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Tapken I, Kuhn D, Hoffmann N, Detering NT, Schüning T, Billaud JN, Tugendreich S, Schlüter N, Green J, Krämer A, Claus P. From data to discovery: AI-guided analysis of disease-relevant molecules in spinal muscular atrophy (SMA). Hum Mol Genet 2024; 33:1367-1377. [PMID: 38704739 DOI: 10.1093/hmg/ddae076] [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: 01/18/2024] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
Spinal Muscular Atrophy is caused by partial loss of survival of motoneuron (SMN) protein expression. The numerous interaction partners and mechanisms influenced by SMN loss result in a complex disease. Current treatments restore SMN protein levels to a certain extent, but do not cure all symptoms. The prolonged survival of patients creates an increasing need for a better understanding of SMA. Although many SMN-protein interactions, dysregulated pathways, and organ phenotypes are known, the connections among them remain largely unexplored. Monogenic diseases are ideal examples for the exploration of cause-and-effect relationships to create a network describing the disease-context. Machine learning tools can utilize such knowledge to analyze similarities between disease-relevant molecules and molecules not described in the disease so far. We used an artificial intelligence-based algorithm to predict new genes of interest. The transcriptional regulation of 8 out of 13 molecules selected from the predicted set were successfully validated in an SMA mouse model. This bioinformatic approach, using the given experimental knowledge for relevance predictions, enhances efficient targeted research in SMA and potentially in other disease settings.
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Affiliation(s)
- Ines Tapken
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Feodor-Lynen-Str. 31, Hannover 30625, Germany
- Center for Systems Neuroscience (ZSN), Bünteweg 2, Hannover 30559, Germany
| | - Daniela Kuhn
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Feodor-Lynen-Str. 31, Hannover 30625, Germany
- Hannover Medical School, Department of Conservative Dentistry, Periodontology and Preventive Dentistry, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Nico Hoffmann
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Feodor-Lynen-Str. 31, Hannover 30625, Germany
| | - Nora T Detering
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Feodor-Lynen-Str. 31, Hannover 30625, Germany
- Center for Systems Neuroscience (ZSN), Bünteweg 2, Hannover 30559, Germany
| | - Tobias Schüning
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Feodor-Lynen-Str. 31, Hannover 30625, Germany
| | - Jean-Noël Billaud
- QIAGEN Digital Insights, 1001 Marshall Street,Redwood City, CA 94063, United States
| | - Stuart Tugendreich
- QIAGEN Digital Insights, 1001 Marshall Street,Redwood City, CA 94063, United States
| | - Nadine Schlüter
- Hannover Medical School, Department of Conservative Dentistry, Periodontology and Preventive Dentistry, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Jeff Green
- QIAGEN Digital Insights, 1001 Marshall Street,Redwood City, CA 94063, United States
| | - Andreas Krämer
- QIAGEN Digital Insights, 1001 Marshall Street,Redwood City, CA 94063, United States
| | - Peter Claus
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Feodor-Lynen-Str. 31, Hannover 30625, Germany
- Center for Systems Neuroscience (ZSN), Bünteweg 2, Hannover 30559, Germany
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Yi X, Jia W, Li W, Jia C, Song C. Diagnostic value of cytokines in severe childhood Mycoplasma pneumoniae pneumonia combined with Adenovirus infection. Ital J Pediatr 2024; 50:92. [PMID: 38715105 PMCID: PMC11077701 DOI: 10.1186/s13052-024-01661-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND To explore the alterations of inflammatory markers and immune-related cytokines in children infected with Mycoplasma pneumoniae (MP) combined with Adenovirus (ADV). METHODS The study population consisted of 201 children with MPP, and they were grouped according to whether they were coinfected with ADV infection and critically ill. Additionally, comparative analyses were performed. The diagnostic value of different indicators and combined indicators for SMPP combined with ADV was assessed using ROC curves. RESULTS There was no difference between group A1 and group A2, group B1 and group B2 in terms of age, gender, duration of hospitalisation and fever. The levels of calcitoninogen(PCT), lactate dehydrogenase concentration(LDH), interleukin(IL)-6, IL-8, IL-10, IL-4, IL-12P70, and IFN-γ in group A were higher than group B. The severe group (A1, B1) was significantly higher than the mild group (A2, B2) in terms of D-dimer, CRP, PCT, LDH, IL-6, IL-8, IL-10, IL-17a and number of patients with pleural effusion, solid lung changes. Among the individual indexes of D-dimer, CRP, N%,LDH, and PCT, the AUC of the combined test was 0.977, which was higher than that of the individual indicators. Among IL-6, IL-8, IL-10, and IL-17a, the AUC of the combined assay was 0.802, which was higher than that of the individual indicators. CONCLUSION MP combined with ADV infection was associated with increased expression levels of IL-6, IL-8, IL-10, IL-4, IL-12P70, IFN-γ, and LDH. IL-6, IL-8, IL-10, IL-17a, LDH, PCT, CRP, and D-dimer could be used as predictors of SMPP and the combined test can improve the diagnostic value.
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Affiliation(s)
- Xiaowen Yi
- Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Longhu Waihuan East Road, Zhengdong New District, Zhengzhou, Henan, 450018, China
| | - Wanyu Jia
- Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Longhu Waihuan East Road, Zhengdong New District, Zhengzhou, Henan, 450018, China
| | - Wanying Li
- Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Longhu Waihuan East Road, Zhengdong New District, Zhengzhou, Henan, 450018, China
| | - Canyang Jia
- Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Longhu Waihuan East Road, Zhengdong New District, Zhengzhou, Henan, 450018, China
| | - Chunlan Song
- Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Longhu Waihuan East Road, Zhengdong New District, Zhengzhou, Henan, 450018, China.
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3
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Yee Mon KJ, Kim S, Dai Z, West JD, Zhu H, Jain R, Grimson A, Rudd BD, Singh A. Functionalized nanowires for miRNA-mediated therapeutic programming of naïve T cells. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01649-7. [PMID: 38684809 DOI: 10.1038/s41565-024-01649-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/13/2024] [Indexed: 05/02/2024]
Abstract
Cellular programming of naïve T cells can improve the efficacy of adoptive T-cell therapy. However, the current ex vivo engineering of T cells requires the pre-activation of T cells, which causes them to lose their naïve state. In this study, cationic-polymer-functionalized nanowires were used to pre-program the fate of primary naïve CD8+ T cells to achieve a therapeutic response in vivo. This was done by delivering single or multiple microRNAs to primary naïve mouse and human CD8+ T cells without pre-activation. The use of nanowires further allowed for the delivery of large, whole lentiviral particles with potential for long-term integration. The combination of deletion and overexpression of miR-29 and miR-130 impacted the ex vivo T-cell differentiation fate from the naïve state. The programming of CD8+ T cells using nanowire-delivered co-delivery of microRNAs resulted in the modulation of T-cell fitness by altering the T-cell proliferation, phenotypic and transcriptional regulation, and secretion of effector molecules. Moreover, the in vivo adoptive transfer of murine CD8+ T cells programmed through the nanowire-mediated dual delivery of microRNAs provided enhanced immune protection against different types of intracellular pathogen (influenza and Listeria monocytogenes). In vivo analyses demonstrated that the simultaneous alteration of miR-29 and miR-130 levels in naïve CD8+ T cells reduces the persistence of canonical memory T cells whereas increases the population of short-lived effector T cells. Nanowires could potentially be used to modulate CD8+ T-cell differentiation and achieve a therapeutic response in vivo without the need for pre-activation.
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Affiliation(s)
- Kristel J Yee Mon
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Sungwoong Kim
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, USA
| | - Zhonghao Dai
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jessica D West
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Hongya Zhu
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Ritika Jain
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Andrew Grimson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA.
| | - Ankur Singh
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
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Baldrighi M, Doreth C, Li Y, Zhao X, Warner E, Chenoweth H, Kishore K, Umrania Y, Minde DP, Thome S, Yu X, Lu Y, Knapton A, Harrison J, Clarke M, Latz E, de Cárcer G, Malumbres M, Ryffel B, Bryant C, Liu J, Lilley KS, Mallat Z, Li X. PLK1 inhibition dampens NLRP3 inflammasome-elicited response in inflammatory disease models. J Clin Invest 2023; 133:e162129. [PMID: 37698938 PMCID: PMC10617773 DOI: 10.1172/jci162129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/06/2023] [Indexed: 09/14/2023] Open
Abstract
Unabated activation of the NLR family pyrin domain-containing 3 (NLRP3) inflammasome is linked with the pathogenesis of various inflammatory disorders. Polo-like kinase 1 (PLK1) has been widely studied for its role in mitosis. Here, using both pharmacological and genetic approaches, we demonstrate that PLK1 promoted NLRP3 inflammasome activation at cell interphase. Using an unbiased proximity-dependent biotin identification (Bio-ID) screen for the PLK1 interactome in macrophages, we show an enhanced proximal association of NLRP3 with PLK1 upon NLRP3 inflammasome activation. We further confirmed the interaction between PLK1 and NLRP3 and identified the interacting domains. Mechanistically, we show that PLK1 orchestrated the microtubule-organizing center (MTOC) structure and NLRP3 subcellular positioning upon inflammasome activation. Treatment with a selective PLK1 kinase inhibitor suppressed IL-1β production in in vivo inflammatory models, including LPS-induced endotoxemia and monosodium urate-induced peritonitis in mice. Our results uncover a role of PLK1 in regulating NLRP3 inflammasome activation during interphase and identify pharmacological inhibition of PLK1 as a potential therapeutic strategy for inflammatory diseases with excessive NLRP3 inflammasome activation.
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Affiliation(s)
- Marta Baldrighi
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Christian Doreth
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yang Li
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiaohui Zhao
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Emily Warner
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Hannah Chenoweth
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Yagnesh Umrania
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - David-Paul Minde
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Thome
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Xian Yu
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yuning Lu
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alice Knapton
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - James Harrison
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Murray Clarke
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital, University of Bonn, Bonn, Germany
| | - Guillermo de Cárcer
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Cell Cycle and Cancer Biomarkers Group, “Alberto Sols” Biomedical Research Institute (IIBM-CSIC), Madrid, Spain
| | - Marcos Malumbres
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Bernhard Ryffel
- UMR7355 INEM, Experimental and Molecular Immunology and Neurogenetics CNRS and Université d’Orleans, Orleans, France
| | - Clare Bryant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jinping Liu
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kathryn S. Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - Ziad Mallat
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Université Paris Cité, PARCC, INSERM, Paris, France
| | - Xuan Li
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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5
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Sheng J, Li L, Lv X, Gao M, Chen Z, Zhou Z, Wang J, Wu A, Jiang T. Integrated interactome and transcriptome analysis reveals key host factors critical for SARS-CoV-2 infection. Virol Sin 2023; 38:508-519. [PMID: 37169126 PMCID: PMC10166720 DOI: 10.1016/j.virs.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has seriously threatened global public health and caused huge economic losses. Omics studies of SARS-CoV-2 can help understand the interaction between the virus and host, thereby providing a new perspective in guiding the intervention and treatment of the SARS-CoV-2 infection. Since large amount of SARS-CoV-2 omics data have been accumulated in public databases, this study aimed to identify key host factors involved in SARS-CoV-2 infection through systematic integration of transcriptome and interactome data. By manually curating published studies, we obtained a comprehensive SARS-CoV-2-human protein-protein interactions (PPIs) network, comprising 3591 human proteins interacting with 31 SARS-CoV-2 viral proteins. Using the RobustRankAggregation method, we identified 123 multiple cell line common genes (CLCGs), of which 115 up-regulated CLCGs showed host enhanced innate immunity and chemotactic response signatures. Combined with network analysis, co-expression and functional enrichment analysis, we discovered four key host factors involved in SARS-CoV-2 infection: IFITM1, SERPINE1, DDX60, and TNFAIP2. Furthermore, SERPINE1 was found to facilitate SARS-CoV-2 replication, and can alleviate the endoplasmic reticulum (ER) stress induced by ORF8 protein through interaction with ORF8. Our findings highlight the importance of systematic integration analysis in understanding SARS-CoV-2-human interactions and provide valuable insights for future research on potential therapeutic targets against SARS-CoV-2 infection.
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Affiliation(s)
- Jie Sheng
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China; Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Lili Li
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Xueying Lv
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China; Department of Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, China
| | - Meiling Gao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Ziyi Chen
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Zhuo Zhou
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Jingfeng Wang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China.
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China.
| | - Taijiao Jiang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China; Guangzhou Laboratory, Guangzhou, 510005, China; State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, China.
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6
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Yokomizo-Nakano T, Hamashima A, Kubota S, Bai J, Sorin S, Sun Y, Kikuchi K, Iimori M, Morii M, Kanai A, Iwama A, Huang G, Kurotaki D, Takizawa H, Matsui H, Sashida G. Exposure to microbial products followed by loss of Tet2 promotes myelodysplastic syndrome via remodeling HSCs. J Exp Med 2023; 220:e20220962. [PMID: 37071125 PMCID: PMC10120406 DOI: 10.1084/jem.20220962] [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: 06/03/2022] [Revised: 01/11/2023] [Accepted: 03/28/2023] [Indexed: 04/19/2023] Open
Abstract
Aberrant innate immune signaling in myelodysplastic syndrome (MDS) hematopoietic stem/progenitor cells (HSPCs) has been implicated as a driver of the development of MDS. We herein demonstrated that a prior stimulation with bacterial and viral products followed by loss of the Tet2 gene facilitated the development of MDS via up-regulating the target genes of the Elf1 transcription factor and remodeling the epigenome in hematopoietic stem cells (HSCs) in a manner that was dependent on Polo-like kinases (Plk) downstream of Tlr3/4-Trif signaling but did not increase genomic mutations. The pharmacological inhibition of Plk function or the knockdown of Elf1 expression was sufficient to prevent the epigenetic remodeling in HSCs and diminish the enhanced clonogenicity and the impaired erythropoiesis. Moreover, this Elf1-target signature was significantly enriched in MDS HSPCs in humans. Therefore, prior infection stress and the acquisition of a driver mutation remodeled the transcriptional and epigenetic landscapes and cellular functions in HSCs via the Trif-Plk-Elf1 axis, which promoted the development of MDS.
