston University, Boston, MA, USA.,Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA
| | | | | | | | - Noyal Joseph
- Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Senbagavalli Babu
- Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | | | - David F Jenkins
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA.,Bioinformatics Program, Boston University, Boston, MA, USA.,Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Yue Zhao
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA.,Bioinformatics Program, Boston University, Boston, MA, USA.,Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Ethel Nankya
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA.,Bioinformatics Program, Boston University, Boston, MA, USA.,Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA
| | - C Robert Horsburgh
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Gautam Roy
- Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Jerrold Ellner
- Department of Medicine, Center for Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Sonali Sarkar
- Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Padmini Salgame
- Department of Medicine, Center for Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Natasha S Hochberg
- Boston Medical Center, Boston, MA, USA.,Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.,Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, USA
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32
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Chaney HL, Grose LF, Charpigny G, Behura SK, Sheldon IM, Cronin JG, Lonergan P, Spencer TE, Mathew DJ. Conceptus-induced, interferon tau-dependent gene expression in bovine endometrial epithelial and stromal cells†. Biol Reprod 2020; 104:669-683. [PMID: 33330929 DOI: 10.1093/biolre/ioaa226] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/13/2020] [Accepted: 12/13/2020] [Indexed: 12/21/2022] Open
Abstract
Bovine endometrium consists of epithelial and stromal cells that respond to conceptus interferon tau (IFNT), the maternal recognition of pregnancy (MRP) signal, by increasing expression of IFN-stimulated genes (ISGs). Endometrial epithelial and stromal-cell-specific ISGs are largely unknown but hypothesized to have essential functions during pregnancy establishment. Bovine endometrial epithelial cells were cultured in inserts above stromal fibroblast (SF) cells for 6 h in medium alone or with IFNT. The epithelial and SF transcriptomic response was analyzed separately using RNA sequencing and compared to a list of 369 DEGs recently identified in intact bovine endometrium in response to elongating bovine conceptuses and IFNT. Bovine endometrial epithelial and SF shared 223 and 70 DEGs in common with the list of 369 endometrial DEGs. Well-known ISGs identified in the epithelial and SF were ISG15, MX1, MX2, and OAS2. DEGs identified in the epithelial but not SF included a number of IRF molecules (IRF1, IRF2, IRF3, and IRF8), mitochondria SLC transporters (SLC25A19, SLC25A28, and SLC25A30), and a ghrelin receptor. Expression of ZC3HAV1, an anti-retroviral gene, increased specifically within the SF. Gene ontology analysis identified the type I IFN signaling pathway and activation of nuclear factor kappa B transcription factors as biological processes associated with the epithelial cell DEGs. This study has identified biologically relevant IFNT-stimulated genes within specific endometrial cell types. The findings provide critical information regarding the effects of conceptus IFNT on specific endometrial compartments during early developmental processes in cattle.
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Affiliation(s)
- Heather L Chaney
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA
| | - Lindsay F Grose
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA
| | - Gilles Charpigny
- INRA, Biologie du Développement et Reproduction, Jouy en Josas, France
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - I Martin Sheldon
- Swansea University Medical School, Swansea University, Swansea, UK
| | - James G Cronin
- Swansea University Medical School, Swansea University, Swansea, UK
| | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Daniel J Mathew
- Department of Animal Science, University of Tennessee, Knoxville, TN, USA
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33
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Sarode AY, Jha MK, Zutshi S, Ghosh SK, Mahor H, Sarma U, Saha B. Residue-Specific Message Encoding in CD40-Ligand. iScience 2020; 23:101441. [PMID: 32827854 PMCID: PMC7452233 DOI: 10.1016/j.isci.2020.101441] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/15/2020] [Accepted: 08/03/2020] [Indexed: 11/15/2022] Open
Abstract
CD40-Ligand (CD40L)-CD40 interaction regulates immune responses against pathogens, autoantigens, and tumor and transplantation antigens. Single amino acid mutations within the 115-155 amino acids stretch, which is responsible for CD40L functions, result in XIgM syndrome. We hypothesize that each of these amino acids of CD40L encodes specific message that, when decoded by CD40 signaling, induces a specific profile of functions. We observed that every single substitution in the XIgM-related amino acids in the 115-155 41-mer peptide in CD40L selectively altered CD40 signaling and effector functions-cytokine productions, HMGCoA reductase, ceramide synthase, inducible nitric oxide synthase and arginase expression, survival of B cells, and control of Leishmania infection and anti-leishmanial T cell response-suggesting residue-specific encoding of a distinct set of messages that collectively define CD40L pleiotropy, serve as a target for engineering the ligand to generate superagonists as immunotherapeutic, and implicate the evolutionary diversification of functions among the ligands in a protein superfamily.
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Affiliation(s)
- Aditya Yashwant Sarode
- National Centre for Cell Science, Lab-5, Pathogenesis and Cellular Response, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Mukesh Kumar Jha
- National Centre for Cell Science, Lab-5, Pathogenesis and Cellular Response, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Shubhranshu Zutshi
- National Centre for Cell Science, Lab-5, Pathogenesis and Cellular Response, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Soumya Kanti Ghosh
- National Centre for Cell Science, Lab-5, Pathogenesis and Cellular Response, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Hima Mahor
- National Centre for Cell Science, Lab-5, Pathogenesis and Cellular Response, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Uddipan Sarma
- National Centre for Cell Science, Lab-5, Pathogenesis and Cellular Response, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Bhaskar Saha
- National Centre for Cell Science, Lab-5, Pathogenesis and Cellular Response, Ganeshkhind, Pune, Maharashtra 411007, India
- Trident Academy of Creative Technology, Bhubaneswar, Orissa 751024, India
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Guo Q, Zhu X, Wei R, Zhao L, Zhang Z, Yin X, Zhang Y, Chu C, Wang B, Li X. miR-130b-3p regulates M1 macrophage polarization via targeting IRF1. J Cell Physiol 2020; 236:2008-2022. [PMID: 32853398 DOI: 10.1002/jcp.29987] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 07/07/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Abstract
Polarized macrophages can be broadly classified into classically activated macrophages (M1) and alternatively activated macrophages (M2) in response to the microenvironment signals. Interferon regulatory factor 1 (IRF1) has been demonstrated to play a critical role in macrophage polarization. However, the mechanisms underlying the regulation of IRF1 expression in macrophage polarization still remain unclear. In this study, IRF1 expression was significantly increased in interferon-γ (IFN-γ) and lipopolysaccharide (LPS)-treated RAW264.7 cells. Moreover, miR-130b-3p was decreased and negatively associated with Irf1 in M1 macrophages. miR-130b-3p repressed M1 polarization by inhibiting IRF1 and subsequently reducing the levels of the targets of IRF1, C-C motif chemokine ligand 5 (CCL5), C-X-C motif chemokine ligand 10 (CXCL10), inducible NO synthase (iNOS), and tumor necrosis factor (TNF). Consistent with these data, overexpressed miR-130b-3p in LPS-treated mice suppressed M1 macrophage polarization in lung macrophages and peritoneal macrophages by inhibiting Irf1 expression and alleviated the inflammation in mouse lung tissues. Furthermore, the predicted binding site between the Irf1 messenger RNA 3'-untranslated region (3'-UTR) and miR-130b-3p was confirmed by the dual-luciferase reporter assay. In conclusion, our research gave the first evidence that miR-130b-3p affected the polarization of M1 macrophages by directly inhibiting Irf1. The miR-130b-3p/IRF1 pathway may be a potential target for regulating macrophage polarization.
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Affiliation(s)
- Qiang Guo
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Xiaoxiao Zhu
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Ran Wei
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Lin Zhao
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Zhen Zhang
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Xunqiang Yin
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.,School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Yunhong Zhang
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.,School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Chu Chu
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.,School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Bin Wang
- Department of Peripheral Vascular Disease, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Xia Li
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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Tagawa H, Kanemaru H, Kimura T, Kuriyama H, Sawamura S, Kajihara I, Miyashita A, Aoi J, Fukushima S, Ihn H. BATF2 expression as a novel marker for invasive phenotype in malignant melanoma. J Dermatol 2020; 47:e372-e373. [PMID: 32696470 DOI: 10.1111/1346-8138.15495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hidemi Tagawa
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hisashi Kanemaru
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Toshihiro Kimura
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Haruka Kuriyama
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Soichiro Sawamura
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Ikko Kajihara
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Azusa Miyashita
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Jun Aoi
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Satoshi Fukushima
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hironobu Ihn
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
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Kayama H, Tani H, Kitada S, Opasawatchai A, Okumura R, Motooka D, Nakamura S, Takeda K. BATF2 prevents T-cell-mediated intestinal inflammation through regulation of the IL-23/IL-17 pathway. Int Immunol 2020; 31:371-383. [PMID: 30753547 PMCID: PMC6528702 DOI: 10.1093/intimm/dxz014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 02/19/2019] [Indexed: 12/15/2022] Open
Abstract
Inappropriate activation of the IL-23 signaling pathway causes chronic inflammation through the induction of immunopathological Th17 cells in several tissues including the intestine, whereas adequate Th17 responses are essential for host defense against harmful organisms. In the intestinal lamina propria, IL-23 is primarily produced by innate myeloid cells including dendritic cells (DCs) and macrophages (Mϕs). However, the molecular mechanisms underlying the regulation of IL-23 production by these cells remains poorly understood. In this study, we demonstrated that BATF2 regulates intestinal homeostasis by inhibiting IL-23-driven T-cell responses. Batf2 was highly expressed in intestinal innate myeloid subsets, such as monocytes, CD11b+ CD64+ Mϕs and CD103+ DCs. Batf2-/- mice spontaneously developed colitis and ileitis with altered microbiota composition. In this context, IL-23, but not TNF-α and IL-10, was produced in high quantities by intestinal CD11b+ CD64+ Mϕs from Batf2-/- mice compared with wild-type mice. Moreover, increased numbers of IFN-γ+, IL-17+ and IFN-γ+ IL-17+ CD4+ T cells, but not IL-10+ CD4+ T cells, accumulated in the colons and small intestines of Batf2-/- mice. In addition, RORγt-expressing innate lymphoid cells were increased in Batf2-/- mice. Batf2-/-Rag2-/- mice showed a reduction in intestinal inflammation present in Batf2-/- mice. Furthermore, the high numbers of intestinal IL-17+ and IFN-γ+ IL-17+ CD4+ T cells were markedly reduced in Batf2-/- mice when introducing Il23a deficiency, which was associated with the abrogation of intestinal inflammation. These results indicated that BATF2 in innate myeloid cells is a key molecule for the suppression of IL-23/IL-17 pathway-mediated adaptive intestinal pathology.