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Affiliation(s)
- Takako Yokomizo-Nakano
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ai Hamashima
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Sho Kubota
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jie Bai
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Supannika Sorin
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Yuqi Sun
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kenta Kikuchi
- Laboratory of Chromatin Organization in Immune Cell Development, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mihoko Iimori
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mariko Morii
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Akinori Kanai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Atsushi Iwama
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Gang Huang
- Department of Cell Systems & Anatomy, Department of Pathology and Laboratory Medicine, UT Health San Antonio, Joe R. and Teresa Lozano Long School of Medicine, Mays Cancer Center at UT Health San Antonio, San Antonio, TX, USA
| | - Daisuke Kurotaki
- Laboratory of Chromatin Organization in Immune Cell Development, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hitoshi Takizawa
- Laboratory of Stem Cell Stress, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Hirotaka Matsui
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Goro Sashida
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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7
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Rathore D, Marino MJ, Nita-Lazar A. Omics and systems view of innate immune pathways. Proteomics 2023; 23:e2200407. [PMID: 37269203 DOI: 10.1002/pmic.202200407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/16/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023]
Abstract
Multiomics approaches to studying systems biology are very powerful techniques that can elucidate changes in the genomic, transcriptomic, proteomic, and metabolomic levels within a cell type in response to an infection. These approaches are valuable for understanding the mechanisms behind disease pathogenesis and how the immune system responds to being challenged. With the emergence of the COVID-19 pandemic, the importance and utility of these tools have become evident in garnering a better understanding of the systems biology within the innate and adaptive immune response and for developing treatments and preventative measures for new and emerging pathogens that pose a threat to human health. In this review, we focus on state-of-the-art omics technologies within the scope of innate immunity.
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Affiliation(s)
- Deepali Rathore
- Functional Cellular Networks Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Matthew J Marino
- Functional Cellular Networks Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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8
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Li H, Liu S, Feng Q, Deng R, Wang J, Wang X, Tian R, Xu Y, Chen S, Liu Q, Wang L, Li X, Wan M, Peng Y, Tang S, Xue B, Zhu H. Regulation of PKR-dependent RNA translation inhibition by TRIM21 upon virus infection or other stress. PLoS Pathog 2023; 19:e1011443. [PMID: 37327222 DOI: 10.1371/journal.ppat.1011443] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/25/2023] [Indexed: 06/18/2023] Open
Abstract
The host always employs various ways to defend against viral infection and spread. However, viruses have evolved their own effective strategies, such as inhibition of RNA translation of the antiviral effectors, to destroy the host's defense barriers. Protein synthesis, commonly controlled by the α-subunit of eukaryotic translation initiation factor 2 (eIF2α), is a basic cellular biological process among all species. In response to viral infection, in addition to inducing the transcription of antiviral cytokines by innate immunity, infected cells also inhibit the RNA translation of antiviral factors by activating the protein kinase R (PKR)-eIF2α signaling pathway. Regulation of innate immunity has been well studied; however, regulation of the PKR-eIF2α signaling pathway remains unclear. In this study, we found that the E3 ligase TRIM21 negatively regulates the PKR-eIF2α signaling pathway. Mechanistically, TRIM21 interacts with the PKR phosphatase PP1α and promotes K6-linked polyubiquitination of PP1α. Ubiquitinated PP1α augments its interaction with PKR, causing PKR dephosphorylation and subsequent translational inhibition release. Furthermore, TRIM21 can constitutively restrict viral infection by reversing PKR-dependent translational inhibition of various previously known and unknown antiviral factors. Our study highlights a previously undiscovered role of TRIM21 in regulating translation, which will provide new insights into the host antiviral response and novel targets for the treatment of translation-associated diseases in the clinic.
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Affiliation(s)
- Huiyi Li
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Shun Liu
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Qing Feng
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Rilin Deng
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Jingjing Wang
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Xintao Wang
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Renyun Tian
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Yan Xu
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Shengwen Chen
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Qian Liu
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Luoling Wang
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Xinran Li
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Mengyu Wan
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Yousong Peng
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Songqing Tang
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Binbin Xue
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Department of Pathogen Biology and Immunology, Institute of Pathogen Biology and Immunology, School of Basic Medicine and Life Science, The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The First Affiliated Hospital and The Second Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan, China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Department of Pathogen Biology and Immunology, Institute of Pathogen Biology and Immunology, School of Basic Medicine and Life Science, The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The First Affiliated Hospital and The Second Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan, China
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9
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Kurland AP, Bonaventure B, Johnson JR. A Chemical Proteomics Approach to Discover Regulators of Innate Immune Signaling. Viruses 2023; 15:v15051112. [PMID: 37243198 DOI: 10.3390/v15051112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Innate immune pathways are tightly regulated to balance an appropriate response to infectious agents and tolerable levels of inflammation. Dysregulation of innate immune pathways can lead to severe autoinflammatory disorders or susceptibility to infections. Here, we aimed to identify kinases in common cellular pathways that regulate innate immune pathways by combining small-scale kinase inhibitor screening with quantitative proteomics. We found that inhibitors of kinases ATM, ATR, AMPK, and PLK1 reduced the induction of interferon-stimulated gene expression in response to innate immune pathway activation by poly(I:C) transfection. However, siRNA depletion of these kinases did not validate findings with kinase inhibitors, suggesting that off-target effects may explain their activities. We mapped the effects of kinase inhibitors to various stages in innate immune pathways. Determining the mechanisms by which kinase inhibitors antagonize these pathways may illuminate novel mechanisms of innate immune pathway control.
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Affiliation(s)
- Andrew P Kurland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Boris Bonaventure
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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10
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Wang S, Li H, Li Q, Yin B, Li S, He J, Li C. Signaling events induced by lipopolysaccharide-activated Toll in response to bacterial infection in shrimp. Front Immunol 2023; 14:1119879. [PMID: 36817428 PMCID: PMC9936618 DOI: 10.3389/fimmu.2023.1119879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Toll-like receptors (TLR) play a crucial role in the detection of microbial infections in vertebrates and invertebrates. Mammalian TLRs directly recognize a variety of structurally conserved microbial components. However, invertebrates such as Drosophila indirectly recognize microbial products by binding to the cytokine-like ligand Spätzle, which activates signaling cascades that are not completely understood. In this study, we investigated the signaling events triggered by Toll in response to lipopolysaccharide (LPS), a cell wall component of gram-negative bacteria, and Vibrio parahaemolyticus infection in the arthropod shrimp Litopenaeus vannamei. We found that five of the nine Tolls from L. vannamei bound to LPS and the RNAi of LvToll1, LvToll2, LvToll3, LvToll5, and LvToll9 weakened LvDorsal-L phosphorylation induced by V. parahaemolyticus. All nine Tolls combined with MyD88 via the TIR domain, thereby conferring signals to the tumor necrosis factor receptor-associated factor 6 (TRAF6)-transforming growth factor-β activated kinase 1 binding protein 2 (TAB2)-transforming growth factor-β activated kinase 1 (TAK1) complex. Further examination revealed that the LvTRAF6-LvTAB2-LvTAK1 complex contributes to Dorsal-L phosphorylation and nuclear translocation during V. parahaemolyticus infection. Overall, shrimp Toll1/2/3/5/9-TRAF6/TAB2/TAK1-Dorsal cascades protect the host from V. parahaemolyticus infection, which provides a better understanding of how the innate immune system recognizes and responds to bacterial infections in invertebrates.
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Affiliation(s)
- Sheng Wang
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, China
- China-Association of Southeast Asian Nations (ASEAN) Belt and Road Joint Laboratory on Marine Aquaculture Technology, Guangzhou, China
| | - Haoyang Li
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, China
- China-Association of Southeast Asian Nations (ASEAN) Belt and Road Joint Laboratory on Marine Aquaculture Technology, Guangzhou, China
| | - Qinyao Li
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, China
| | - Bin Yin
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, China
| | - Sedong Li
- Guangdong Evergreen Feed Industry Co., Ltd, Zhanjiang, China
| | - Jianguo He
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, China
- China-Association of Southeast Asian Nations (ASEAN) Belt and Road Joint Laboratory on Marine Aquaculture Technology, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Chaozheng Li
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, China
- China-Association of Southeast Asian Nations (ASEAN) Belt and Road Joint Laboratory on Marine Aquaculture Technology, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
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11
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Geiger-Schuller K, Eraslan B, Kuksenko O, Dey KK, Jagadeesh KA, Thakore PI, Karayel O, Yung AR, Rajagopalan A, Meireles AM, Yang KD, Amir-Zilberstein L, Delorey T, Phillips D, Raychowdhury R, Moussion C, Price AL, Hacohen N, Doench JG, Uhler C, Rozenblatt-Rosen O, Regev A. Systematically characterizing the roles of E3-ligase family members in inflammatory responses with massively parallel Perturb-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525198. [PMID: 36747789 PMCID: PMC9900845 DOI: 10.1101/2023.01.23.525198] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
E3 ligases regulate key processes, but many of their roles remain unknown. Using Perturb-seq, we interrogated the function of 1,130 E3 ligases, partners and substrates in the inflammatory response in primary dendritic cells (DCs). Dozens impacted the balance of DC1, DC2, migratory DC and macrophage states and a gradient of DC maturation. Family members grouped into co-functional modules that were enriched for physical interactions and impacted specific programs through substrate transcription factors. E3s and their adaptors co-regulated the same processes, but partnered with different substrate recognition adaptors to impact distinct aspects of the DC life cycle. Genetic interactions were more prevalent within than between modules, and a deep learning model, comβVAE, predicts the outcome of new combinations by leveraging modularity. The E3 regulatory network was associated with heritable variation and aberrant gene expression in immune cells in human inflammatory diseases. Our study provides a general approach to dissect gene function.
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12
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Bhowmik KK, Barek MA, Aziz MA, Islam MS. Susceptibility of TNFAIP8, TNFAIP8L1, and TNFAIP2 Gene Polymorphisms on Cancer Risk: A Comprehensive Review and Meta-Analysis of Case-Control Studies. Technol Cancer Res Treat 2022; 21:15330338221123109. [PMID: 36254562 PMCID: PMC9580160 DOI: 10.1177/15330338221123109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Objectives: The TNFAIP8 gene family and TNFAIP2 gene are inextricably linked to an elevated risk of cancer development. This systemic review and meta-analysis seeks to establish the relationship between TNFAIP8 (rs11064, rs1045241, rs1045242, and rs3813308), TNFAIP8L1 (rs1060555), and TNFAIP2 (rs710100 and rs8126) polymorphisms with the risk of cancer. Methods and Materials: A systematic search of multiple databases from January 2022 to April 2022 was used to identify relevant studies. Odds ratios (ORs) with corresponding 95% CI and p-value were calculated to assess the association. Bonferroni correction was performed to correct p-values. Trial sequential analysis (TSA) and in-silico messenger RNA expression were also performed. Review Manager 5.4 software was used for performing this meta-analysis. Results: This study comprised 6909 cancer patients and 7087 healthy participants from 14 studies. Four genetic models of rs11064 (codominant 2 [COD2]: OR = 2.30, p = 7.83 × 10-5; codominant 3 [COD3]: OR = 2.10, p = .0006; recessive model [RM]: OR = 2.24, p = .0001; AC: OR = 1.47, p = .037), two genetic models of rs1045241 (codominant 1 [COD1]: OR = 1.27, p = .009; overdominant model [ODM]: OR = 1.24, p = .018), four genetic models of rs1045242 (COD1: OR = 1.52, p = .005; dominant model (DM): OR = 1.56, p = .002; OD: OR = 1.48, p = .008; AC: OR = 1.48, p = .002), and three genetic models of rs8126 (COD2: OR = 1.41, p = .0005; COD3: OR = 1.44, p = .0002; RM: OR = 1.43, p = .0001) were statistically linked to cancer risk. Only one genetic model of rs1060555 polymorphism showed a significant protective association with cancer (COD2: OR = 0.80, p = .048). The outcomes of TSA also validated the findings of the meta-analysis. Conclusion: This study summarizes that rs11064, rs1045241, and rs1045242 polymorphisms of TNFAIP8 gene and rs8126 polymorphism of TNFAIP2 gene are significantly linked with the risk of cancer development. This meta-analysis was registered at INPLASY (registration number: INPLASY202270073).
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Affiliation(s)
- Khokon Kanti Bhowmik
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Bangladesh,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Abdul Barek
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Bangladesh,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md. Abdul Aziz
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | - Mohammad Safiqul Islam
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Bangladesh,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Bangladesh,Mohammad Safiqul Islam, Department of Pharmacy, Noakhali Science and Technology University, Noakhali-3814, Bangladesh.
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13
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Lin MS, Zhong HY, Yim RLH, Chen QY, Du HL, He HQ, Lin K, Zhao P, Gao R, Gao F, Zhang MY. Pan-cancer analysis of oncogenic TNFAIP2 identifying its prognostic value and immunological function in acute myeloid leukemia. BMC Cancer 2022; 22:1068. [PMID: 36243694 PMCID: PMC9571470 DOI: 10.1186/s12885-022-10155-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tumor necrosis factor alpha-induced protein 2 (TNFAIP2), a TNFα-inducible gene, appears to participate in inflammation, immune response, hematopoiesis, and carcinogenesis. However, the potential role of TNFAIP2 in the development of acute myeloid leukemia (AML) remains unknow yet. Therefore, we aimed to study the biological role of TNFAIP2 in leukemogenesis. METHODS TNFAIP2 mRNA level, prognostic value, co-expressed genes, differentially expressed genes, DNA methylation, and functional enrichment analysis in AML patients were explored via multiple public databases, including UALCAN, GTEx portal, Timer 2.0, LinkedOmics, SMART, MethSurv, Metascape, GSEA and String databases. Data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and Beat AML database were used to determine the associations between TNFAIP2 expression and various clinical or genetic parameters of AML patients. Moreover, the biological functions of TNFAIP2 in AML were investigated through in vitro experiments. RESULTS By large-scale data mining, our study indicated that TNFAIP2 was differentially expressed across different normal and tumor tissues. TNFAIP2 expression was significantly increased in AML, particularly in French-American-British (FAB) classification M4/M5 patients, compared with corresponding control tissues. Overexpression of TNFAIP2 was an independent poor prognostic factor of overall survival (OS) and was associated with unfavorable cytogenetic risk and gene mutations in AML patients. DNA hypermethylation of TNFAIP2 at gene body linked to upregulation of TNFAIP2 and inferior OS in AML. Functional enrichment analysis indicated immunomodulation function and inflammation response of TNFAIP2 in leukemogenesis. Finally, the suppression of TNFAIP resulted in inhibition of proliferation by altering cell-cycle progression and increase of cell death by promoting early and late apoptosis in THP-1 and U937AML cells. CONCLUSION Collectively, the oncogenic TNFAIP2 can function as a novel biomarker and prognostic factor in AML patients. The immunoregulation function of TNFAIP2 warrants further validation in AML.