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Affiliation(s)
- Hisako Kayama
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Haruka Tani
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Shoko Kitada
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Anunya Opasawatchai
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Ryu Okumura
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Kiyoshi Takeda
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
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Freem L, Summers KM, Gheyas AA, Psifidi A, Boulton K, MacCallum A, Harne R, O’Dell J, Bush SJ, Hume DA. Analysis of the Progeny of Sibling Matings Reveals Regulatory Variation Impacting the Transcriptome of Immune Cells in Commercial Chickens. Front Genet 2019; 10:1032. [PMID: 31803225 PMCID: PMC6870463 DOI: 10.3389/fgene.2019.01032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/25/2019] [Indexed: 01/05/2023] Open
Abstract
There is increasing recognition that the underlying genetic variation contributing to complex traits influences transcriptional regulation and can be detected at a population level as expression quantitative trait loci. At the level of an individual, allelic variation in transcriptional regulation of individual genes can be detected by measuring allele-specific expression in RNAseq data. We reasoned that extreme variants in gene expression could be identified by analysis of inbred progeny with shared grandparents. Commercial chickens have been intensively selected for production traits. Selection is associated with large blocks of linkage disequilibrium with considerable potential for co-selection of closely linked "hitch-hiker alleles" affecting traits unrelated to the feature being selected, such as immune function, with potential impact on the productivity and welfare of the animals. To test this hypothesis that there is extreme allelic variation in immune-associated genes we sequenced a founder population of commercial broiler and layer birds. These birds clearly segregated genetically based upon breed type. Each genome contained numerous candidate null mutations, protein-coding variants predicted to be deleterious and extensive non-coding polymorphism. We mated selected broiler-layer pairs then generated cohorts of F2 birds by sibling mating of the F1 generation. Despite the predicted prevalence of deleterious coding variation in the genomic sequence of the founders, clear detrimental impacts of inbreeding on survival and post-hatch development were detected in only one F2 sibship of 15. There was no effect on circulating leukocyte populations in hatchlings. In selected F2 sibships we performed RNAseq analysis of the spleen and isolated bone marrow-derived macrophages (with and without lipopolysaccharide stimulation). The results confirm the predicted emergence of very large differences in expression of individual genes and sets of genes. Network analysis of the results identified clusters of co-expressed genes that vary between individuals and suggested the existence of trans-acting variation in the expression in macrophages of the interferon response factor family that distinguishes the parental broiler and layer birds and influences the global response to lipopolysaccharide. This study shows that the impact of inbreeding on immune cell gene expression can be substantial at the transcriptional level, and potentially opens a route to accelerate selection using specific alleles known to be associated with desirable expression levels.
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Affiliation(s)
- Lucy Freem
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Kim M. Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Almas A. Gheyas
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Androniki Psifidi
- Department of Clinical Sciences and Services, Royal Veterinary College, University of London, London, United Kingdom
| | - Kay Boulton
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Amanda MacCallum
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Rakhi Harne
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Jenny O’Dell
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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Liu Q, Ou Q, Shen L, Qiu C, Zhang B, Zhang W, Shao L, Gao Y, Chen ZW. BATF Potentially Mediates Negative Regulation of PD-1/PD-Ls Pathway on T Cell Functions in Mycobacterium tuberculosis Infection. Front Immunol 2019; 10:2430. [PMID: 31681314 PMCID: PMC6803382 DOI: 10.3389/fimmu.2019.02430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
Background: Previously, we have found that blockade of PD-1/PD-Ls pathway could enhance CD4+ T cells-mediated protective immunity in patients with active tuberculosis (ATB). However, the mechanism of PD-1/PD-Ls pathway involved in negative regulation of anti-TB immunity has been still unclear. Recently, the study of human immunodeficiency virus (HIV) infection demonstrated that PD-1 could induce the expression of basic leucine zipper ATF-like transcription factor (BATF) to inhibit CD8+ T cell function. While the mechanism of immune regulation of BATF in Mycobacterium tuberculosis (M. tb) infection has not yet been elucidated. Methods: We enrolled 104 participants including ATB patients (n = 66), latent tuberculosis infection (LTBI) (n = 16) and healthy control (HC) (n = 22). The expressions of BATF in peripheral blood CD4+ and CD8+ T cells from enrolled subjects were determined using flow cytometry. Intervention with PD-1/PD-Ls pathway was performed by using blocking antibodies or human PD-L1 fusion protein. Silencing BATF in peripheral blood mononuclear cells (PBMCs) by electroporation with siRNA. Real-time quantitative PCR, CFSE dilution assay and enzyme linked immunosorbent assay (ELISA) were employed to test T cell functions after BATF knockdown. Results: The percentages of BATF+CD4+ (P = 0.0003 and P < 0.0001, respectively) and BATF+CD8+ (P = 0.0003 and P = 0.0003, respectively) cells were significantly increased in ATB patients compared with LTBI and HC. BATF-expressing PD-1+ T cells in CD4+ and CD8+ T cells were much higher in ATB group than those in LTBI group (P = 0.0426 and 0.0104, respectively) and HC group (P = 0.0133 and 0.0340, respectively). There was a positive correlation between BATF expression and PD-1 expression in ATB patients (for CD4+ T cells, r = 0.6761, P = 0.0158; for CD8+ T cells, r = 0.6104, P = 0.0350). BATF knockdown could enhance IL-2 and IFN-γ secretions (P = 0.0485 and 0.0473, respectively) and CD4+ T cells proliferation (P = 0.0041) in vitro. Conclusions: In the context of tuberculosis, BATF mediates negative regulation of PD-1/PD-Ls pathway on T cell functions. BATF knockdown can improve cytokine secretion and cells proliferation in vitro.