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Affiliation(s)
- Mei-Si Lin
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy School, Chengdu University of Traditional Chinese Medicine, Chengdu, 611730, China
| | - Hui-Yun Zhong
- Sichuan Vocational College of Health and Rehabilitation, Zigong, 643000, China
| | - Rita Lok-Hay Yim
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong, SAR, China
| | - Qi-Yan Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy School, Chengdu University of Traditional Chinese Medicine, Chengdu, 611730, China
| | - Hong-Ling Du
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy School, Chengdu University of Traditional Chinese Medicine, Chengdu, 611730, China
| | - Hao-Qi He
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy School, Chengdu University of Traditional Chinese Medicine, Chengdu, 611730, China
| | - Ke Lin
- School of Medical Information Engineering, Chengdu University of Traditional Chinese Medicine, Chengdu, 611730, China
| | - Peng Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy School, Chengdu University of Traditional Chinese Medicine, Chengdu, 611730, China
| | - Ru Gao
- Department of Nursing, Chengdu Wenjiang People's Hospital, Chengdu, 611100, Sichuan, China.
| | - Fei Gao
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy School, Chengdu University of Traditional Chinese Medicine, Chengdu, 611730, China.
| | - Min-Yue Zhang
- Division of Hematology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China.
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14
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Weier AK, Homrich M, Ebbinghaus S, Juda P, Miková E, Hauschild R, Zhang L, Quast T, Mass E, Schlitzer A, Kolanus W, Burgdorf S, Gruß OJ, Hons M, Wieser S, Kiermaier E. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. J Cell Biol 2022; 221:213533. [PMID: 36214847 PMCID: PMC9555069 DOI: 10.1083/jcb.202107134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 03/01/2022] [Accepted: 09/12/2022] [Indexed: 12/13/2022] Open
Abstract
Centrosomes play a crucial role during immune cell interactions and initiation of the immune response. In proliferating cells, centrosome numbers are tightly controlled and generally limited to one in G1 and two prior to mitosis. Defects in regulating centrosome numbers have been associated with cell transformation and tumorigenesis. Here, we report the emergence of extra centrosomes in leukocytes during immune activation. Upon antigen encounter, dendritic cells pass through incomplete mitosis and arrest in the subsequent G1 phase leading to tetraploid cells with accumulated centrosomes. In addition, cell stimulation increases expression of polo-like kinase 2, resulting in diploid cells with two centrosomes in G1-arrested cells. During cell migration, centrosomes tightly cluster and act as functional microtubule-organizing centers allowing for increased persistent locomotion along gradients of chemotactic cues. Moreover, dendritic cells with extra centrosomes display enhanced secretion of inflammatory cytokines and optimized T cell responses. Together, these results demonstrate a previously unappreciated role of extra centrosomes for regular cell and tissue homeostasis.
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Affiliation(s)
- Ann-Kathrin Weier
- Life and Medical Sciences Institute, Immune and Tumor Biology, University of Bonn, Bonn, Germany
| | - Mirka Homrich
- Life and Medical Sciences Institute, Immune and Tumor Biology, University of Bonn, Bonn, Germany
| | - Stephanie Ebbinghaus
- Life and Medical Sciences Institute, Immune and Tumor Biology, University of Bonn, Bonn, Germany
| | - Pavel Juda
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Eliška Miková
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Robert Hauschild
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Lili Zhang
- Life and Medical Sciences Institute, Quantitative Systems Biology, University of Bonn, Bonn, Germany
| | - Thomas Quast
- Life and Medical Sciences Institute, Molecular Immunology and Cell Biology, University of Bonn, Bonn, Germany
| | - Elvira Mass
- Life and Medical Sciences Institute, Developmental Biology of the Immune System, University of Bonn, Bonn, Germany
| | - Andreas Schlitzer
- Life and Medical Sciences Institute, Quantitative Systems Biology, University of Bonn, Bonn, Germany
| | - Waldemar Kolanus
- Life and Medical Sciences Institute, Molecular Immunology and Cell Biology, University of Bonn, Bonn, Germany
| | - Sven Burgdorf
- Life and Medical Sciences Institute, Cellular Immunology, University of Bonn, Bonn, Germany
| | - Oliver J. Gruß
- Institute of Genetics, University of Bonn, Bonn, Germany
| | - Miroslav Hons
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Stefan Wieser
- Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Spain
| | - Eva Kiermaier
- Life and Medical Sciences Institute, Immune and Tumor Biology, University of Bonn, Bonn, Germany,Correspondence to Eva Kiermaier:
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15
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Zhang C, Ni C, Lu H. Polo-Like Kinase 2: From Principle to Practice. Front Oncol 2022; 12:956225. [PMID: 35898867 PMCID: PMC9309260 DOI: 10.3389/fonc.2022.956225] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/14/2022] [Indexed: 11/21/2022] Open
Abstract
Polo-like kinase (PLK) 2 is an evolutionarily conserved serine/threonine kinase that shares the n-terminal kinase catalytic domain and the C-terminal Polo Box Domain (PBD) with other members of the PLKs family. In the last two decades, mounting studies have focused on this and tried to clarify its role in many aspects. PLK2 is essential for mitotic centriole replication and meiotic chromatin pairing, synapsis, and crossing-over in the cell cycle; Loss of PLK2 function results in cell cycle disorders and developmental retardation. PLK2 is also involved in regulating cell differentiation and maintaining neural homeostasis. In the process of various stimuli-induced stress, including oxidative and endoplasmic reticulum, PLK2 may promote survival or apoptosis depending on the intensity of stimulation and the degree of cell damage. However, the role of PLK2 in immunity to viral infection has been studied far less than that of other family members. Because PLK2 is extensively and deeply involved in normal physiological functions and pathophysiological mechanisms of cells, its role in diseases is increasingly being paid attention to. The effect of PLK2 in inhibiting hematological tumors and fibrotic diseases, as well as participating in neurodegenerative diseases, has been gradually recognized. However, the research results in solid organ tumors show contradictory results. In addition, preliminary studies using PLK2 as a disease predictor and therapeutic target have yielded some exciting and promising results. More research will help people better understand PLK2 from principle to practice.
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Affiliation(s)
- Chuanyong Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Chuangye Ni
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Hao Lu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
- *Correspondence: Hao Lu,
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16
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Naqvi I, Giroux N, Olson L, Morrison SA, Llanga T, Akinade TO, Zhu Y, Zhong Y, Bose S, Arvai S, Abramson K, Chen L, Que L, Kraft B, Shen X, Lee J, Leong KW, Nair SK, Sullenger B. DAMPs/PAMPs induce monocytic TLR activation and tolerance in COVID-19 patients; nucleic acid binding scavengers can counteract such TLR agonists. Biomaterials 2022; 283:121393. [PMID: 35349874 PMCID: PMC8797062 DOI: 10.1016/j.biomaterials.2022.121393] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 01/24/2022] [Indexed: 12/13/2022]
Abstract
Millions of COVID-19 patients have succumbed to respiratory and systemic inflammation. Hyperstimulation of toll-like receptor (TLR) signaling is a key driver of immunopathology following infection by viruses. We found that severely ill COVID-19 patients in the Intensive Care Unit (ICU) display hallmarks of such hyper-stimulation with abundant agonists of nucleic acid-sensing TLRs present in their blood and lungs. These nucleic acid-containing Damage and Pathogen Associated Molecular Patterns (DAMPs/PAMPs) can be depleted using nucleic acid-binding microfibers to limit the patient samples' ability to hyperactivate such innate immune receptors. Single-cell RNA-sequencing revealed that CD16+ monocytes from deceased but not recovered ICU patients exhibit a TLR-tolerant phenotype and a deficient anti-viral response after ex vivo TLR stimulation. Plasma proteomics confirmed such myeloid hyperactivation and revealed DAMP/PAMP carrier consumption in deceased patients. Treatment of these COVID-19 patient samples with MnO nanoparticles effectively neutralizes TLR activation by the abundant nucleic acid-containing DAMPs/PAMPs present in their lungs and blood. Finally, MnO nanoscavenger treatment limits the ability of DAMPs/PAMPs to induce TLR tolerance in monocytes. Thus, treatment with microfiber- or nanoparticle-based DAMP/PAMP scavengers may prove useful for limiting SARS-CoV-2 induced hyperinflammation, preventing monocytic TLR tolerance, and improving outcomes in severely ill COVID-19 patients.
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Affiliation(s)
- Ibtehaj Naqvi
- Duke University School of Medicine, Department of Surgery, Division of Surgical Sciences, USA
| | - Nicholas Giroux
- Duke University, Department of Biomedical Engineering, Pratt School of Engineering, USA; Duke University, Graduate School, USA
| | - Lyra Olson
- Duke University, Graduate School, USA; Duke University School of Medicine, Department of Pharmacology and Cancer Biology, USA
| | - Sarah Ahn Morrison
- Duke University School of Medicine, Department of Surgery, Division of Surgical Sciences, USA
| | | | - Tolu O Akinade
- Columbia University, Department of Biomedical Engineering, USA
| | - Yuefei Zhu
- Columbia University, Department of Biomedical Engineering, USA
| | - Yiling Zhong
- Columbia University, Department of Biomedical Engineering, USA
| | - Shree Bose
- Duke University, Graduate School, USA; Duke University School of Medicine, Department of Pharmacology and Cancer Biology, USA
| | - Stephanie Arvai
- Duke University Center for Genomic and Computational Biology, RNA Sequencing Core, USA
| | - Karen Abramson
- Duke University Center for Genomic and Computational Biology, RNA Sequencing Core, USA
| | - Lingye Chen
- Duke University School of Medicine, Department of Medicine, Division of Pulmonary Medicine, USA
| | - Loretta Que
- Duke University School of Medicine, Department of Medicine, Division of Pulmonary Medicine, USA
| | - Bryan Kraft
- Duke University School of Medicine, Department of Medicine, Division of Pulmonary Medicine, USA
| | - Xiling Shen
- Duke University, Department of Biomedical Engineering, Pratt School of Engineering, USA
| | - Jaewoo Lee
- Duke University School of Medicine, Department of Surgery, Division of Surgical Sciences, USA
| | - Kam W Leong
- Columbia University, Department of Biomedical Engineering, USA
| | - Smita K Nair
- Duke University School of Medicine, Department of Surgery, Division of Surgical Sciences, USA; Duke University School of Medicine, Department of Pathology, USA; Duke University School of Medicine, Department of Neurosurgery, USA.
| | - Bruce Sullenger
- Duke University School of Medicine, Department of Surgery, Division of Surgical Sciences, USA; Duke University, Department of Biomedical Engineering, Pratt School of Engineering, USA; Duke University School of Medicine, Department of Pharmacology and Cancer Biology, USA; Duke University School of Medicine, Department of Neurosurgery, USA.
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17
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TIR-Domain-Containing Adapter-Inducing Interferon-β (TRIF)-Dependent Antiviral Responses Protect Mice against Ross River Virus Disease. mBio 2022; 13:e0336321. [PMID: 35089088 PMCID: PMC8725586 DOI: 10.1128/mbio.03363-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Ross River virus (RRV) is the major mosquito-borne virus in the South Pacific region. RRV infections are characterized by arthritic symptoms, which can last from several weeks to months. Type I interferon (IFN), the primary antiviral innate immune response, is able to modulate adaptive immune responses. The relationship between the protective role of type I IFN and the induction of signaling proteins that drive RRV disease pathogenesis remains poorly understood. In the present study, the role of TIR-domain-containing adapter-inducing interferon-β (TRIF), an essential signaling adaptor protein downstream of Toll-like receptor (TLR) 3, a key single-stranded RNA (ssRNA)-sensing receptor, was investigated. We found that TRIF-/- mice were highly susceptible to RRV infection, with severe disease, high viremia, and a low type I IFN response early during disease development, which suggests the TLR3-TRIF axis may engage early in response to RRV infection. The number and the activation level of CD4+ T cells, CD8+ T cells, and NK cells were reduced in TRIF-/- mice compared to those in infected wild-type (WT) mice. In addition, the number of germinal center B cells was lower in TRIF-/- mice than WT mice following RRV infection, with lower titers of IgG antibodies detected in infected TRIF-/- mice compared to WT. Interestingly, the requirement for TRIF to promote immunoglobulin class switch recombination was at the level of the local immune microenvironment rather than B cells themselves. The slower resolution of RRV disease in TRIF-/- mice was associated with persistence of the RRV genome in muscle tissue and a continuing IFN response. IMPORTANCE RRV has been prevalent in the South Pacific region for decades and causes substantial economic and social costs. Though RRV is geographically restricted, a number of other alphaviruses have spread globally due to expansion of the mosquito vectors and increased international travel. Since over 30 species of mosquitoes have been implicated as potent vectors for RRV dissemination, RRV has the potential to further expand its distribution. In the pathogenesis of RRV disease, it is still not clear how innate immune responses synergize with adaptive immune responses. Type I IFN is crucial for bridging innate to adaptive immune responses to viral invasion. Hence, key signaling proteins in type I IFN induction pathways, which are important for type I IFN modulation, may also play critical roles in viral pathogenesis. This study provides insight into the role of TRIF in RRV disease development.
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microRNA-Mediated Encoding and Decoding of Time-Dependent Signals in Tumorigenesis. Biomolecules 2022; 12:biom12020213. [PMID: 35204714 PMCID: PMC8961662 DOI: 10.3390/biom12020213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 02/01/2023] Open
Abstract
microRNAs, pivotal post-transcriptional regulators of gene expression, in the past decades have caught the attention of researchers for their involvement in different biological processes, ranging from cell development to cancer. Although lots of effort has been devoted to elucidate the topological features and the equilibrium properties of microRNA-mediated motifs, little is known about how the information encoded in frequency, amplitude, duration, and other features of their regulatory signals can affect the resulting gene expression patterns. Here, we review the current knowledge about microRNA-mediated gene regulatory networks characterized by time-dependent input signals, such as pulses, transient inputs, and oscillations. First, we identify the general characteristic of the main motifs underlying temporal patterns. Then, we analyze their impact on two commonly studied oncogenic networks, showing how their dysfunction can lead to tumorigenesis.