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Affiliation(s)
- Qianqian Liu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Qinfang Ou
- Department of Pulmonary Diseases, Wuxi Infectious Diseases Hospital, Wuxi, China
| | - Lei Shen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Shanghai, China
| | - Chao Qiu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Institutes of Biomedical Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bingyan Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Institutes of Biomedical Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lingyun Shao
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yan Gao
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Zheng W Chen
- Department of Microbiology and Immunology, Center for Primate Biomedical Research, University of Illinois College of Medicine, Chicago, IL, United States
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SARI attenuates colon inflammation by promoting STAT1 degradation in intestinal epithelial cells. Mucosal Immunol 2019; 12:1130-1140. [PMID: 31182817 DOI: 10.1038/s41385-019-0178-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/30/2019] [Accepted: 05/26/2019] [Indexed: 02/05/2023]
Abstract
SARI functions as a suppressor of colon cancer and predicts survival of colon cancer patients, but its role in regulating colitis has not been characterized. Here we show that SARI-/- mice were highly susceptible to colitis, which was associated with enhanced macrophage infiltration and inflammatory cytokine production. Bone marrow reconstitution experiments demonstrated that disease susceptibility was not dependent on the deficiency of SARI in the immune compartment but on the protective role of SARI in the intestinal epithelial cells (IECs). Furthermore, SARI deficiency enhanced Chemokine (C-C motif) Ligand 2 (CCL2) production and knockout of CCR2 blocks the promoting role of SARI deficiency on colitis. Mechanistically, SARI directly targets and promotes signal transducer and activator of transcription 1 (STAT1) degradation in IECs, followed by persistent inactivation of the STAT1/CCL2 transcription complex. In summary, SARI attenuated colitis in mice by impairing colitis-dependent STAT1/CCL2 transcriptional activation in IECs and macrophages recruitment in colon tissue.
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40
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Antonczyk A, Krist B, Sajek M, Michalska A, Piaszyk-Borychowska A, Plens-Galaska M, Wesoly J, Bluyssen HAR. Direct Inhibition of IRF-Dependent Transcriptional Regulatory Mechanisms Associated With Disease. Front Immunol 2019; 10:1176. [PMID: 31178872 PMCID: PMC6543449 DOI: 10.3389/fimmu.2019.01176] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/09/2019] [Indexed: 12/24/2022] Open
Abstract
Interferon regulatory factors (IRFs) are a family of homologous proteins that regulate the transcription of interferons (IFNs) and IFN-induced gene expression. As such they are important modulating proteins in the Toll-like receptor (TLR) and IFN signaling pathways, which are vital elements of the innate immune system. IRFs have a multi-domain structure, with the N-terminal part acting as a DNA binding domain (DBD) that recognizes a DNA-binding motif similar to the IFN-stimulated response element (ISRE). The C-terminal part contains the IRF-association domain (IAD), with which they can self-associate, bind to IRF family members or interact with other transcription factors. This complex formation is crucial for DNA binding and the commencing of target-gene expression. IRFs bind DNA and exert their activating potential as homo or heterodimers with other IRFs. Moreover, they can form complexes (e.g., with Signal transducers and activators of transcription, STATs) and collaborate with other co-acting transcription factors such as Nuclear factor-κB (NF-κB) and PU.1. In time, more of these IRF co-activating mechanisms have been discovered, which may play a key role in the pathogenesis of many diseases, such as acute and chronic inflammation, autoimmune diseases, and cancer. Detailed knowledge of IRFs structure and activating mechanisms predisposes IRFs as potential targets for inhibition in therapeutic strategies connected to numerous immune system-originated diseases. Until now only indirect IRF modulation has been studied in terms of antiviral response regulation and cancer treatment, using mainly antisense oligonucleotides and siRNA knockdown strategies. However, none of these approaches so far entered clinical trials. Moreover, no direct IRF-inhibitory strategies have been reported. In this review, we summarize current knowledge of the different IRF-mediated transcriptional regulatory mechanisms and how they reflect the diverse functions of IRFs in homeostasis and in TLR and IFN signaling. Moreover, we present IRFs as promising inhibitory targets and propose a novel direct IRF-modulating strategy employing a pipeline approach that combines comparative in silico docking to the IRF-DBD with in vitro validation of IRF inhibition. We hypothesize that our methodology will enable the efficient identification of IRF-specific and pan-IRF inhibitors that can be used for the treatment of IRF-dependent disorders and malignancies.