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MicroRNA-376b-3p Promotes Porcine Reproductive and Respiratory Syndrome Virus Replication by Targeting Viral Restriction Factor TRIM22. J Virol 2021; 96:e0159721. [PMID: 34757838 DOI: 10.1128/jvi.01597-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus is a major economically significant pathogen and has evolved several strategies to evade host's antiviral response and provide favorable conditions for survival. In the present study, we demonstrated that a host microRNA, miR-376b-3p, was upregulated by PRRSV infection through the viral components, nsp4 and nsp11, and miR-376b-3p can directly target tripartite motif-containing 22 (TRIM22) to impair its anti-PRRSV activity, thus facilitating the replication of PRRSV. Meanwhile, we found that TRIM22 induced degradation of the nucleocapsid protein (N) of PRRSV by interacting with N protein to inhibit PRRSV replication, and further study indicated that TRIM22 could enhance the activation of lysosomal pathway by interacting with LC3 to induce lysosomal degradation of N protein. In conclusion, PRRSV increased miR-376b-3p expression and hijacked the host miR-376b-3p to promote PRRSV replication by impairing the antiviral effect of TRIM22. Therefore, our finding outlines a novel strategy of immune evasion exerted by PRRSV, which is helpful for better understanding the pathogenesis of PRRSV. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) causes enormous economic losses each year in the swine industry worldwide. MicroRNAs (miRNAs) play important roles during viral infections via modulating the expression of viral or host genes at post-transcriptional level. TRIM22 has recently been identified as a key restriction factor that inhibited the replication of a number of human virus such as HIV, ECMV, HCV, HBV, IAV, and RSV. Here we showed that host miR-376b-3p could be up-regulated by PRRSV and functioned to impair the anti-PRRSV role of TRIM22 to facilitate PRRSV replication. Meanwhile, we found that TRIM22 inhibited the replication of PRRSV by interacting with viral N protein and accelerating its degradation through the lysosomal pathway. Collectively, the paper described a novel mechanism that PRRSV exploited the host miR-376b-3p to evade antiviral responses and provided a new insight into the study of virus-host interactions.
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Chiappini C, Chen Y, Aslanoglou S, Mariano A, Mollo V, Mu H, De Rosa E, He G, Tasciotti E, Xie X, Santoro F, Zhao W, Voelcker NH, Elnathan R. Tutorial: using nanoneedles for intracellular delivery. Nat Protoc 2021; 16:4539-4563. [PMID: 34426708 DOI: 10.1038/s41596-021-00600-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/30/2021] [Indexed: 02/08/2023]
Abstract
Intracellular delivery of advanced therapeutics, including biologicals and supramolecular agents, is complex because of the natural biological barriers that have evolved to protect the cell. Efficient delivery of therapeutic nucleic acids, proteins, peptides and nanoparticles is crucial for clinical adoption of emerging technologies that can benefit disease treatment through gene and cell therapy. Nanoneedles are arrays of vertical high-aspect-ratio nanostructures that can precisely manipulate complex processes at the cell interface, enabling effective intracellular delivery. This emerging technology has already enabled the development of efficient and non-destructive routes for direct access to intracellular environments and delivery of cell-impermeant payloads. However, successful implementation of this technology requires knowledge of several scientific fields, making it complex to access and adopt by researchers who are not directly involved in developing nanoneedle platforms. This presents an obstacle to the widespread adoption of nanoneedle technologies for drug delivery. This tutorial aims to equip researchers with the knowledge required to develop a nanoinjection workflow. It discusses the selection of nanoneedle devices, approaches for cargo loading and strategies for interfacing to biological systems and summarises an array of bioassays that can be used to evaluate the efficacy of intracellular delivery.
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Affiliation(s)
- Ciro Chiappini
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK.
- London Centre for Nanotechnology, King's College London, London, UK.
| | - Yaping Chen
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, Victoria, Australia
| | - Stella Aslanoglou
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, Victoria, Australia
- CSIRO Manufacturing, Clayton, Victoria, Australia
| | - Anna Mariano
- Center for Advanced Biomaterials for Healthcare, Istituto Italiano di Tecnologia, Naples, Italy
| | - Valentina Mollo
- Center for Advanced Biomaterials for Healthcare, Istituto Italiano di Tecnologia, Naples, Italy
| | - Huanwen Mu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Enrica De Rosa
- Center for Musculoskeletal Regeneration, Orthopedics & Sports Medicine, Houston Methodist Research Institute, Houston, TX, USA
| | - Gen He
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, China
| | - Ennio Tasciotti
- IRCCS San Raffaele Pisana Hospital, Rome, Italy
- San Raffaele University, Rome, Italy
- Sclavo Pharma, Siena, Italy
| | - Xi Xie
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, China.
| | - Francesca Santoro
- Center for Advanced Biomaterials for Healthcare, Istituto Italiano di Tecnologia, Naples, Italy.
| | - Wenting Zhao
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Nicolas H Voelcker
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, Victoria, Australia.
- CSIRO Manufacturing, Clayton, Victoria, Australia.
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria, Australia.
| | - Roey Elnathan
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, Victoria, Australia.
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria, Australia.
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21
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Nazitto R, Amon LM, Mast FD, Aitchison JD, Aderem A, Johnson JS, Diercks AH. ILF3 Is a Negative Transcriptional Regulator of Innate Immune Responses and Myeloid Dendritic Cell Maturation. THE JOURNAL OF IMMUNOLOGY 2021; 206:2949-2965. [PMID: 34031149 DOI: 10.4049/jimmunol.2001235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/31/2021] [Indexed: 12/31/2022]
Abstract
APCs such as myeloid dendritic cells (DCs) are key sentinels of the innate immune system. In response to pathogen recognition and innate immune stimulation, DCs transition from an immature to a mature state that is characterized by widespread changes in host gene expression, which include the upregulation of cytokines, chemokines, and costimulatory factors to protect against infection. Several transcription factors are known to drive these gene expression changes, but the mechanisms that negatively regulate DC maturation are less well understood. In this study, we identify the transcription factor IL enhancer binding factor 3 (ILF3) as a negative regulator of innate immune responses and DC maturation. Depletion of ILF3 in primary human monocyte-derived DCs led to increased expression of maturation markers and potentiated innate responses during stimulation with viral mimetics or classic innate agonists. Conversely, overexpression of short or long ILF3 isoforms (NF90 and NF110) suppressed DC maturation and innate immune responses. Through mutagenesis experiments, we found that a nuclear localization sequence in ILF3, and not its dual dsRNA-binding domains, was required for this function. Mutation of the domain associated with zinc finger motif of ILF3's NF110 isoform blocked its ability to suppress DC maturation. Moreover, RNA-sequencing analysis indicated that ILF3 regulates genes associated with cholesterol homeostasis in addition to genes associated with DC maturation. Together, our data establish ILF3 as a transcriptional regulator that restrains DC maturation and limits innate immune responses through a mechanism that may intersect with lipid metabolism.
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Affiliation(s)
- Rodolfo Nazitto
- Department of Immunology, University of Washington School of Medicine, Seattle, WA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Lynn M Amon
- Center for Infectious Disease Research, Seattle, WA; and
| | - Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Alan Aderem
- Department of Immunology, University of Washington School of Medicine, Seattle, WA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Jarrod S Johnson
- Center for Infectious Disease Research, Seattle, WA; and.,Department of Biochemistry, University of Utah, Salt Lake City, UT
| | - Alan H Diercks
- Department of Immunology, University of Washington School of Medicine, Seattle, WA;
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22
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Johnson JS, De Veaux N, Rives AW, Lahaye X, Lucas SY, Perot BP, Luka M, Garcia-Paredes V, Amon LM, Watters A, Abdessalem G, Aderem A, Manel N, Littman DR, Bonneau R, Ménager MM. A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV. Cell Rep 2021; 30:914-931.e9. [PMID: 31968263 PMCID: PMC7039998 DOI: 10.1016/j.celrep.2019.12.054] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/25/2019] [Accepted: 12/13/2019] [Indexed: 01/12/2023] Open
Abstract
Transcriptional programming of the innate immune response is pivotal for host protection. However, the transcriptional mechanisms that link pathogen sensing with innate activation remain poorly under-stood. During HIV-1 infection, human dendritic cells (DCs) can detect the virus through an innate sensing pathway, leading to antiviral interferon and DC maturation. Here, we develop an iterative experimental and computational approach to map the HIV-1 innate response circuitry in monocyte-derived DCs (MDDCs). By integrating genome-wide chromatin accessibility with expression kinetics, we infer a gene regulatory network that links 542 transcription factors with 21,862 target genes. We observe that an interferon response is required, yet insufficient, to drive MDDC maturation and identify PRDM1 and RARA as essential regulators of the interferon response and MDDC maturation, respectively. Our work provides a resource for interrogation of regulators of HIV replication and innate immunity, highlighting complexity and cooperativity in the regulatory circuit controlling the response to infection. Pathogen sensing leads to host transcriptional reprogramming to protect against infection. However, it is unclear how transcription factor activity is coordinated across the genome. Johnson et al. integrate chromatin accessibility and gene expression data to infer and validate a gene regulatory network that directs the innate immune response to HIV.
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Affiliation(s)
- Jarrod S Johnson
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA; Center for Infectious Disease Research, Seattle, WA 98109, USA.
| | - Nicholas De Veaux
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA
| | - Alexander W Rives
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA
| | - Xavier Lahaye
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Sasha Y Lucas
- Center for Infectious Disease Research, Seattle, WA 98109, USA
| | - Brieuc P Perot
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Imagine Institute, INSERM UMR 1163, ATIP-Avenir Team, Université de Paris, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Marine Luka
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Imagine Institute, INSERM UMR 1163, ATIP-Avenir Team, Université de Paris, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Victor Garcia-Paredes
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Imagine Institute, INSERM UMR 1163, ATIP-Avenir Team, Université de Paris, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Lynn M Amon
- Center for Infectious Disease Research, Seattle, WA 98109, USA
| | - Aaron Watters
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA
| | - Ghaith Abdessalem
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Imagine Institute, INSERM UMR 1163, ATIP-Avenir Team, Université de Paris, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Alan Aderem
- Center for Infectious Disease Research, Seattle, WA 98109, USA; Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Nicolas Manel
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Dan R Littman
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Richard Bonneau
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA; Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Data Science, New York University, New York, NY 10011, USA
| | - Mickaël M Ménager
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Imagine Institute, INSERM UMR 1163, ATIP-Avenir Team, Université de Paris, 24 Boulevard du Montparnasse, 75015 Paris, France; The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA.
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23
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Alam MM, Jarvis CM, Hincapie R, McKay CS, Schimer J, Sanhueza-Chavez CA, Xu K, Diehl RC, Finn MG, Kiessling LL. Glycan-Modified Virus-like Particles Evoke T Helper Type 1-like Immune Responses. ACS NANO 2021; 15:309-321. [PMID: 32790346 PMCID: PMC8249087 DOI: 10.1021/acsnano.0c03023] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Dendritic cells (DCs) are highly effective antigen-presenting cells that shape immune responses. Vaccines that deliver antigen to the DCs can harness their power. DC surface lectins recognize glycans not typically present on host tissue to facilitate antigen uptake and presentation. Vaccines that target these surface lectins should offer improved antigen delivery, but their efficacy will depend on how lectin targeting influences the T cell subtypes that result. We examined how antigen structure influences uptake and signaling from the C-type lectin DC-SIGN (dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin or CD209). Virus-like particles (VLPs) were engineered from bacteriophage Qβ to present an array of mannoside ligands. The VLPs were taken up by DCs and efficiently trafficked to endosomes. The signaling that ensued depended on the ligand displayed on the VLP: only those particles densely functionalized with an aryl mannoside, Qβ-Man540, elicited DC maturation and induced the expression of the proinflammatory cytokines characteristic of a T helper type 1 (TH1)-like immune response. This effect was traced to differential binding to DC-SIGN at the acidic pH of the endosome. Mice immunized with a VLP bearing the aryl mannoside, and a peptide antigen (Qβ-Ova-Man540) had antigen-specific responses, including the production of CD4+ T cells producing the activating cytokines interferon-γ and tumor necrosis factor-α. A TH1 response is critical for intracellular pathogens (e.g., viruses) and cancer; thus, our data highlight the value of targeting DC lectins for antigen delivery and validate the utility of DC-targeted VLPs as vaccine vehicles that induce cellular immunity.
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Affiliation(s)
- Mohammad Murshid Alam
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA
| | - Cassie M. Jarvis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA
| | - Robert Hincapie
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Craig S. McKay
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Jiri Schimer
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Carlos A Sanhueza-Chavez
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
- Current address: Department of Pharmaceutical Sciences, St. John’s University, 8000 Utopia Pkwy. Queens, NY 11439, USA
| | - Ke Xu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Roger C Diehl
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA
| | - M. G. Finn
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA
- Corresponding Author: Laura L. Kiessling,
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Hao J, Shen C, Wei N, Yan M, Zhang X, Xu G, Zhang D, Hou J, Cao W, Jin Y, Zhang K, Zheng H, Liu X. Foot-and-Mouth Disease Virus Capsid Protein VP1 Antagonizes TPL2-Mediated Activation of the IRF3/IFN-β Signaling Pathway to Facilitate the Virus Replication. Front Immunol 2021; 11:580334. [PMID: 33488582 PMCID: PMC7821752 DOI: 10.3389/fimmu.2020.580334] [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] [Received: 07/22/2020] [Accepted: 11/18/2020] [Indexed: 11/13/2022] Open
Abstract
Foot-and-mouth disease (FMD) is a severe, highly contagious viral disease of cloven-hoofed animals. In order to establish an infection, the FMD virus (FMDV) needs to counteract host antiviral responses. Tumor progression locus 2 (TPL2), a mitogen-activated protein kinase, can regulate innate and adaptive immunity; however, its exact mechanisms underlying TPL2-mediated regulation of the pathogenesis of FMDV infection remain unknown. In this study, we confirmed that TPL2 could inhibit FMDV replication in vitro and in vivo. The virus replication increased in Tpl2-deficient suckling mice in association with reduced expression of interferon-stimulated genes interferon-α (IFN-α) and myxovirus resistance (MX2) and significantly reduced expression of C-X-C motif chemokine ligand 10 (CXCL10), interferon regulatory factor 3 (IRF3), and IRF7, while the phosphorylation of IRF3 was not detected. Moreover, the interactions between TPL2 and VP1 were also confirmed. The overexpression of TPL2 promoted IRF3-mediated dose-dependent activation of the IFN-β signaling pathway in association with interactions between IRF3 and TPL2. VP1 also inhibited phosphorylation of TPL2 at Thr290, while Thr290 resulted as the key functional site associated with the TPL2-mediated antiviral response. Taken together, this study indicated that FMDV capsid protein VP1 antagonizes TPL2-mediated activation of the IRF3/IFN-β signaling pathway for immune escape and facilitated virus replication.