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Affiliation(s)
- Aleksandra Antonczyk
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Bart Krist
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Malgorzata Sajek
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Agata Michalska
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Anna Piaszyk-Borychowska
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Martyna Plens-Galaska
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Wesoly
- Laboratory of High Throughput Technologies, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Hans A R Bluyssen
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
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41
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Sepehri Z, Kiani Z, Kohan F, Ghavami S. Toll-Like Receptor 4 as an Immune Receptor Against Mycobacterium tuberculosis: A Systematic Review. Lab Med 2019; 50:117-129. [PMID: 30124945 DOI: 10.1093/labmed/lmy047] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVE To review the main Mycobacterium tuberculosis (Mtb) pathogen-associated molecular patterns (PAMPs) and the roles played by toll-like receptor (TLR)4 in determination of Mtb infection outcome. METHODS Several scientific databases, including Scopus, PubMed, and Google Scholar, were used for searching appropriate research articles from the literature for information on our topic. RESULTS TLR4 plays positive roles in induction of immune responses against Mtb and participates in eradication of the infection. Some limited investigations approved the roles of TLR4 in induction of apoptosis in macrophages during tuberculosis (TB) and attenuation of immune responses in some situations. CONCLUSIONS TB outcome appears to be dependent on TLR4/Mtb interaction and several factors, including bacterial load and immune or nonimmune cells, as hosts. Also, other TLR/Mtb interactions can affect TLR4 responses.
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Affiliation(s)
- Zahra Sepehri
- Department of Internal Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Zohre Kiani
- Zabol Medicinal Plant Research Center, Zabol University of Medical Sciences, Zabol, Iran and Kerman University of Medical Sciences, Kerman, Iran
| | - Farhad Kohan
- Zabol University of Medical Sciences, Zabol, Iran
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Sciences, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
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Wang Q, Dai L, Wang Y, Deng J, Lin Y, Wang Q, Fang C, Ma Z, Wang H, Shi G, Cheng L, Liu Y, Chen S, Li J, Dong Z, Su X, Yang L, Zhang S, Jiang M, Huang M, Yang Y, Yu D, Zhou Z, Wei Y, Deng H. Targeted demethylation of the SARI promotor impairs colon tumour growth. Cancer Lett 2019; 448:132-143. [DOI: 10.1016/j.canlet.2019.01.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 10/27/2022]
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43
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Denisenko E, Guler R, Mhlanga M, Suzuki H, Brombacher F, Schmeier S. Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection. BMC Genomics 2019; 20:71. [PMID: 30669987 PMCID: PMC6341744 DOI: 10.1186/s12864-019-5450-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 01/11/2019] [Indexed: 12/18/2022] Open
Abstract
Background Tuberculosis is a life-threatening infectious disease caused by Mycobacterium tuberculosis (M.tb). M.tb subverts host immune responses to build a favourable niche and survive inside of host macrophages. Macrophages can control or eliminate the infection, if acquire appropriate functional phenotypes. Transcriptional regulation is a key process that governs the activation and maintenance of these phenotypes. Among the factors orchestrating transcriptional regulation during M.tb infection, transcriptional enhancers still remain unexplored. Results We analysed transcribed enhancers in M.tb-infected mouse bone marrow-derived macrophages. We established a link between known M.tb-responsive transcription factors and transcriptional activation of enhancers and their target genes. Our data suggest that enhancers might drive macrophage response via transcriptional activation of key immune genes, such as Tnf, Tnfrsf1b, Irg1, Hilpda, Ccl3, and Ccl4. We report enhancers acquiring transcription de novo upon infection. Finally, we link highly transcriptionally induced enhancers to activation of genes with previously unappreciated roles in M.tb infection, such as Fbxl3, Tapt1, Edn1, and Hivep1. Conclusions Our findings suggest the importance of macrophage host transcriptional enhancers during M.tb infection. Our study extends current knowledge of the regulation of macrophage responses to M.tb infection and provides a basis for future functional studies on enhancer-gene interactions in this process. Electronic supplementary material The online version of this article (10.1186/s12864-019-5450-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena Denisenko
- Massey University, Institute of Natural and Mathematical Sciences, Albany, Auckland, New Zealand
| | - Reto Guler
- Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, South Africa
| | - Musa Mhlanga
- Gene Expression and Biophysics Group, CSIR Synthetic Biology ERA, Pretoria, South Africa.,Division of Chemical Systems and Synthetic Biology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
| | - Harukazu Suzuki
- Division of Genomic Technologies, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Frank Brombacher
- Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, South Africa
| | - Sebastian Schmeier
- Massey University, Institute of Natural and Mathematical Sciences, Albany, Auckland, New Zealand.