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Affiliation(s)
- Junhong Hao
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
| | - Chaochao Shen
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
| | - Nannan Wei
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
| | - Minghao Yan
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
| | - Xuegang Zhang
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
| | - Guowei Xu
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
| | - Dajun Zhang
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
| | - Jing Hou
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
| | - Weijun Cao
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
| | - Ye Jin
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
| | - Keshan Zhang
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
| | - Xiangtao Liu
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute of Chinese Academy of Agriculture Science, Lanzhou, China
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25
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Pandey S, Gruenbaum A, Kanashova T, Mertins P, Cluzel P, Chevrier N. Pairwise Stimulations of Pathogen-Sensing Pathways Predict Immune Responses to Multi-adjuvant Combinations. Cell Syst 2020; 11:495-508.e10. [PMID: 33113356 DOI: 10.1016/j.cels.2020.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/29/2020] [Accepted: 09/30/2020] [Indexed: 12/31/2022]
Abstract
The immune system makes decisions in response to combinations of multiple microbial inputs. We do not understand the combinatorial logic governing how higher-order combinations of microbial signals shape immune responses. Here, using coculture experiments and statistical analyses, we discover a general property for the combinatorial sensing of microbial signals, whereby the effects of triplet combinations of microbial signals on immune responses can be predicted by combining the effects of single and pairs. Mechanistically, we find that singles and pairs dictate the information signaled by triplets in mouse and human DCs at the levels of transcription, chromatin, and protein secretion. We exploit this simplifying property to develop cell-based immunotherapies prepared with adjuvant combinations that trigger protective responses in mouse models of cancer. We conclude that the processing of multiple input signals by innate immune cells is governed by pairwise effects, which will inform the rationale combination of adjuvants to manipulate immunity.
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Affiliation(s)
- Surya Pandey
- Pritzker School of Molecular Engineering, the University of Chicago, Chicago, IL 60637, USA
| | - Adam Gruenbaum
- Pritzker School of Molecular Engineering, the University of Chicago, Chicago, IL 60637, USA
| | - Tamara Kanashova
- Proteomics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Society, and Berlin Institute of Health, 13125 Berlin, Germany
| | - Philipp Mertins
- Proteomics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Society, and Berlin Institute of Health, 13125 Berlin, Germany
| | - Philippe Cluzel
- School of Engineering and Applied Science & Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nicolas Chevrier
- Pritzker School of Molecular Engineering, the University of Chicago, Chicago, IL 60637, USA.
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26
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Chen Y, Wang J, Li X, Hu N, Voelcker NH, Xie X, Elnathan R. Emerging Roles of 1D Vertical Nanostructures in Orchestrating Immune Cell Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2001668. [PMID: 32844502 PMCID: PMC7461044 DOI: 10.1002/adma.202001668] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/16/2020] [Indexed: 05/07/2023]
Abstract
Engineered nano-bio cellular interfaces driven by 1D vertical nanostructures (1D-VNS) are set to prompt radical progress in modulating cellular processes at the nanoscale. Here, tuneable cell-VNS interfacial interactions are probed and assessed, highlighting the use of 1D-VNS in immunomodulation, and intracellular delivery into immune cells-both crucial in fundamental and translational biomedical research. With programmable topography and adaptable surface functionalization, 1D-VNS provide unique biophysical and biochemical cues to orchestrate innate and adaptive immunity, both ex vivo and in vivo. The intimate nanoscale cell-VNS interface leads to membrane penetration and cellular deformation, facilitating efficient intracellular delivery of diverse bioactive cargoes into hard-to-transfect immune cells. The unsettled interfacial mechanisms reported to be involved in VNS-mediated intracellular delivery are discussed. By identifying up-to-date progress and fundamental challenges of current 1D-VNS technology in immune-cell manipulation, it is hoped that this report gives timely insights for further advances in developing 1D-VNS as a safe, universal, and highly scalable platform for cell engineering and enrichment in advanced cancer immunotherapy such as chimeric antigen receptor-T therapy.
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Affiliation(s)
- Yaping Chen
- Monash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
- Melbourne Centre for NanofabricationVictorian Node of the Australian National Fabrication Facility151 Wellington RoadClayton3168Australia
| | - Ji Wang
- The First Affiliated Hospital of Sun Yat‐sen UniversitySun Yat‐sen UniversityGuangzhou510006China
| | - Xiangling Li
- State Key Laboratory of Optoelectronic Materials and TechnologiesSchool of Electronics and Information TechnologySun Yat‐sen UniversityGuangzhou510006China
| | - Ning Hu
- State Key Laboratory of Optoelectronic Materials and TechnologiesSchool of Electronics and Information TechnologySun Yat‐sen UniversityGuangzhou510006China
| | - Nicolas H. Voelcker
- Monash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
- Melbourne Centre for NanofabricationVictorian Node of the Australian National Fabrication Facility151 Wellington RoadClayton3168Australia
- Department of Materials Science and EngineeringMonash University22 Alliance LaneClaytonVIC3168Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)ClaytonVIC3168Australia
- INM‐Leibniz Institute for New MaterialsCampus D2 2Saarbrücken66123Germany
| | - Xi Xie
- The First Affiliated Hospital of Sun Yat‐sen UniversitySun Yat‐sen UniversityGuangzhou510006China
- State Key Laboratory of Optoelectronic Materials and TechnologiesSchool of Electronics and Information TechnologySun Yat‐sen UniversityGuangzhou510006China
| | - Roey Elnathan
- Monash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
- Melbourne Centre for NanofabricationVictorian Node of the Australian National Fabrication Facility151 Wellington RoadClayton3168Australia
- Department of Materials Science and EngineeringMonash University22 Alliance LaneClaytonVIC3168Australia
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27
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Shimamoto-Mitsuyama C, Nakaya A, Esaki K, Balan S, Iwayama Y, Ohnishi T, Maekawa M, Toyota T, Dean B, Yoshikawa T. Lipid Pathology of the Corpus Callosum in Schizophrenia and the Potential Role of Abnormal Gene Regulatory Networks with Reduced Microglial Marker Expression. Cereb Cortex 2020; 31:448-462. [PMID: 32924060 PMCID: PMC7727339 DOI: 10.1093/cercor/bhaa236] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Structural changes in the corpus callosum have been reported in schizophrenia; however, the underlying molecular mechanism remains unclear. As the corpus callosum is high in lipid content, we analyzed the lipid contents of the corpora callosa from 15 patients with schizophrenia and 15 age- and sex-matched controls using liquid chromatography coupled to tandem mass spectrometry and identified lipid combinations associated with schizophrenia. Real-time quantitative polymerase chain reaction analyses using extended samples (schizophrenia, n = 95; control, n = 91) showed low expression levels of lipid metabolism-related genes and their potential upstream transcription factors in schizophrenia. Subsequent pathway analysis identified a gene regulatory network where nuclear factor of activated T cells 2 (NFATC2) is placed most upstream. We also observed low gene expression levels of microglial markers, inflammatory cytokines, and colony-stimulating factor 1 receptor (CSF1R), which is known to regulate the density of microglia, in the corpus callosum in schizophrenia. The interactions between CSF1R and several genes in the presently identified gene network originating from NFATC2 have been reported. Collectively, this study provides evidence regarding lipid abnormalities in the corpora callosa of patients with schizophrenia and proposes the potential role of impaired “NFATC2-relevant gene network-microglial axis” as its underlying mechanism.
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Affiliation(s)
| | - Akihiro Nakaya
- Laboratory of Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama, Japan.,Laboratory of Genome Data Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kayoko Esaki
- Laboratory of Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Shabeesh Balan
- Laboratory of Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Yoshimi Iwayama
- Laboratory of Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama, Japan.,Support Unit for Bio-Material Analysis, Research Resources Division, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Tetsuo Ohnishi
- Laboratory of Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Motoko Maekawa
- Laboratory of Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Tomoko Toyota
- Laboratory of Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Brian Dean
- The Florey Institute of Neuroscience and Mental Health, Howard Florey Laboratories, The University of Melbourne, Parkville, Victoria, Australia.,The Centre for Mental Health, Swinburne University, Hawthorn, Victoria, Australia
| | - Takeo Yoshikawa
- Laboratory of Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama, Japan
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28
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Wang JL, Cai F, Liu XH, Li LM, He X, Hu XM, Kang CM, Bai HL, Zhang RY, Wu CM, Wu LM, Wang J, Zheng L, Ping BH, Hu YW, Wang Q. Lipopolysaccharide Promotes Inflammatory Response via Enhancing IFIT1 Expression in Human Umbilical Vein Endothelial Cells. DNA Cell Biol 2020; 39:1274-1281. [PMID: 32551893 DOI: 10.1089/dna.2020.5454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Jia-Li Wang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Linyi People's Hospital of Shandong Province, Linyi, China
| | - Fen Cai
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, China
| | - Xue-Hui Liu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Clinical Laboratory, Guangzhou Twelfth People's Hospital, Guangzhou, China
| | - Li-Min Li
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xin He
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiu-Mei Hu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chun-Min Kang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huan-Lan Bai
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ru-Yi Zhang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chang-Meng Wu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Li-Mei Wu
- Department of Clinical Laboratory, Guangzhou Twelfth People's Hospital, Guangzhou, China
| | - Jia Wang
- Rizhao People's Hospital of Shandong Province, Rizhao, China
| | - Lei Zheng
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bao-Hong Ping
- Department of Hui Qiao, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yan-Wei Hu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qian Wang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
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29
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Gillen J, Bridgwater C, Nita-Lazar A. Approaching complexity: systems biology and ms-based techniques to address immune signaling. Expert Rev Proteomics 2020; 17:341-354. [PMID: 32552048 DOI: 10.1080/14789450.2020.1780920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Studying immune signaling has been critical for our understanding of immunology, pathogenesis, cancer, and homeostasis. To enhance the breadth of the analysis, high throughput methods have been developed to survey multiple areas simultaneously, including transcriptomics, reporter assays, and ELISAs. While these techniques have been extremely informative, mass-spectrometry-based technologies have been gaining momentum and starting to be widely used in the studies of immune signaling and systems immunology. AREAS COVERED We present established proteomic methods that have been used to address immune signaling and discuss the new mass-spectrometry- based techniques of interest to the expanding field of systems immunology. Established and new proteomic methods and their applications discussed here include post-translational modification analysis, protein quantification, secretome analysis, and interactomics. In addition, we present developments in small molecule and metabolite analysis, mass spectrometry imaging, and single cell analysis. Finally, we discuss the role of multi-omic integration in aiding leading edge investigation. EXPERT OPINION In science, available techniques enhance the breadth and depth of the studies. By incorporating proteomic techniques and their innovative use, it will be possible to expand the current studies and to address novel questions at the forefront of scientific discovery.
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Affiliation(s)
- Joseph Gillen
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, MD, USA
| | - Caleb Bridgwater
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, MD, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, MD, USA
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30
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Scholz A, Rappl P, Böffinger N, Mota AC, Brüne B, Schmid T. Translation of TNFAIP2 is tightly controlled by upstream open reading frames. Cell Mol Life Sci 2020; 77:2017-2027. [PMID: 31392347 PMCID: PMC11104949 DOI: 10.1007/s00018-019-03265-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022]
Abstract
Translation is a highly regulated process, both at the global as well as on a transcript-specific level. Regulatory upstream open reading frames (uORFs) represent a mode to alter cap-dependent translation efficiency in a transcript-specific manner and are found in numerous mRNAs. In the majority of cases, uORFs inhibit the translation of their associated main ORFs. Consequently, their inactivation results in enhanced translation of the main ORF, a phenomenon best characterized in the context of the integrated stress response. In the present study, we identified potent translation-inhibitory uORFs in the transcript leader sequence (TLS) of tumor necrosis factor alpha induced protein 2 (TNFAIP2). The initial description of the uORFs was based on the observation that despite a massive induction of TNFAIP2 mRNA expression in response to interleukin 1β (IL1β), TNFAIP2 protein levels remained low in MCF7 cells. While we were able to characterize the uORFs with respect to their exact size and sequential requirements in this cellular context, only TPA stimulation partially overcame the translation-inhibitory activity of the TNFAIP2 uORFs. Characterization of TNFAIP2 translation in the context of monocyte-to-macrophage differentiation suggested that, while the uORFs efficiently block TNFAIP2 protein synthesis in monocytes, they are inactivated in mature macrophages, thus allowing for a massive increase in TNFAIP2 protein expression. In summary, we establish TNFAIP2 as a novel target of uORF-mediated translational regulation. Furthermore, our findings suggest that during macrophage differentiation a major uORF-dependent translational switch occurs.
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Affiliation(s)
- Anica Scholz
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Peter Rappl
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Nicola Böffinger
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Ana Carolina Mota
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Bernhard Brüne
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Tobias Schmid
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.