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44
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Guler R, Mpotje T, Ozturk M, Nono JK, Parihar SP, Chia JE, Abdel Aziz N, Hlaka L, Kumar S, Roy S, Penn-Nicholson A, Hanekom WA, Zak DE, Scriba TJ, Suzuki H, Brombacher F. Batf2 differentially regulates tissue immunopathology in Type 1 and Type 2 diseases. Mucosal Immunol 2019; 12:390-402. [PMID: 30542107 PMCID: PMC7051910 DOI: 10.1038/s41385-018-0108-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 10/04/2018] [Accepted: 10/07/2018] [Indexed: 02/04/2023]
Abstract
Basic leucine zipper transcription factor 2 (Batf2) activation is detrimental in Type 1-controlled infectious diseases, demonstrated during infection with Mycobacterium tuberculosis (Mtb) and Listeria monocytogenes Lm. In Batf2-deficient mice (Batf2-/-), infected with Mtb or Lm, mice survived and displayed reduced tissue pathology compared to infected control mice. Indeed, pulmonary inflammatory macrophage recruitment, pro-inflammatory cytokines and immune effectors were also decreased during tuberculosis. This explains that batf2 mRNA predictive early biomarker found in active TB patients is increased in peripheral blood. Similarly, Lm infection in human macrophages and mouse spleen and liver also increased Batf2 expression. In striking contrast, Type 2-controlled schistosomiasis exacerbates during infected Batf2-/- mice with increased intestinal fibro-granulomatous inflammation, pro-fibrotic immune cells, and elevated cytokine production leading to wasting disease and early death. Together, these data strongly indicate that Batf2 differentially regulates Type 1 and Type 2 immunity in infectious diseases.
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Affiliation(s)
- Reto Guler
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, 7925 South Africa ,0000 0004 1937 1151grid.7836.aDepartment 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 ,0000 0004 1937 1151grid.7836.aWellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, 7925 South Africa
| | - Thabo Mpotje
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, 7925 South Africa ,0000 0004 1937 1151grid.7836.aDepartment 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
| | - Mumin Ozturk
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, 7925 South Africa ,0000 0004 1937 1151grid.7836.aDepartment 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 (ICGEB), Cape Town Component, Cape Town, 7925 South Africa ,0000 0004 1937 1151grid.7836.aDepartment 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 ,0000 0004 0595 6917grid.500526.4The Medical Research Centre, Institute of Medical Research and Medicinal Plant Studies (IMPM), Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | - Suraj P. Parihar
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, 7925 South Africa ,0000 0004 1937 1151grid.7836.aDepartment 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 ,0000 0004 1937 1151grid.7836.aWellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, 7925 South Africa ,0000 0004 1937 1151grid.7836.aDivision of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925 South Africa
| | - Julius Ebua Chia
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, 7925 South Africa ,0000 0004 1937 1151grid.7836.aDepartment 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
| | - Nada Abdel Aziz
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, 7925 South Africa ,0000 0004 1937 1151grid.7836.aDepartment 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 ,0000 0004 0639 9286grid.7776.1Department of Chemistry, Faculty of Science, Cairo University, Cairo, Egypt
| | - Lerato Hlaka
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, 7925 South Africa ,0000 0004 1937 1151grid.7836.aDepartment 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
| | - Santosh Kumar
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, 7925 South Africa ,0000 0004 1937 1151grid.7836.aDepartment 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
| | - Sugata Roy
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Adam Penn-Nicholson
- 0000 0004 1937 1151grid.7836.aSouth African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925 South Africa
| | - Willem A. Hanekom
- 0000 0004 1937 1151grid.7836.aSouth African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925 South Africa
| | - Daniel E. Zak
- 0000 0004 0463 2611grid.53964.3dThe Center for Infectious Disease Research, Seattle, WA 98109 USA
| | - Thomas J. Scriba
- 0000 0004 1937 1151grid.7836.aSouth African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925 South Africa
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, 7925 South Africa ,0000 0004 1937 1151grid.7836.aDepartment 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 ,0000 0004 1937 1151grid.7836.aWellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, 7925 South Africa
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45
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Rajaraman S, Canjuga D, Ghosh M, Codrea MC, Sieger R, Wedekink F, Tatagiba M, Koch M, Lauer UM, Nahnsen S, Rammensee HG, Mühlebach MD, Stevanovic S, Tabatabai G. Measles Virus-Based Treatments Trigger a Pro-inflammatory Cascade and a Distinctive Immunopeptidome in Glioblastoma. MOLECULAR THERAPY-ONCOLYTICS 2018; 12:147-161. [PMID: 30775418 PMCID: PMC6365369 DOI: 10.1016/j.omto.2018.12.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 12/23/2018] [Indexed: 12/26/2022]
Abstract
Glioblastoma is an aggressive primary brain tumor with bad prognosis. On the other hand, oncolytic measles virus (MeV) therapy is an experimental glioma treatment strategy with clinical safety and first evidence of anti-tumoral efficacy. Therefore, we investigated the combination of MeV with conventional therapies by cytotoxic survival assays in long-term glioma cell lines LN229, LNZ308, and glioma stem-like GS8 cells, as well as the basal viral infectivity in primary glioblastoma cultures T81/16, T1094/17, and T708/16. We employed Chou-Talalay analysis to identify the synergistic treatment sequence chemotherapy, virotherapy, and finally radiotherapy (CT-VT-RT). RNA sequencing and immunopeptidome analyses were used to delineate treatment-induced molecular and immunological profiles. CT-VT-RT displayed synergistic anti-glioma activity and initiated a type 1 interferon response, along with canonical Janus kinase-signal transducers and activators of transcription (JAK-STAT) signaling, and downstream interferon-stimulated genes were induced, resulting in apoptotic cascades. Furthermore, antigen presentation along with immunostimulatory chemokines was increased in CT-VT-RT-treated glioma cells, indicating a treatment-induced pro-inflammatory phenotype. We identified novel treatment-induced viral and tumor-associated peptides through HLA ligandome analysis. Our data delineate an actionable treatment-induced molecular and immunological signature of CT-VT-RT, and they could be exploited for the design of novel tailored treatment strategies involving virotherapy and immunotherapy.
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Affiliation(s)
- Srinath Rajaraman
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Denis Canjuga
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Michael Ghosh
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen 72076, Germany
| | - Marius Cosmin Codrea
- Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Raika Sieger
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Florian Wedekink
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Marcos Tatagiba
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Marilin Koch
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Ulrich M Lauer
- Department of Internal Medicine VIII, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany.,German Translational Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen 72076, Germany.,German Translational Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
| | - Michael D Mühlebach
- Division of Veterinary Medicine, Paul-Ehrlich-Institut, Langen 63225, Germany
| | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen 72076, Germany.,German Translational Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
| | - Ghazaleh Tabatabai
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany.,German Translational Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
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46
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Barreira-Silva P, Torrado E, Nebenzahl-Guimaraes H, Kallenius G, Correia-Neves M. Aetiopathogenesis, immunology and microbiology of tuberculosis. Tuberculosis (Edinb) 2018. [DOI: 10.1183/2312508x.10020917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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47
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Dunlap MD, Howard N, Das S, Scott N, Ahmed M, Prince O, Rangel-Moreno J, Rosa BA, Martin J, Kaushal D, Kaplan G, Mitreva M, Kim KW, Randolph GJ, Khader SA. A novel role for C-C motif chemokine receptor 2 during infection with hypervirulent Mycobacterium tuberculosis. Mucosal Immunol 2018; 11:1727-1742. [PMID: 30115997 PMCID: PMC6279476 DOI: 10.1038/s41385-018-0071-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 06/26/2018] [Accepted: 07/10/2018] [Indexed: 02/08/2023]
Abstract
C-C motif chemokine receptor 2 (CCR2) is a major chemokine axis that recruits myeloid cells including monocytes and macrophages. Thus far, CCR2-/- mice have not been found to be susceptible to infection with Mycobacterium tuberculosis (Mtb). Here, using a prototype W-Beijing family lineage 2 Mtb strain, HN878, we show that CCR2-/- mice exhibit increased susceptibility to tuberculosis (TB). Following exposure to Mtb HN878, alveolar macrophages (AMs) are amongst the earliest cells infected. We show that AMs accumulate early in the airways following infection and express CCR2. During disease progression, CCR2-expressing AMs exit the airways and localize within the TB granulomas. RNA-sequencing of sorted airway and non-airway AMs from infected mice show distinct gene expression profiles, suggesting that upon exit from airways and localization within granulomas, AMs become classically activated. The absence of CCR2+ cells specifically at the time of AM egress from the airways resulted in enhanced susceptibility to Mtb infection. Furthermore, infection with an Mtb HN878 mutant lacking phenolic glycolipid (PGL) expression still resulted in increased susceptibility in CCR2-/- mice. Together, these data show a novel role for CCR2 in protective immunity against clinically relevant Mtb infections.
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Affiliation(s)
- Micah D Dunlap
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Nicole Howard
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Shibali Das
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Ninecia Scott
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Mushtaq Ahmed
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Oliver Prince
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | | | - Bruce A Rosa
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - John Martin
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Deepak Kaushal
- Division of Bacteriology and Parasitology, Tulane National Primate Research Center, Covington, LA, 70118, USA
| | - Gilla Kaplan
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Makedonka Mitreva
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Ki-Wook Kim
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Gwendalyn J Randolph
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Shabaana A Khader
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
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48
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Yurchenko AA, Daetwyler HD, Yudin N, Schnabel RD, Vander Jagt CJ, Soloshenko V, Lhasaranov B, Popov R, Taylor JF, Larkin DM. Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation. Sci Rep 2018; 8:12984. [PMID: 30154520 PMCID: PMC6113280 DOI: 10.1038/s41598-018-31304-w] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/16/2018] [Indexed: 01/08/2023] Open
Abstract
Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, 3083, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, 3083, Victoria, Australia
| | - Nikolay Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211-5300, USA
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, 3083, Victoria, Australia
| | | | | | - Ruslan Popov
- Yakutian Research Institute of Agriculture, 677001, Yakutsk, Russia
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211-5300, USA
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia.
- Royal Veterinary College, University of London, NW01 0TU, London, UK.