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31
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Yang X, Li W, Zhang S, Wu D, Jiang X, Tan R, Niu X, Wang Q, Wu X, Liu Z, Chen L, Qin J, Su B. PLK4 deubiquitination by Spata2-CYLD suppresses NEK7-mediated NLRP3 inflammasome activation at the centrosome. EMBO J 2020; 39:e102201. [PMID: 31762063 PMCID: PMC6960439 DOI: 10.15252/embj.2019102201] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 10/13/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
The innate immune sensor NLRP3 assembles an inflammasome complex with NEK7 and ASC to activate caspase-1 and drive the maturation of proinflammatory cytokines IL-1β and IL-18. NLRP3 inflammasome activity must be tightly controlled, as its over-activation is involved in the pathogenesis of inflammatory diseases. Here, we show that NLRP3 inflammasome activation is suppressed by a centrosomal protein Spata2. Spata2 deficiency enhances NLRP3 inflammasome activity both in the macrophages and in an animal model of peritonitis. Mechanistically, Spata2 recruits the deubiquitinase CYLD to the centrosome for deubiquitination of polo-like kinase 4 (PLK4), the master regulator of centrosome duplication. Deubiquitination of PLK4 facilitates its binding to and phosphorylation of NEK7 at Ser204. NEK7 phosphorylation in turn attenuates NEK7 and NLRP3 interaction, which is required for NLRP3 inflammasome activation. Pharmacological or shRNA-mediated inhibition of PLK4, or mutation of the NEK7 Ser204 phosphorylation site, augments NEK7 interaction with NLRP3 and causes increased NLRP3 inflammasome activation. Our study unravels a novel centrosomal regulatory pathway of inflammasome activation and may provide new therapeutic targets for the treatment of NLRP3-associated inflammatory diseases.
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Affiliation(s)
- Xiao‐Dong Yang
- Shanghai Jiao Tong University School of Medicine‐Yale Institute for Immune MetabolismShanghai Jiao Tong University School of MedicineShanghaiChina§
| | - Wenguo Li
- Shanghai Jiao Tong University School of Medicine‐Yale Institute for Immune MetabolismShanghai Jiao Tong University School of MedicineShanghaiChina§
| | - Shuangyan Zhang
- Shanghai Jiao Tong University School of Medicine‐Yale Institute for Immune MetabolismShanghai Jiao Tong University School of MedicineShanghaiChina§
| | - Dandan Wu
- Shanghai Jiao Tong University School of Medicine‐Yale Institute for Immune MetabolismShanghai Jiao Tong University School of MedicineShanghaiChina§
| | - Xiaoli Jiang
- Shanghai Jiao Tong University School of Medicine‐Yale Institute for Immune MetabolismShanghai Jiao Tong University School of MedicineShanghaiChina§
| | - Rong Tan
- Xiangya HospitalCentral South UniversityChangshaChina
| | - Xiaoyin Niu
- Shanghai Jiao Tong University School of Medicine‐Yale Institute for Immune MetabolismShanghai Jiao Tong University School of MedicineShanghaiChina§
| | - Qijun Wang
- Shanghai Jiao Tong University School of Medicine‐Yale Institute for Immune MetabolismShanghai Jiao Tong University School of MedicineShanghaiChina§
| | - Xuefeng Wu
- Shanghai Jiao Tong University School of Medicine‐Yale Institute for Immune MetabolismShanghai Jiao Tong University School of MedicineShanghaiChina§
| | - Zhiduo Liu
- Shanghai Jiao Tong University School of Medicine‐Yale Institute for Immune MetabolismShanghai Jiao Tong University School of MedicineShanghaiChina§
| | - Lin‐Feng Chen
- Department of BiochemistryUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Jun Qin
- Department of Biochemistry and Molecular BiologyBaylor College of MedicineHoustonTXUSA
| | - Bing Su
- Shanghai Jiao Tong University School of Medicine‐Yale Institute for Immune MetabolismShanghai Jiao Tong University School of MedicineShanghaiChina§
- Yale University Institute for Immune MetabolismShanghai Jiao Tong University School of MedicineShanghaiChina
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32
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John SP, Sun J, Carlson RJ, Cao B, Bradfield CJ, Song J, Smelkinson M, Fraser IDC. IFIT1 Exerts Opposing Regulatory Effects on the Inflammatory and Interferon Gene Programs in LPS-Activated Human Macrophages. Cell Rep 2020; 25:95-106.e6. [PMID: 30282041 PMCID: PMC6492923 DOI: 10.1016/j.celrep.2018.09.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 07/06/2018] [Accepted: 08/30/2018] [Indexed: 12/15/2022] Open
Abstract
Activation of the TLR4 signaling pathway by lipopolysaccharide (LPS) leads to induction of both inflammatory and interferon-stimulated genes, but the mechanisms through which these coordinately activated transcriptional programs are balanced to promote an optimal innate immune response remain poorly understood. In a genome-wide small interfering RNA (siRNA) screen of the LPS-induced tumor necrosis factor α (TNF-α) response in macrophages, we identify the interferon-stimulated protein IFIT1 as a negative regulator of the inflammatory gene program. Transcriptional profiling further identifies a positive regulatory role for IFIT1 in type I interferon expression, implicating IFIT1 as a reciprocal modulator of LPS-induced gene classes. We demonstrate that these effects of IFIT1 are mediated through modulation of a Sin3A-HDAC2 transcriptional regulatory complex at LPS-induced gene loci. Beyond the well-studied role of cytosolic IFIT1 in restricting viral replication, our data demonstrate a function for nuclear IFIT1 in differential transcriptional regulation of separate branches of the LPS-induced gene program.
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Affiliation(s)
- Sinu P John
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
| | - Jing Sun
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Rebecca J Carlson
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Binh Cao
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Clinton J Bradfield
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jian Song
- Bioinformatics Group, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Margery Smelkinson
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Iain D C Fraser
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
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33
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Ritter JL, Zhu Z, Thai TC, Mahadevan NR, Mertins P, Knelson EH, Piel BP, Han S, Jaffe JD, Carr SA, Barbie DA, Barbie TU. Phosphorylation of RAB7 by TBK1/IKKε Regulates Innate Immune Signaling in Triple-Negative Breast Cancer. Cancer Res 2019; 80:44-56. [PMID: 31662325 DOI: 10.1158/0008-5472.can-19-1310] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/06/2019] [Accepted: 10/25/2019] [Indexed: 12/31/2022]
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease enriched for mutations in PTEN and dysregulation of innate immune signaling. Here, we demonstrate that Rab7, a recently identified substrate of PTEN phosphatase activity, is also a substrate of the innate immune signaling kinases TANK-binding kinase 1 (TBK1)/IκB kinase ε (IKKε) on the same serine-72 (S72) site. An unbiased search for novel TBK1/IKKε substrates using stable isotope labeling with amino acids in cell culture phosphoproteomic analysis identified Rab7-S72 as a top hit. PTEN-null TNBC cells expressing a phosphomimetic version of Rab7-S72 exhibited diffuse cytosolic Rab7 localization and enhanced innate immune signaling, in contrast to a kinase-resistant version, which localized to active puncta that promote lysosomal-mediated stimulator of interferon genes (STING) degradation. Thus, convergence of PTEN loss and TBK1/IKKε activation on Rab7-S72 phosphorylation limited STING turnover and increased downstream production of IRF3 targets including CXCL10, CCL5, and IFNβ. Consistent with this data, PTEN-null TNBC tumors expressed higher levels of STING, and PTEN-null TNBC cell lines were hyperresponsive to STING agonists. Together, these findings begin to uncover how innate immune signaling is dysregulated downstream of TBK1/IKKε in a subset of TNBCs and reveals previously unrecognized cross-talk with STING recycling that may have implications for STING agonism in the clinic. SIGNIFICANCE: These findings identify Rab7 as a substrate for TBK1 for regulation of innate immune signaling, thereby providing important insight for strategies aimed at manipulating the immune response to enhance therapeutic efficacy in TNBC.
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Affiliation(s)
- Jessica L Ritter
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA
| | - Zehua Zhu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Tran C Thai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Navin R Mahadevan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Philipp Mertins
- Broad Institute of Harvard and MIT, Cambridge, MA.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Erik H Knelson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Brandon P Piel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Saemi Han
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Thanh U Barbie
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA. .,Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA
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34
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El Maadidi S, Weber ANR, Motshwene P, Schüssler JM, Backes D, Dickhöfer S, Wang H, Liu X, Garcia MD, Taumer C, Soufi B, Wolz OO, Klimosch SN, Franz-Wachtel M, Macek B, Gay NJ. Putative link between Polo-like kinases (PLKs) and Toll-like receptor (TLR) signaling in transformed and primary human immune cells. Sci Rep 2019; 9:13168. [PMID: 31511529 PMCID: PMC6739412 DOI: 10.1038/s41598-019-49017-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/15/2019] [Indexed: 12/21/2022] Open
Abstract
Toll-like receptors (TLRs) are important sentinels of bacterial and viral infection and thus fulfil a critical sensory role in innate immunity. Polo-like kinases (PLKs), a five membered family of Ser/Thr protein kinases, have long been studied for their role in mitosis and thus represent attractive therapeutic targets in cancer therapy. Recently, PLKs were implicated in TLR signaling in mice but the role of PLKs in TLR signaling in untransformed primary immune cells has not been addressed, even though PLK inhibitors are in clinical trials. We here identified several phospho-serine and phospho-threonine residues in the known TLR pathway kinases, Interleukin-1 receptor-associated kinase (IRAK) 2 and IRAK4. These sites lie in canonical polo-box motifs (PBM), sequence motifs known to direct recruitment of PLKs to client proteins. Interestingly, PLK1 was phosphorylated and PLK 2 and 3 mRNA induced upon TLR stimulation in primary immune cells, respectively. In whole blood, PLK inhibition disparately affected TLR mediated cytokine responses in a donor- and inhibitor-dependent fashion. Collectively, PLKs may thus potentially interface with TLR signaling in humans. We propose that temporary PLK inhibitor-mediated blockade of TLR-signaling in certain patients receiving such inhibitors during cancer treatment may cause adverse effects such as an increased risk of infections due to a then compromised ability of the TLR recognition system to sense and initiate cytokine responses to invading microbes.
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Affiliation(s)
- Souhayla El Maadidi
- Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Alexander N R Weber
- Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076, Tübingen, Germany.
| | - Precious Motshwene
- Department of Biochemistry, Cambridge University, 80 Tennis Court Road, Cambridge, CB2 2GA, UK
- University of Pretoria, Agricultural Sciences Building, University & Lynwood rds, Hatfield, Pretoria, 0083, South Africa
| | - Jan Moritz Schüssler
- Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Daniel Backes
- Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Sabine Dickhöfer
- Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Hui Wang
- Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076, Tübingen, Germany
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, No. 818, Tianyuan East Rd, Jiangning District, 211166, Nanjing, China
| | - Xiao Liu
- Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Magno Delmiro Garcia
- Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Christoph Taumer
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Boumediene Soufi
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Olaf-Oliver Wolz
- Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Sascha N Klimosch
- Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076, Tübingen, Germany
- HOT Screen GmbH, Aspenhaustr. 25, 72770, Reutlingen, Germany
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Nicholas J Gay
- Department of Biochemistry, Cambridge University, 80 Tennis Court Road, Cambridge, CB2 2GA, UK.
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35
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Abariute L, Lard M, Hebisch E, Prinz CN. Uptake of nanowires by human lung adenocarcinoma cells. PLoS One 2019; 14:e0218122. [PMID: 31226121 PMCID: PMC6588221 DOI: 10.1371/journal.pone.0218122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/27/2019] [Indexed: 12/23/2022] Open
Abstract
Semiconductor nanowires are increasingly used in optoelectronic devices. However, their effects on human health have not been assessed fully. Here, we investigate the effects of gallium phosphide nanowires on human lung adenocarcinoma cells. Four different geometries of nanowires were suspended in the cell culture for 48 hours. We show that cells internalize the nanowires and that the nanowires have no effect on cell proliferation rate, motility, viability and intracellular ROS levels. By blocking specific internalization pathways, we demonstrate that the nanowire uptake is the result of a combination of processes, requiring dynamin and actin polymerization, which suggests an internalization through macropinocytosis and phagocytosis.
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Affiliation(s)
- Laura Abariute
- Division of Solid State Physics, Lund University, Lund, Sweden
- NanoLund, Lund University, Lund, Sweden
| | - Mercy Lard
- Division of Solid State Physics, Lund University, Lund, Sweden
- NanoLund, Lund University, Lund, Sweden
| | - Elke Hebisch
- Division of Solid State Physics, Lund University, Lund, Sweden
- NanoLund, Lund University, Lund, Sweden
| | - Christelle N. Prinz
- Division of Solid State Physics, Lund University, Lund, Sweden
- NanoLund, Lund University, Lund, Sweden
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36
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Martins Gomes SF, Westermann AJ, Sauerwein T, Hertlein T, Förstner KU, Ohlsen K, Metzger M, Shusta EV, Kim BJ, Appelt-Menzel A, Schubert-Unkmeir A. Induced Pluripotent Stem Cell-Derived Brain Endothelial Cells as a Cellular Model to Study Neisseria meningitidis Infection. Front Microbiol 2019; 10:1181. [PMID: 31191497 PMCID: PMC6548865 DOI: 10.3389/fmicb.2019.01181] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/09/2019] [Indexed: 11/13/2022] Open
Abstract
Meningococcal meningitis is a severe central nervous system infection that occurs when Neisseria meningitidis (Nm) penetrates brain endothelial cells (BECs) of the meningeal blood-cerebrospinal fluid barrier. As a human-specific pathogen, in vivo models are greatly limited and pose a significant challenge. In vitro cell models have been developed, however, most lack critical BEC phenotypes limiting their usefulness. Human BECs generated from induced pluripotent stem cells (iPSCs) retain BEC properties and offer the prospect of modeling the human-specific Nm interaction with BECs. Here, we exploit iPSC-BECs as a novel cellular model to study Nm host-pathogen interactions, and provide an overview of host responses to Nm infection. Using iPSC-BECs, we first confirmed that multiple Nm strains and mutants follow similar phenotypes to previously described models. The recruitment of the recently published pilus adhesin receptor CD147 underneath meningococcal microcolonies could be verified in iPSC-BECs. Nm was also observed to significantly increase the expression of pro-inflammatory and neutrophil-specific chemokines IL6, CXCL1, CXCL2, CXCL8, and CCL20, and the secretion of IFN-γ and RANTES. For the first time, we directly observe that Nm disrupts the three tight junction proteins ZO-1, Occludin, and Claudin-5, which become frayed and/or discontinuous in BECs upon Nm challenge. In accordance with tight junction loss, a sharp loss in trans-endothelial electrical resistance, and an increase in sodium fluorescein permeability and in bacterial transmigration, was observed. Finally, we established RNA-Seq of sorted, infected iPSC-BECs, providing expression data of Nm-responsive host genes. Altogether, this model provides novel insights into Nm pathogenesis, including an impact of Nm on barrier properties and tight junction complexes, and suggests that the paracellular route may contribute to Nm traversal of BECs.
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Affiliation(s)
- Sara F Martins Gomes
- Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Alexander J Westermann
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Till Sauerwein
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.,ZB MED, Information Centre for Life Sciences, Cologne, Germany.,TH Köln, University of Applied Sciences, Faculty of Information Science and Communication Studies, Cologne, Germany
| | - Tobias Hertlein
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Konrad U Förstner
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.,ZB MED, Information Centre for Life Sciences, Cologne, Germany.,TH Köln, University of Applied Sciences, Faculty of Information Science and Communication Studies, Cologne, Germany
| | - Knut Ohlsen
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Marco Metzger
- Chair Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Würzburg, Germany.,Fraunhofer Institute for Silicate Research ISC, Translational Center Regenerative Therapies (TLC-RT), Würzburg, Germany
| | - Eric V Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Brandon J Kim
- Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany.,Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Antje Appelt-Menzel
- Chair Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Würzburg, Germany.,Fraunhofer Institute for Silicate Research ISC, Translational Center Regenerative Therapies (TLC-RT), Würzburg, Germany
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Subbannayya Y, Pinto SM, Bösl K, Prasad TSK, Kandasamy RK. Dynamics of Dual Specificity Phosphatases and Their Interplay with Protein Kinases in Immune Signaling. Int J Mol Sci 2019; 20:ijms20092086. [PMID: 31035605 PMCID: PMC6539644 DOI: 10.3390/ijms20092086] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 12/12/2022] Open
Abstract
Dual specificity phosphatases (DUSPs) have a well-known role as regulators of the immune response through the modulation of mitogen-activated protein kinases (MAPKs). Yet the precise interplay between the various members of the DUSP family with protein kinases is not well understood. Recent multi-omics studies characterizing the transcriptomes and proteomes of immune cells have provided snapshots of molecular mechanisms underlying innate immune response in unprecedented detail. In this study, we focus on deciphering the interplay between members of the DUSP family with protein kinases in immune cells using publicly available omics datasets. Our analysis resulted in the identification of potential DUSP-mediated hub proteins including MAPK7, MAPK8, AURKA, and IGF1R. Furthermore, we analyzed the association of DUSP expression with TLR4 signaling and identified VEGF, FGFR, and SCF-KIT pathway modules to be regulated by the activation of TLR4 signaling. Finally, we identified several important kinases including LRRK2, MAPK8, and cyclin-dependent kinases as potential DUSP-mediated hubs in TLR4 signaling. The findings from this study have the potential to aid in the understanding of DUSP signaling in the context of innate immunity. Further, this will promote the development of therapeutic modalities for disorders with aberrant DUSP signaling.
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Affiliation(s)
- Yashwanth Subbannayya
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Sneha M Pinto
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Korbinian Bösl
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Richard K Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, N-0349 Oslo, Norway.
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38
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Wang H, Zhou Q, Dai W, Feng X, Lu Z, Yang Z, Liu Y, Xie G, Yang Y, Shen K, Li Y, Li SC, Xu X, Shen Y, Li D, Zheng Y. Lung Microbiota and Pulmonary Inflammatory Cytokines Expression Vary in Children With Tracheomalacia and Adenoviral or Mycoplasma pneumoniae Pneumonia. Front Pediatr 2019; 7:265. [PMID: 31316955 PMCID: PMC6611399 DOI: 10.3389/fped.2019.00265] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/12/2019] [Indexed: 12/14/2022] Open
Abstract
Community-acquired pneumonia (CAP) is a worldwide infectious disease caused by bacteria, viruses, or a combination of these infectious agents. Mycoplasma pneumoniae is an atypical pneumonia pathogen that causes high morbidity and mortality in children, and adenovirus can lead to severe pneumonia. However, the etiology of different types of pneumonia is still unclear. In this study, we selected a total of 52 inpatients with M. pneumoniae pneumonia (MPP) (n = 21), adenovirus pneumonia (AVP) (n = 16), or tracheomalacia (n = 15) to serve as a disease control. Bronchoalveolar lavage fluid (BALF) samples that had been obtained for clinical use were analyzed. We compared the differences in microbiota and the expression of 10 inflammatory cytokines in samples between MPP, AVP, and tracheomalacia. We found that the bacterial diversity in MPP was lower than that in AVP and tracheomalacia. Mycoplasma, Streptococcus, and Pseudomonas were predominant in samples of MPP, AVP, and tracheomalacia, respectively. The expression levels of IL-6, IL-8, and IL-10 were significantly higher in inpatients with AVP compared to children hospitalized with tracheomalacia or MPP. The lung microbiota in MPP was remarkably correlated with IL-2, IL-4, IL-5, IL-6, TNF-α, and IL-1α expressions, while this was not found in tracheomalacia and AVP. Microbiota analysis identified a high load of multi-drug resistant Acinetobacter baumannii in the lung microbiota of several inpatients, which might be associated with the long hospitalization length and intra-group differences at the individual level. This study will help to understand the microbial etiology of tracheomalacia, AVP, and MPP and to identify effective therapies for these diseases.
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Affiliation(s)
- Heping Wang
- Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China
| | - Qian Zhou
- Department of Microbial Research, WeHealthGene Institute, Shenzhen, China
| | - Wenkui Dai
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Xin Feng
- Department of Microbial Research, WeHealthGene Institute, Shenzhen, China
| | - Zhiwei Lu
- Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China
| | - Zhenyu Yang
- Department of Microbial Research, WeHealthGene Institute, Shenzhen, China
| | - Yanhong Liu
- Department of Microbial Research, WeHealthGene Institute, Shenzhen, China
| | - Gan Xie
- Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China
| | - Yonghong Yang
- Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China.,Department of Microbial Research, WeHealthGene Institute, Shenzhen, China.,Department of Respiratory Diseases, Beijing Children's Hospital, Beijing, China
| | - Kunling Shen
- Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China.,Department of Respiratory Diseases, Beijing Children's Hospital, Beijing, China
| | - Yinhu Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Ximing Xu
- Institute of Statistics, NanKai University, Tianjin, China
| | - Yongshun Shen
- Department of Pediatrics, Shenzhen Dapeng District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Dongfang Li
- Department of Microbial Research, WeHealthGene Institute, Shenzhen, China.,Institute of Statistics, NanKai University, Tianjin, China
| | - Yuejie Zheng
- Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China
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39
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Wen Z, Xie G, Zhou Q, Qiu C, Li J, Hu Q, Dai W, Li D, Zheng Y, Wen F. Distinct Nasopharyngeal and Oropharyngeal Microbiota of Children with Influenza A Virus Compared with Healthy Children. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6362716. [PMID: 30581863 PMCID: PMC6276510 DOI: 10.1155/2018/6362716] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 10/24/2018] [Accepted: 11/06/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Influenza A virus (IAV) has had the highest morbidity globally over the past decade. A growing number of studies indicate that the upper respiratory tract (URT) microbiota plays a key role for respiratory health and that a dysfunctional respiratory microbiota is associated with disease; but the impact of microbiota during influenza is understudied. METHODS We recruited 180 children, including 121 IAV patients and 59 age-matched healthy children. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected to conduct 16S rDNA sequencing and compare microbiota structures in different individuals. RESULTS Both NP and OP microbiota in IAV patients differed from those in healthy individuals. The NP dominated genera in IVA patients, such as Moraxella, Staphylococcus, Corynebacterium, and Dolosigranulum, showed lower abundance than in healthy children. The Streptococcus significantly enriched in patients' NP and Phyllobacterium could be generally detected in patients' NP microbiota. The most abundant genera in OP microbiota showed a decline tendency in patients, including Streptococcus, Neisseria, and Haemophilus. The URT's bacterial concurrence network changed dramatically in patients. NP and OP samples were clustered into subgroups by different dominant genera; and NP and OP microbiota provided the precise indicators to distinguish IAV patients from healthy children. CONCLUSION This is the first respiratory microbiome analysis on pediatric IAV infection which reveals distinct NP and OP microbiota in influenza patients. It provides a new insight into IAV research from the microecology aspect and promotes the understanding of IAV pathogenesis.
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Affiliation(s)
- Zhixin Wen
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen 518026, China
| | - Gan Xie
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen 518026, China
| | - Qian Zhou
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, Dayun Software Town, Shenzhen 518000, China
| | - Chuangzhao Qiu
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, Dayun Software Town, Shenzhen 518000, China
| | - Jing Li
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen 518026, China
| | - Qian Hu
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen 518026, China
| | - Wenkui Dai
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, Dayun Software Town, Shenzhen 518000, China
| | - Dongfang Li
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, Dayun Software Town, Shenzhen 518000, China
| | - Yuejie Zheng
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen 518026, China
| | - Feiqiu Wen
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Shenzhen 518038, China
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40
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Crow MK, Olferiev M, Kirou KA. Type I Interferons in Autoimmune Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2018; 14:369-393. [PMID: 30332560 DOI: 10.1146/annurev-pathol-020117-043952] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Type I interferons, which make up the first cytokine family to be described and are the essential mediators of antivirus host defense, have emerged as central elements in the immunopathology of systemic autoimmune diseases, with systemic lupus erythematosus as the prototype. Lessons from investigation of interferon regulation following virus infection can be applied to lupus, with the conclusion that sustained production of type I interferon shifts nearly all components of the immune system toward pathologic functions that result in tissue damage and disease. We review recent data, mainly from studies of patients with systemic lupus erythematosus, that provide new insights into the mechanisms of induction and the immunologic consequences of chronic activation of the type I interferon pathway. Current concepts implicate endogenous nucleic acids, driving both cytosolic sensors and endosomal Toll-like receptors, in interferon pathway activation and suggest targets for development of novel therapeutics that may restore the immune system to health.
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Affiliation(s)
- Mary K Crow
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, New York, New York 10021, USA;
| | - Mikhail Olferiev
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, New York, New York 10021, USA;
| | - Kyriakos A Kirou
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, New York, New York 10021, USA;
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41
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Jia L, Shi Y, Wen Y, Li W, Feng J, Chen C. The roles of TNFAIP2 in cancers and infectious diseases. J Cell Mol Med 2018; 22:5188-5195. [PMID: 30145807 PMCID: PMC6201362 DOI: 10.1111/jcmm.13822] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/21/2018] [Accepted: 07/05/2018] [Indexed: 12/30/2022] Open
Abstract
TNFα‐induced protein 2 (TNFAIP2) is a primary response gene of TNFα. TNFAIP2 is highly expressed in immune cells and the urinary bladder. The expression of TNFAIP2 is regulated by multiple transcription factors and signalling pathways, including NF‐κB, KLF5 and retinoic acid. Physiologically, TNFAIP2 appears to be a multiple functional mediator not only for inflammation, angiogenesis and tunneling nanotube (TNT) formation but also as a regulator of cell proliferation and migration. The expression of TNFAIP2 is frequently abnormal in human cancers and in infectious diseases. Due to its significant functions in cell proliferation, angiogenesis, migration and invasion, TNFAIP2 could be a potential diagnostic biomarker and therapeutic target for cancer.
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Affiliation(s)
- Lin Jia
- Department of Biology, Yuxi Normal University, Yuxi, China
| | - Yundong Shi
- Department of Biology, Yuxi Normal University, Yuxi, China
| | - Yi Wen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wei Li
- Department of Urology of the First People's Hospital of Yunnan Province, Kunming, China.,Medical College of Kunming University of Science and Technology, Kunming, China
| | - Jing Feng
- Department of Laboratory Medicine & Central Laboratory, Southern Medical University Affiliated Fengxian Hospital, Shanghai, China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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42
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Luk ADW, Ni K, Wu Y, Lam KT, Chan KW, Lee PP, Tu W, Mao H, Lau YL. Type I and III Interferon Productions Are Impaired in X-Linked Agammaglobulinemia Patients Toward Poliovirus but Not Influenza Virus. Front Immunol 2018; 9:1826. [PMID: 30147693 PMCID: PMC6095995 DOI: 10.3389/fimmu.2018.01826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/24/2018] [Indexed: 12/20/2022] Open
Abstract
Background X-linked agammaglobulinemia (XLA) is a primary immunodeficiency caused by Bruton's tyrosine kinase (BTK) mutation. Patients are susceptible to severe enterovirus infections. The underlying mechanism remains unknown. BTK is involved in toll-like receptors pathway, which initiates antiviral responses including interferon (IFN) productions. Objective To demonstrate type I and III IFN productions in dendritic cells of XLA patients is decreased in response to oral poliovirus vaccine (OPV) but not H1N1 virus. Methods Monocyte-derived dendritic cells (MoDCs) were derived from nine XLA patients aged 22-32 years old and 23 buffy coats from Hong Kong Red Cross blood donors. LFM-A13 was used to inhibit BTK. OPV Sabin type 1 and H1N1 influenza virus were used to stimulate MoDCs with RPMI as mock stimulation. The antiviral cytokine productions and phenotypic maturation of MoDCs were determined 24 h post-stimulation. OPV RNA was determined at 0, 6, 12, and 24 h post-stimulation. Results Upon OPV stimulation, IFN-α2, IFN-β, and IFN-λ1 productions in MoDCs from XLA patients and BTK-inhibited MoDCs of healthy controls were significantly lower than that from healthy controls. Whereas upon H1N1 stimulation, the IFN-α2, IFN-β, and IFN-λ1 productions were similar in MoDCs from XLA patients, BTK-inhibited MoDCs of healthy controls and healthy controls. The mean fluorescent intensities (MFI) of CD83, CD86, and MHC-II in MoDCs from XLA patients in response to OPV was similar to that in response to mock stimulation, while the MFI of CD83, CD86, and MHC-II were significantly higher in response to H1N1 stimulation than that in response to mock stimulation. Whereas, the MFI of CD83, CD86, and MHC-II in MoDCs of healthy controls were significantly higher in response to both OPV and H1N1 stimulation compared to that in response to mock stimulation. Conclusion Production of type I and III IFN in response to OPV was deficient in MoDCs from XLA patients, but was normal in response to H1N1 due to deficient BTK function. Moreover, phenotypic maturation of MoDCs from XLA patients was impaired in response to OPV but not to H1N1. These selective impairments may account for the unique susceptibility of XLA patients toward severe enterovirus infections.