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49
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Li Y, Li Y, Lu W, Li H, Wang Y, Luo H, Wu Y, Dong W, Bai G, Zhang Y. Integrated Network Pharmacology and Metabolomics Analysis of the Therapeutic Effects of Zi Dian Fang on Immune Thrombocytopenic Purpura. Front Pharmacol 2018; 9:597. [PMID: 29971001 PMCID: PMC6018083 DOI: 10.3389/fphar.2018.00597] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/18/2018] [Indexed: 12/25/2022] Open
Abstract
Current hormone-based treatments for immune thrombocytopenic purpura (ITP) are associated with potentially serious adverse reactions. Zi Dian Fang (ZDF) is a multi-target Traditional Chinese Medicine (TCM) used to treat both the symptoms and root causes of ITP, with fewer side effects than hormone-based treatments. This study analysis of the therapeutic effects of ZDF on ITP from three aspects: platelet proliferation, immunoregulation, and inflammation. After detection of 52 chemical constituents of ZDF by UPLC-Q-TOF/MS, The main targets and pathways affected by ZDF were screened by network pharmacology and verified by Western blot and ELISA. Meanwhile, metabolomics analysis were applied to a mouse model of ITP to identify and screen endogenous terminal metabolites differentially regulated by ZDF. Integrated network pharmacology and metabolomics analysis of the therapeutic effects of ZDF on ITP may be as follows: ZDF counteracts ITP symptoms mainly by inhibiting Ras/MAPKs (Ras/Mitogen-activated protein kinases) pathway, and the expression of upstream protein (Ras) and downstream protein (p-ERK, p-JNK, p-p38) were inhibited, which affects the content of effect index associated with proliferation (Thrombopoietin, TPO; Granulocyte-macrophage colony stimulating factor, GM-CSF), inflammation (Tumor necrosis factor-α, TNF-α; Interleukin-6, IL-6), immune (Interleukin-2, IL-2; Interferon-gamma, IFN-γ; Interleukin-4, IL-4), so that the body’s arginine, Δ12-prostaglandin j2 (Δ12-PGJ2), 9-cis-Retinoic Acid, sphingosine-1-phosphate (S1P), oleic acid amide and other 12 endogenous metabolites significantly changes. Considering the established safety profile, the present study suggests ZDF may be a useful alternative to hormone-based therapies for the treatment of ITP.
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Affiliation(s)
- Yubo Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yamei Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wenliang Lu
- Tasly Institute, Tasly Pharmaceutical Group, Tianjin, China
| | - Hongbin Li
- Tasly Institute, Tasly Pharmaceutical Group, Tianjin, China
| | - Yuming Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Houmin Luo
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yuanyuan Wu
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wenying Dong
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Gang Bai
- College of Pharmacy, Nankai University, Tianjin, China
| | - Yanjun Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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50
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Verma S, Du P, Nakanjako D, Hermans S, Briggs J, Nakiyingi L, Ellner JJ, Manabe YC, Salgame P. "Tuberculosis in advanced HIV infection is associated with increased expression of IFNγ and its downstream targets". BMC Infect Dis 2018; 18:220. [PMID: 29764370 PMCID: PMC5952419 DOI: 10.1186/s12879-018-3127-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 05/02/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is the major cause of death in Human Immunodeficiency Virus (HIV)-infected individuals. However, diagnosis of TB in HIV remains challenging particularly when HIV infection is advanced. Several gene signatures and serum protein biomarkers have been identified that distinguish active TB from latent infection. Our study was designed to assess if gene expression signatures and cytokine levels would distinguish active TB in advanced HIV. METHODS We conducted a case-control study of whole blood RNA-Seq and plasma cytokine/chemokine analysis in HIV-infected with CD4+ T cell count of ≤ 100 cells/μl, with and without active TB. Next, the overlap of the differentially expressed genes (DEG) with the published signatures was performed and then receiver operator characteristic (ROC) analysis was done on small gene discriminators to determine their performance in distinguishing TB in advanced HIV. ELISA was performed on plasma to evaluate cytokine and chemokine levels. RESULTS Hierarchical clustering of the transcriptional profiles showed that, in general, HIV-infected individuals with TB (TB-HIV) clustered separately from those without TB. IPA indicated that the TB-HIV signature was characterized by an increase in inflammatory signaling pathways. Analysis of overlaps between DEG in our data set with published TB signatures revealed that significant overlap was seen with one TB signature and one TB-IRIS signature. ROC analysis revealed that transcript levels of FcGR1A (AUC = 0.85) and BATF2 (AUC = 0.82), previously reported as consistent single gene classifiers of active TB irrespective of HIV status, performed successfully even in advanced HIV. Plasma protein levels of IFNγ, a stimulator of FcGR1A and BATF2, and CXCL10, also up-regulated by IFNγ, accurately classified active TB (AUC = 0.98 and 0.91, respectively) in advanced HIV. Neither of these genes nor proteins distinguished between TB and TB-IRIS. CONCLUSIONS Gene expression of FcGR1A and BATF2, and plasma protein levels of IFNγ and CXCL10 have the potential to independently detect TB in advanced HIV. However, since other lung diseases were not included in this study, these final candidates need to be validated as specific to TB in the advanced HIV population with TB.
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Affiliation(s)
- Sheetal Verma
- Department of Medicine, Center for Emerging Pathogens, Rutgers University New Jersey Medical School, Newark, NJ USA
| | - Peicheng Du
- Office of Advanced Research Computing, Rutgers University New Jersey Medical School, Newark, NJ USA
| | - Damalie Nakanjako
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Sabine Hermans
- Amsterdam Institute of Global Health and Development, Amsterdam Medical Center, Amsterdam, Netherlands
| | - Jessica Briggs
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Present address: UCSF, Division of Infectious Diseases, San Francisco, CA USA
| | - Lydia Nakiyingi
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Jerrold J. Ellner
- Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA USA
| | - Yukari C. Manabe
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Padmini Salgame
- Department of Medicine, Center for Emerging Pathogens, Rutgers University New Jersey Medical School, Newark, NJ USA
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