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Affiliation(s)
- Anderson Dik Wai Luk
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Ke Ni
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yuet Wu
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Kwok-Tai Lam
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Koon-Wing Chan
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Pamela P. Lee
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Shenzhen Primary Immunodeficiency Diagnostic and Therapeutic Laboratory, Department of Paediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Wenwei Tu
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Shenzhen Primary Immunodeficiency Diagnostic and Therapeutic Laboratory, Department of Paediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Huawei Mao
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Department of Rheumatology and Immunology, Ministry of Education Key Laboratory of Child Development and Disorder, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Shenzhen Primary Immunodeficiency Diagnostic and Therapeutic Laboratory, Department of Paediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
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Mass Spectrometry-based Structural Analysis and Systems Immunoproteomics Strategies for Deciphering the Host Response to Endotoxin. J Mol Biol 2018; 430:2641-2660. [PMID: 29949751 DOI: 10.1016/j.jmb.2018.06.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/23/2018] [Accepted: 06/15/2018] [Indexed: 02/06/2023]
Abstract
One cause of sepsis is systemic maladaptive immune response of the host to bacteria and specifically, to Gram-negative bacterial outer-membrane glycolipid lipopolysaccharide (LPS). On the host myeloid cell surface, proinflammatory LPS activates the innate immune system via Toll-like receptor-4/myeloid differentiation factor-2 complex. Intracellularly, LPS is also sensed by the noncanonical inflammasome through caspase-11 in mice and 4/5 in humans. The minimal functional determinant for innate immune activation is the membrane anchor of LPS called lipid A. Even subtle modifications to the lipid A scaffold can enable, diminish, or abolish immune activation. Bacteria are known to modify their LPS structure during environmental stress and infection of hosts to alter cellular immune phenotypes. In this review, we describe how mass spectrometry-based structural analysis of endotoxin helped uncover major determinations of molecular pathogenesis. Through characterization of LPS modifications, we now better understand resistance to antibiotics and cationic antimicrobial peptides, as well as how the environment impacts overall endotoxin structure. In addition, mass spectrometry-based systems immunoproteomics approaches can assist in elucidating the immune response against LPS. Many regulatory proteins have been characterized through proteomics and global/targeted analysis of protein modifications, enabling the discovery and characterization of novel endotoxin-mediated protein translational modifications.
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44
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Sueyoshi T, Kawasaki T, Kitai Y, Ori D, Akira S, Kawai T. Hu Antigen R Regulates Antiviral Innate Immune Responses through the Stabilization of mRNA for Polo-like Kinase 2. THE JOURNAL OF IMMUNOLOGY 2018; 200:3814-3824. [PMID: 29678949 DOI: 10.4049/jimmunol.1701282] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 04/03/2018] [Indexed: 12/29/2022]
Abstract
Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), RIG-I, and melanoma differentiation-associated gene 5 (MDA5) play a critical role in inducing antiviral innate immune responses by activating IFN regulatory factor 3 (IRF3) and NF-κB, which regulates the transcription of type I IFN and inflammatory cytokines. Antiviral innate immune responses are also regulated by posttranscriptional and translational mechanisms. In this study, we identified an RNA-binding protein HuR as a regulator for RLR signaling. Overexpression of HuR, but not of other Hu members, increased IFN-β promoter activity. HuR-deficient macrophage cells exhibited decreased Ifnb1 expression after RLR stimulation, whereas they showed normal induction after stimulation with bacterial LPS or immunostimulatory DNA. Moreover, HuR-deficient cells displayed impaired nuclear translocation of IRF3 after RLR stimulation. In HuR-deficient cells, the mRNA expression of Polo-like kinase (PLK) 2 was markedly reduced. We found that HuR bound to the 3' untranslated region of Plk2 mRNA and increased its stabilization. PLK2-deficient cells also showed reduced IRF3 nuclear translocation and Ifnb mRNA expression during RLR signaling. Together, these findings suggest that HuR bolsters RLR-mediated IRF3 nuclear translocation by controlling the stability of Plk2 mRNA.
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Affiliation(s)
- Takuya Sueyoshi
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takumi Kawasaki
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yuichi Kitai
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan
| | - Daisuke Ori
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shizuo Akira
- Laboratory of Host Defense, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan; and.,Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Taro Kawai
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan;
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45
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Hung YF, Chen CY, Shih YC, Liu HY, Huang CM, Hsueh YP. Endosomal TLR3, TLR7, and TLR8 control neuronal morphology through different transcriptional programs. J Cell Biol 2018; 217:2727-2742. [PMID: 29777026 PMCID: PMC6080926 DOI: 10.1083/jcb.201712113] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 04/09/2018] [Accepted: 05/03/2018] [Indexed: 02/07/2023] Open
Abstract
Neuroinflammation is associated with diverse neurological disorders. Endosomal Toll-like receptors (TLRs) including TLR3, TLR7, and TLR8 cell-autonomously regulate neuronal differentiation. However, the mechanisms by which these three TLRs affect neuronal morphology are unclear. In this study, we compare these TLRs in mouse neurons. By combining in vitro neuronal cultures, in utero electroporation, and transcriptomic profiling, we show that TLR8, TLR7, and TLR3 promote dendritic pruning via MYD88 signaling. However, they induce different transcriptomic profiles related to innate immunity, signaling, and neuronal development. The temporal expression patterns and the effects on neuronal morphology are not identical upon activation of these endosomal TLRs. Pathway analyses and in vitro studies specifically implicate mitogen-activated protein kinase signaling in TLR8-mediated dendritic pruning. We further show that TLR8 is more critical for dendritic arborization at a late development stage in vivo. The activation of TLR8, TLR7, or TLR3 results in dendritic shortening, and TLR7 and TLR3 but not TLR8 also control axonal growth. In-depth transcriptomic analyses show that TLRs use different downstream pathways to control neuronal morphology, which may contribute to neuronal development and pathological responses.
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Affiliation(s)
- Yun-Fen Hung
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chiung-Ya Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Chun Shih
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hsin-Yu Liu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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46
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Mertins P, Przybylski D, Yosef N, Qiao J, Clauser K, Raychowdhury R, Eisenhaure TM, Maritzen T, Haucke V, Satoh T, Akira S, Carr SA, Regev A, Hacohen N, Chevrier N. An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling. Cell Rep 2018; 19:2853-2866. [PMID: 28658630 DOI: 10.1016/j.celrep.2017.06.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 04/11/2017] [Accepted: 06/01/2017] [Indexed: 10/19/2022] Open
Abstract
Building an integrated view of cellular responses to environmental cues remains a fundamental challenge due to the complexity of intracellular networks in mammalian cells. Here, we introduce an integrative biochemical and genetic framework to dissect signal transduction events using multiple data types and, in particular, to unify signaling and transcriptional networks. Using the Toll-like receptor (TLR) system as a model cellular response, we generate multifaceted datasets on physical, enzymatic, and functional interactions and integrate these data to reveal biochemical paths that connect TLR4 signaling to transcription. We define the roles of proximal TLR4 kinases, identify and functionally test two dozen candidate regulators, and demonstrate a role for Ap1ar (encoding the Gadkin protein) and its binding partner, Picalm, potentially linking vesicle transport with pro-inflammatory responses. Our study thus demonstrates how deciphering dynamic cellular responses by integrating datasets on various regulatory layers defines key components and higher-order logic underlying signaling-to-transcription pathways.
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Affiliation(s)
- Philipp Mertins
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Dariusz Przybylski
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Nir Yosef
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jana Qiao
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Karl Clauser
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Thomas M Eisenhaure
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Tanja Maritzen
- Molecular Physiology and Cell Biology Section, Leibniz-Institute for Molecular Pharmacology (FMP), 13125 Berlin, Germany
| | - Volker Haucke
- Molecular Physiology and Cell Biology Section, Leibniz-Institute for Molecular Pharmacology (FMP), 13125 Berlin, Germany
| | - Takashi Satoh
- WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Shizuo Akira
- WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Steven A Carr
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA 02142, USA.
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Center for Immunology and Inflammatory Diseases and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA.
| | - Nicolas Chevrier
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
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47
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Martin-Gayo E, Cole MB, Kolb KE, Ouyang Z, Cronin J, Kazer SW, Ordovas-Montanes J, Lichterfeld M, Walker BD, Yosef N, Shalek AK, Yu XG. A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers. Genome Biol 2018; 19:10. [PMID: 29378643 PMCID: PMC5789701 DOI: 10.1186/s13059-017-1385-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 12/23/2017] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-sequencing to examine viral responses among the dendritic cells (DCs) of three elite controllers (ECs) of HIV-1 infection. RESULTS To overcome the potentially confounding effects of donor-to-donor variability, we present a generally applicable computational framework for identifying reproducible patterns in gene expression across donors who share a unifying classification. Applying it, we discover a highly functional antiviral DC state in ECs whose fractional abundance after in vitro exposure to HIV-1 correlates with higher CD4+ T cell counts and lower HIV-1 viral loads, and that effectively primes polyfunctional T cell responses in vitro. By integrating information from existing genomic databases into our reproducibility-based analysis, we identify and validate select immunomodulators that increase the fractional abundance of this state in primary peripheral blood mononuclear cells from healthy individuals in vitro. CONCLUSIONS Overall, our results demonstrate how single-cell approaches can reveal previously unappreciated, yet important, immune behaviors and empower rational frameworks for modulating systems-level immune responses that may prove therapeutically and prophylactically useful.
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Affiliation(s)
| | - Michael B Cole
- Department of Physics, University of California, Berkeley, CA, USA
| | - Kellie E Kolb
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zhengyu Ouyang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | | | - Samuel W Kazer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jose Ordovas-Montanes
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Nir Yosef
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. .,Electrical Engineering & Computer Sciences, UC Berkeley, Berkeley, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| | - Alex K Shalek
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. .,Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. .,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
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48
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Cellular Decision Making by Non-Integrative Processing of TLR Inputs. Cell Rep 2017; 19:125-135. [PMID: 28380352 DOI: 10.1016/j.celrep.2017.03.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/11/2017] [Accepted: 03/06/2017] [Indexed: 02/06/2023] Open
Abstract
Cells receive a multitude of signals from the environment, but how they process simultaneous signaling inputs is not well understood. Response to infection, for example, involves parallel activation of multiple Toll-like receptors (TLRs) that converge on the nuclear factor κB (NF-κB) pathway. Although we increasingly understand inflammatory responses for isolated signals, it is not clear how cells process multiple signals that co-occur in physiological settings. We therefore examined a bacterial infection scenario involving co-stimulation of TLR4 and TLR2. Independent stimulation of these receptors induced distinct NF-κB dynamic profiles, although surprisingly, under co-stimulation, single cells continued to show ligand-specific dynamic responses characteristic of TLR2 or TLR4 signaling rather than a mixed response, comprising a cellular decision that we term "non-integrative" processing. Iterating modeling and microfluidic experiments revealed that non-integrative processing occurred through interaction of switch-like NF-κB activation, receptor-specific processing timescales, cell-to-cell variability, and TLR cross-tolerance mediated by multilayer negative feedback.
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49
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Ghodke-Puranik Y, Dorschner JM, Vsetecka DM, Amin S, Makol A, Ernste F, Osborn T, Moder K, Chowdhary V, Eliopoulos E, Zervou MI, Goulielmos GN, Jensen MA, Niewold TB. Lupus-Associated Functional Polymorphism in PNP Causes Cell Cycle Abnormalities and Interferon Pathway Activation in Human Immune Cells. Arthritis Rheumatol 2017; 69:2328-2337. [PMID: 28859258 DOI: 10.1002/art.40304] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 08/25/2017] [Indexed: 01/12/2023]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is frequently characterized by activation of the type I interferon (IFN) pathway. We previously observed that a missense single-nucleotide polymorphism (rs1049564) in the purine nucleoside phosphorylase (PNP) gene was associated with high levels of IFN in SLE. PNP is a key enzyme involved in purine metabolism. In this study, we performed functional follow-up of this polymorphism in human cells. METHODS Type I IFN was measured in patient sera, using a reporter cell assay. Structural modeling of the PNP variant was performed using PyMOL software. PNP messenger RNA (mRNA) and protein levels and type I IFN-induced gene expression were measured in lymphoblastoid cell lines with known PNP rs1049564 genotypes. The cell cycle was assayed using flow cytometry. RESULTS Structural modeling indicated no major disruption in folding related to rs1049564. We observed that homozygous rs1049564 TT lymphoblastoid cells had decreased PNP mRNA expression and protein levels, and that cells with the TT genotype had reduced PNP enzymatic activity even when the amount of PNP was controlled. Cells with the TT genotype had a 2-fold increase in S-phase block as compared with cells with the homozygous CC phenotype. The S-phase block could be pharmacologically reversed with hypoxanthine and adenosine, supporting the notion that relative PNP deficiency is the cause of the S-phase block. Type I IFN-induced transcripts were increased in a dose-response manner related to the rs1049564 T allele, at both baseline and after type I IFN stimulation. CONCLUSION The PNP rs1049564 T allele is a loss-of-function variant that induces S-phase block and IFN pathway activation in lymphocytes. The S-phase block could be rescued in our in vitro experiments, suggesting the potential for personalized treatment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Mark A Jensen
- New York University School of Medicine, New York, New York
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50
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Kimura S. Molecular insights into the mechanisms of M-cell differentiation and transcytosis in the mucosa-associated lymphoid tissues. Anat Sci Int 2017; 93:23-34. [PMID: 29098649 DOI: 10.1007/s12565-017-0418-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/13/2017] [Indexed: 02/07/2023]
Abstract
Microfold cells (M cells), which are located in the follicle-associated epithelium (FAE) covering mucosal lymphoid follicles, are specialized epithelial cells that initiate mucosal immune responses. These cells take luminal antigens and transport them via transcytosis across the FAE to the antigen-presenting cells underneath. Several intestinal pathogens exploit M cells as their portal for entry to invade the host and cause disease conditions. Recent studies have revealed that the uptake of antigens by M cells is essential for efficient antigen-specific IgA production and that this process likely maintains the homeostasis of mucosal tissues. The present article reviews recent advances in understanding the molecular mechanism of M-cell differentiation and describes the molecules expressed by M cells that are associated with antigen uptake and/or the transcytosis process. Current efforts to augment M-cell-mediated uptake for use in the development of effective mucosal vaccines are also discussed.
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Affiliation(s)
- Shunsuke Kimura
- Laboratory of Histology and Cytology, Graduate School of Medicine, Hokkaido University, North 15, West 7, Kita-ku, Sapporo, 060-8638, Japan.
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